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Muriel Gargaud 
William M. Irvine 

Editors-in-Chief Danie l Rou an 

Ricardo Amils Tilman Spohn 

Jose Cernicharo Quintanilla Stephane Tirard 

Henderson James Cleaves II Michel Viso 

Daniele L. Pinti Editors 


Encyclopedia of 
Astrobiology 

Second Edition 


Springer Reference 


EXTRAS ONLINE 



Encyclopedia of Astrobiology 




Muriel Gargaud • William M. Irvine 
Editors-in-Chief 

Ricardo Amils • Henderson James (Jim) 
Cleaves II • Daniele L. Pinti 
Jose Cernicharo Quintanilla 
Daniel Rouan • Tilman Spohn 
Stephane Tirard • Michel Viso 
Editors 


Encyclopedia of 
Astrobiology 

Second Edition 


With 703 Figures and 99 Tables 


4^ Springer Reference 


Editor s-in-Chief 
Muriel Gargaud 
CNRS-Universite de Bordeaux 
Laboratoire d’Astrophysique 
de Bordeaux 
Floirac, France 

Editors 
Ricardo Amils 

Departamento de Biologia Molecular 
Universidad Autonoma de Madrid 
Madrid, Spain 

Daniele L. Pinti 
GEOTOP Research Center for 
Geochemistry and Geodynamics 
Universite du Quebec a Montreal 
Montreal, QC, Canada 

Daniel Rouan 

LESIA, Observatoire Paris-Site 
de Meudon 
Meudon, France 

Stephane Tirard 

Centre Frangois Viete d’Histoire 
des Sciences et des Techniques EA 1161 
Faculte des Sciences et des 
Techniques de Nantes 
Nantes, France 


William M. Irvine 
University of Massachusetts 
Amherst, MA, USA 


Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI) 
Tokyo Institute of Technology 
Meguro-ku, Tokyo, Japan 

Jose Cernicharo Quintanilla 
Department of Astrophysics 
Laboratory of Molecular Astrophysics 
Iorrejon de Ardoz 
Madrid, Spain 

Tilman Spohn 

Deutsches Zentrum fiir Luft- und 
Raumfahrt (DLR), Institut fiir 
Planetenforschung 
Berlin, Germany 

Michel Viso 

CNES/DSP/SME, Veterinaire/DVM 

Astro/Exobiology 

Paris Cedex 1, France 


ISBN 978-3-662-44184-8 ISBN 978-3-662-44185-5 (eBook) 

ISBN 978-3-662-44186-2 (print and electronic bundle) 

DOI 10.1007/978-3-662-44185-5 

Library of Congress Control Number: 2015947250 

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Foreword to the First Edition 


Are we alone? Long an object of speculation or fiction, if not heresy, this 
question entered the field of science on November 1, 1961, at the National 
Radio Astronomy Observatory in Green Bank, Virginia, where a number of 
scientists, including Melvin Calvin, who had just been awarded the Nobel 
prize in chemistry for his work on photosynthesis, and the charismatic Carl 
Sagan, gathered at the invitation of a young astronomer, Frank Drake, to 
launch the Search for Extra-Terrestrial Intelligence (SETI) project. Since 
then, batteries of increasingly powerful radiotelescopes have been scanning 
space for messages sent out by some extraterrestrial civilization, so far 
in vain. 

At the same time, in the wake of widening space exploration, a new 
discipline was born that has the distinctive peculiarity of having three 
names - exobiology, astrobiology, and bioastronomy - and no as-yet-known 
object. The purpose of this new discipline is more modest than that of the 
SETI project: to detect signs of extraterrestrial life, not necessarily intelligent. 

To guide this quest, we have available vast knowledge that has been gained 
in the last few decades concerning the basic mechanisms of life. This knowl¬ 
edge, in turn, has illuminated our concept of the origin of life. Even though we 
do not know how or under what conditions this phenomenon took place, we 
may safely affirm that if life arose naturally, which is the only scientifically 
acceptable assumption, its origin must have depended on “chemistry.” By its 
very nature, chemistry deals with highly deterministic, reproducible events 
that are bound to take place under prevailing physical-chemical conditions. If 
even a very slight element of chance affected chemical reactions, there would 
be no chemical laboratories, no chemical factories. We could not afford 
the risk. 

A conclusion that emerges from this consideration is that life, as a product 
of environmentally enforced chemistry, was bound to arise under the 
physical-chemical conditions that prevailed at the site of its birth. 

This statement, at least, holds true for the early steps in the origin of life, 
until the appearance of the first replicable substance, most likely RNA. Once 
this happened, “selection” became added to chemistry, introducing an ele¬ 
ment of chance in the development of life. Contrary to what has often been 
claimed in the past, this fact does not necessarily imply that the process was 
ruled by contingency. There are reasons to believe that, in many instances, 


v 



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Foreword to the First Edition 


chance provided enough opportunities for selection to be optimizing and, 
therefore, likewise obligatory under prevailing conditions. 

Thus, in so far as chemistry and optimizing selection played a dominant 
role in the process, the development of life appears as the obligatory outcome 
of prevailing conditions. Hence the assumption that the probability of the 
appearance elsewhere in the universe of forms of life resembling Earth life in 
their basic properties is approximately equal to the probability of the occur¬ 
rence elsewhere in the universe of the physical conditions obtained at the site 
where Earth life arose. 

In the eyes of many astronomers, this probability is very high. It is 
estimated that some 30 billion sun-like stars exist in our galaxy alone and 
that the total number of galaxies in the universe is on the order of 100 billion. 
This means, to the extent that our galaxy may be taken as a representative 
sample of galaxies in general, there may be some 3,000 billion sun-like stars 
in the universe. Unless our solar system should be the product of extremely 
unlikely events, the probability of there being planets similar to Earth (or to 
whatever celestial object served as the cradle of Earth life) seems very strong. 

Recent findings are most encouraging in this respect, by revealing that 
planet formation is not a rare event, with more than 400 planets already 
identified around a number of nearby stars. Although no habitable Earthlike 
extrasolar planet has yet been found, this may be partly due to technical 
limitations. The prospects that, with improved technologies, such a planet 
may be discovered some time in the future are far from negligible. Signs of 
life on such a planet, although more difficult to detect, may likewise yield 
technological progress. 

As by now, the enormous research effort expended within the framework 
of the new discipline of exobiology-cum-bioastronomy-cum-astrobiology 
has already produced a wealth of new findings, in fields ranging from physics 
and cosmology to chemistry, biochemistry, and molecular biology. These 
findings have provided rich material for this Encyclopedia. Its editors and 
authors are to be commended for making this material widely available in 
easily accessible form. 

14 January 2011 Christian de Duve 


References 

1. de Duve C (2005) Singularities landmarks on the pathways of life. Cambridge Univer¬ 
sity Press, New York 



Preface to the First Edition 


Where do we come from? Are we alone in the Universe? Where are we going? 
These are the questions addressed by astrobiology - the study of the origin, 
evolution, distribution, and the future of life in the Universe. 

Encyclopedias are unusual works. A quote from the prologue of one of the 
more famous early encyclopedias is instructive: 

“.. .the purpose of an encyclopedia is to collect knowledge disseminated 
around the globe; to set forth its general system to the men with whom we 
live, and transmit it to those who will come after us, so that the work of 
preceding centuries will not become useless to the centuries to come; and so 
that our offspring, becoming better instructed, will at the same time become 
more virtuous and happy, and that we should not die without having rendered 
a service to the human race in the future years to come”. Diderot and 
d’Alembert, Encyclopedic (1751). 1 

Diderot and d’Alembert’s eighteenth century Encyclopedic was indeed 
ground-breaking, but perhaps more remarkable is the degree to which their 
description resembles the modern concept of genetic inheritance and natural 
selection: a civilization’s accumulated knowledge being analogous to the 
traits encoded in an organism’s time-tested DNA genome. In many ways, 
the Encyclopedic addressed the goals of astrobiology; between the lines, we 
find aspects of what makes biology biology. 

Encyclopedias have now existed for approximately 2,000 years, the first 
being Pliny the Elder’s Naturalis Historia, which was a compendium of the 
knowledge available to a citizen of the Roman Empire as documented by the 
first century AD. 2 It contained - 20,000 facts from 2,000 sources written by 
200 authors. The present volume contains an unknown number of “facts” 
(indeed, some of the content will likely be proven false, as science is a living, 
breathing accumulation of presently accepted knowledge, all subject to future 
revision), but it does include more than 1,700 contributions, references 
uncounted thousands of prior publications, and is written by 385 authors. 

Modern encyclopedias are derived from the dictionaries of the eighteenth 
century. The two are similar in that both are arranged alphabetically and 
generally are the work of a team of expert contributors. They differ in that 
encyclopedias contain a deeper level of analysis of the included terms and 
attempt to cross-reference and place the assembled contents in a useful context. 

The first encyclopedias attempted to cover all human knowledge. This is 
now impossible for a printed work because the body of human knowledge is 

vii 



Preface to the First Edition 


viii 

presently growing exponentially, with no end in sight. Encyclopedias now 
exist for almost every definable field of study. A field requires a certain degree 
of maturity to have an encyclopedia, and conversely, the publication of an 
encyclopedia commonly records the birth of a definable field of study. 
Astrobiology is an interdisciplinary field, spanning geology, chemistry, phys¬ 
ics, astronomy, biology, engineering, and computer science, to name only the 
core fields of study. 

While some of these fields of research are fairly well mapped, many others 
are in rapid flux, and still others remain perennially enigmatic, awaiting future 
breakthroughs by the scientists of tomorrow. To this end, the Encyclopedia of 
Astrobiology is primarily aimed at younger scientists or scientists new to the 
field who wish to understand how their expertise coincides with current 
knowledge in other areas of study. It is hoped that the encyclopedia will 
serve to orient researchers to the current state of the art. A more in-depth 
discussion of many of the topic areas can be obtained by referring to college 
or graduate level texts or to the articles cited at the end of many of the entries. 

Encyclopedias are snapshots of the state of knowledge at a particular time. 
In 1844, the book Vestiges of the Natural History of Creation was published 
anonymously (it was later found to have been written by Scottish publisher 
William Chambers) and created a public sensation. 3 It offered a sweeping and 
very secular view of the development of the Solar System, stretching from the 
nebular hypothesis to the development of man. While primitive by modern 
standards (it was, after all, based on state-of-the-art early nineteenth century 
science), it was in many ways remarkably similar to modern cosmology. In 
broad brushstrokes, it is the precursor to the worldview developed in Carl 
Sagan’s Cosmos 4 and the grand view of myriads of habitable planets implicit 
in the Drake equation. The implication of Vestiges was simply this: the 
Universe operates everywhere and at all times according to physical princi¬ 
ples, and the evolution of matter is largely predictable and often progressive, 
proceeding from the simple to the complex. 

Science has advanced dramatically since Chambers’ book was published. 
It is truly a long way from Sir William Hershel’s 40-ft telescope to the 
Herschel Space Telescope, 5 and from a Universe with seven known planets 
orbiting the Sun to one with more than 500 planets orbiting other stars. It is 
also a long way from the work of Black, Priestly, and Lavoisier 6 to SELEX 
technology and high-throughput automated chemical screening and analysis, 
and from Lyell’s Principles of Geology 7 to plate tectonics and isotope geo¬ 
chemistry. Nonetheless, certain questions permeate the sciences across time 
and discipline. Woese’s three domains of life 8 are direct descendents of 
Linnaeus’ early classification scheme, and both are attempts to unify and 
classify terrestrial organisms. Darwinism has offered an underlying mecha¬ 
nism for doing so that has allowed for unification of the assorted observations 
of the living world. However, the question of whether terrestrial life is unique 
in the universe has fascinated mankind for millennia. 

It was not until 1959, when NASA began funding the search for life in the 
Universe in its Exobiology program, that we at last achieved the technological 
prowess to try to answer this question. 9 The paleontologist George Gaylord 



Preface to the First Edition 


ix 

Simpson famously noted shortly thereafter that Exobiology was a science 
“that has yet to demonstrate that its subject matter exists.” 

NASA’s first exobiology grant was awarded to Wolf Vishniac for the 
construction of the Wolf Trap, a device for detecting bacteria on Mars. Due 
to size limitations, the device never flew, but various descendants have made 
the trip to Mars and returned various negative or tantalizingly ambiguous 
results. These results are, amusingly, either disappointingly or encouragingly 
ambiguous, depending on one’s point of view. Despite remarkable progress in 
the sciences, humanity still has no answer to the question, “Are we alone?,” 
though the question is in principle answerable. The search continues 
enthusiastically. 

Why should we think there might be life elsewhere in the Universe? In 
1960, the radio-astronomer Frank Drake developed his now-famous equation 
for estimating the number of communicating civilizations in the Galaxy: 


N = R* x f p x n e x f e x fi x f c x L, 


where N is the number of civilizations in our galaxy for which communica¬ 
tion might be possible, R* is the average rate of star formation per year, f p is 
the fraction of stars that have planets, n e is the average number of planets that 
can support life per star with planets, is the fraction of the planets that can 
support life on which life actually develops, f A is the fraction of those on which 
intelligent life develops, f c is the fraction of those on which civilizations 
communicate using detectable signals, and L is the length of time these 
civilizations communicate. 

When Drake unveiled his equation in 1960 and estimated that there were 
maybe ten communicating civilizations in the Galaxy, few of the parameters 
were known with any certainty; the rate of star formation was perhaps the 
only solid measurable value. Fifty years later, the flourishing search for 
exoplanets has placed the focus on the second value (notably, it now appears 
to be close to what Drake estimated, ~50 %). Hundreds of exoplanets have 
been found around other stars, and current technology allows the observation 
of even small planets. Theory suggests that the fraction of stars with Earthlike 
planets is somewhere near 10 % (again, surprisingly, and a tribute to back-of- 
the-envelope calculations, not far from Drake’s initial estimate). 

The least well-known value is the question of how difficult is it for life to 
begin (one of the “perennially enigmatic” facts mentioned above). Based on 
present knowledge, the fraction of planets on which life actually emerges 
(fl) could be anywhere from very, very close to 0 or far closer to 1. We simply 
do not know. On the ends of the spectrum, the scientific community is divided 
into two equally “hunch-”based camps: first, life is inevitable and is a cosmic 
imperative (where conditions are appropriate) and, second, the origin of life 
requires such a concatenation of improbable events that it is the scientific 
equivalent of a miracle. 

On the one planet we know of with life, our own, putative evidence in the 
form of isotopically light carbon appears in the earliest known sedimentary 



X 


Preface to the First Edition 


rocks, suggesting life emerged relatively early in the history of the planet, 
although we do not know whether this took place 100 years or 700 million 
years after the planet formed. This implies that either something extraordi¬ 
nary happened on Earth, or that the origin of life is a mundane phenomenon 
on young planets, given appropriate chemistry, environmental conditions, 
and enough time. Radioastronomy has provided a glimpse of the chemical 
inventory of the cosmos which does appear to be universal. Spectral signa¬ 
tures of a veritable zoo of organic compounds suggest that the Universe is 
strewn with the potential precursors of life. Organic carbon (in the form of 
carbon monoxide) has now been observed as far back as 13 billion years ago, 
only some 700 million years after the birth of the Universe in the Big Bang. 
The picture emerging, reminiscent of Chambers’ universe, is that physics and 
chemistry are the same everywhere in the Universe, and that the Earth, 
although remarkable in many respects, may not be unique. 

As in any factorial equation, the most important values are the ones with 
the largest uncertainty. Two approaches could shed light on the “fl problem”: 
the duplication of the process in the laboratory or the discovery of life on 
another planet. It is difficult to say whether the first approach will ever 
succeed to anyone’s complete satisfaction, given that the origin of life on 
Earth was a historical event that happened when no one was around to witness 
it. The second approach, while fraught with technological difficulties, is 
perhaps more promising. To that end, numerous instruments and space mis¬ 
sions have been designed and launched to explore the Solar System and 
beyond. The spectral signatures of planets around nearby stars are being 
monitored for the characteristic signs of life such as the signature of disequi¬ 
librium chemistry in the form of the presence in their atmospheres of both 
oxidized and reduced gases. 

While the answers to the vast questions that define astrobiology as a field 
of study are unclear, it is evident that answering them will require an 
interdisciplinary effort, stretching across international borders. One is hesi¬ 
tant to speculate what the answer to the question, “Are we alone?” will 
ultimately be. As good scientists, we should probably withhold judgment 
until the data are in. As better scientists, we must join hands and find the data. 
The editors of the Encyclopedia of Astrobiology hope that this volume will 
contribute to this effort. 


The Editors 


Notes 

1. A complete English and French version of the Encyclopedic can be found at http://quod. 
lib.umich.edu/d/did/ 

2. For a complete English translation of Pliny the Elder’s The Natural History by John 
Bostock see http://www.perseus.tufts.edu/hopper/text?doc=Plin.+Nat.+toc&redirect= 
true. A complete Latin version can be found at http://www.perseus.tufts.edu/hopper/ 
text?doc=Perseus:text:1999.02.0138:toc&redirect=true 

3. Chambers R (1994) Vestiges of the natural history of creation and other evolutionary 
writings. University of Chicago Press 




Preface to the First Edition 


XI 


4. Cosmos was a remarkable 13-part popular science series narrated by Carl Sagan which 
aired in 1980. Most if not all of the episodes can be viewed on line, and a book was spun 
off: Sagan C (1985) Cosmos. Ballantine Books 

5. For a survey of the early developments in astronomy, see Lankford J (ed) (1996) History 
of astronomy: an encyclopedia, 1st edn. Routledge 

6. For an excellent discussion of the early history of chemistry (including the work of 
Black, Priestly and Lavoisier) see Partington JR (1989) A short history of chemistry, 3rd 
revised edn. Dover Publications 

7. Lyell C (2010) Principles of geology: being an inquiry how far the former changes of the 
earth’s surface are referable to causes now in operation. Nabu Press (March 1, 2010). 
Originally published in three volumes between 1830-1833 

8. Woese C, Kandler O, Wheelis M (1990) Towards a natural system of organisms: 
proposal for the domains Archaea, Bacteria, and Eucarya. Proc Nat Acad Sci USA 
87(12): 4576^579 

9. For an insightful recounting of the early history of NASA’s early efforts in exo- and 
astrobiology (including discussion of the roles of Wolf Vishniac and Frank Drake) see 
Dick SJ, Strick JE (2005) The living universe: NASA and the development of astrobi¬ 
ology. Rutgers University Press 




Preface to the Second Edition 


The Encyclopedia of Astrobiology serves as the key to a common under¬ 
standing of the astrobiology field among astronomers and astrophysicists, 
biologists and biochemists, chemists, geologists and geochemists, space 
scientists, historians of science, and others working in this interdisciplinary 
and rapidly expanding field. In the past few years, the pace of advancement in 
astrobiology has become so rapid that we have felt it necessary to update and 
expand many of the earlier entries and to augment the original edition of this 
Encyclopedia, published in 2011, with some 300 new entries. Exciting results 
include the discovery of some 1,200 planets (as of early 2015) orbiting stars 
other than the Sun, some with masses close to that of Earth; the continuing 
exploration of the conditions possibly relevant to life on Solar System bodies 
such as Mars, Saturn’s satellites Titan and Enceladus, and comets; the in vitro 
evolution of increasingly capable and diverse ribozymes; the progress toward 
synthetic cellular systems that can undergo Darwinian evolution; the discov¬ 
ery of increasingly complex organic molecules in interstellar space; and the 
recently launched and newly planned space missions and telescopes that will 
further our knowledge of the universe and make significant contributions to 
the goals of astrobiology. All of this research is relevant to our increasingly 
detailed understanding concerning the origin of life on our own planet and the 
possible occurrence of life elsewhere in the universe. Finally, the History of 
Science section is expanded to include speculation on topics such as the origin 
of species and the possibility of inhabited planets beyond the Earth by 
classical and medieval scholars, the latter from both Europe and the Islamic 
world. 

We believe that both new and experienced researchers as well as graduate 
students - either in the adjacent fields of astrobiology or those new to the 
subject - will appreciate this reference work during their quest to understand 
the whole picture. To aid this process, we introduce in this edition a Table of 
Contents, broken down by research area, which nicely illustrates the breadth 
and the depth of the field of astrobiology. Although members of the different 
disciplines commonly employ their own terminology and technical language, 
here we have made a special effort to eliminate specialized jargon and 
overtechnical terms from the Encyclopedia. Synonyms and keywords from 


xiii 



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Preface to the Second Edition 


the 1st edition have been carefully revisited, with many newly added and 
redundant terms deleted. 

Both the carefully selected group of active researchers contributing to this 
work as well as the expert field editors hope that this new edition will be 
valuable to the scientific community and accelerate the interdisciplinary 
advance of astrobiology. 

The Editors 



Acknowledgement to the Second Edition 


A brief note is warranted about how we constructed the Encyclopedia. 
A glossary of terms was first compiled by a team of experts in each field. It 
was then cross-referenced between fields to check for conceptual overlap and 
was then both expanded and pared down to produce a consensus entry list. 

Authors with peer-recognized contributions to their fields of study were 
then invited to contribute entries appropriate to their expertise. After a final 
draft was submitted, entries were proofread and vetted for scientific accuracy 
and readability by a team of field editors, then edited and modified to be 
accessible by a reader with general knowledge of college-level science. 
Finally, the entries were cross-referenced and edited for stylistic consistency 
and ease of reading. 

The editors would like to sincerely thank all the authors of the content of 
the Encyclopedia for their efforts and understanding throughout the long and 
at times difficult triple review process. We are particularly grateful to those 
who also accepted to act as nonspecialist reviewers for fields other than 
their own. 

We would also like to thank several people who, although not authors, 
served as external reviewers for a significant number of entries: Maxence 
Claeys (Ecole Centrale Paris, France), Carlos Garcia-Ferris (Universitat de 
Valencia, Spain), David Hochberg (CAB, Madrid, Spain), Pierre Fena 
(Academie des Sciences, Paris, France), Susan Feschine (University of Mas¬ 
sachusetts Amherst, USA), and Jean Vandenhaute (University of Namur, 
Belgium). 

We express our gratitude to our respective institutions, especially those 
who facilitated and aided in the organization and funding of editorial meet¬ 
ings: Centre National de la Recherche Scientifique (CNRS, France), Centre 
National d’Etudes Spatiales (CNES, France), Faboratoire d’Astrophysique de 
Bordeaux (France), Universite Bordeaux 1 (France), GEOTOP Research 
Center for Geochemistry and Geodynamics (Universite de Quebec a Mon¬ 
treal, Canada), Natural Sciences and Engineering Research Council of Can¬ 
ada, European Science Foundation (Archean Environment Research 
Networking Program), Centro de Astrobiologia (CAB, INTA-CSIC, Madrid, 
Spain), Universidad Autonoma de Madrid, NASA Goddard Space Flight 
Center Cooperative Agreement NNX09AH33A with the University of Mas¬ 
sachusetts. This work was also supported by the European COST Action TD 


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Acknowledgement to the Second Edition 


1308 “Origins and evolution of life on Earth and in the Universe” and the 
Erasmus + European Astrobiology Campus. 

Last, but certainly not least, we express our sincere appreciation to the 
editorial staff of Springer, in particular Saskia Ellis and Daniela Graf, who 
lent technical and administrative support throughout the entire process. 

The Editors 



Editors-in-Chief 


Muriel Gargaud CNRS-Universite de Bordeaux, Laboratoire 
d’Astrophysique de Bordeaux, Floirac, France 

William M. Irvine University of Massachusetts, Amherst, MA, USA 


XVII 




Field Editors 


Ricardo Amils Departamento de Biologia Molecular, Universidad 
Autonoma de Madrid, Madrid, Spain 

Field: Life Sciences 

Henderson James (Jim) Cleaves II Earth-Life Science Institute (ELSI), 
Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan 

Field: Chemical Sciences 

Daniele L. Pinti GEOTOP Research Center for Geochemistry and 
Geodynamics, Universite du Quebec a Montreal, Montreal, QC, Canada 

Field: Earth Sciences 

Jose Cernicharo Quintanilla Department of Astrophysics, Laboratory of 
Molecular Astrophysics, Iorrejon de Ardoz, Madrid, Spain 

Field: Astrophysics and Astrochemistry 

Daniel Rouan LESIA, Observatoire Paris-Site de Meudon, Meudon, France 
Field: Astrophysics and Astrochemistry 

Tilman Spohn Deutsches Zentrum fur Luft- und Raumfahrt (DLR), Institut 
fur Planetenforschung, Berlin, Germany 

Field: Planetary Sciences and Exoplanets 

Stephane Tirard Centre Francois Viete d’Histoire des Sciences et des 
Techniques EA 1161, Faculte des Sciences et des Techniques de Nantes, 
Nantes, France 

Field: History and Philosophy of Science 

Michel Viso CNES/DSP/SME, Veterinaire/DVM, Astro/Exobiology, Paris 
Cedex 1, France 

Field: Space Missions , Ground Facilities and Planetary Protection 
and 

Institutions and Organizations 


XIX 




Section Editors 


Alessandro Airo Institut fur Geologische Wissenschaften Tektonik und 
Sedimentare Geologie, Freie Universitat Berlin, Fachbereich 
Geowissenschaften, Berlin, Germany 

Section: Inner Solar System 

Francis Albarede Ecole Normale Superieure de Lyon, Lyon, France 
Section: Early Earth Geochemistry 

Yann Alibert Space Research and Planetary Sciences, Physics Institute, 
University of Bern, Bern, Swiss 

Section: Planetary Formation and Dynamics 

Philippe Andre Laboratoire AIM, IRFU/Service d’Astrophysique, CEA 
Saclay, Gif-sur-Yvette, France 

Section: Stars - Formation and Evolution 

Kristin Bartik Universite libre de Bruxelles, Brussels, Belgium 

Section: Chemistry - General Definitions 

Hugues Bersini IRIDIA, Universite Libre de Bruxelles, Brussels, Belgium 
Section: Artificial Life 

Carlos Briones Centro de Astrobiologia (CSIC/INTA), Consejo Superior de 
Investigaciones Cientificas, Torrejon de Ardoz, Madrid, Spain 

Section: Genetics and Evolution 

Therese Encrenaz LESIA, Observatoire de Paris - Section de Meudon, 
France 

Section: Outer Solar System 

Fernando B. Figueiredo CITEUC, University of Coimbra, Coimbra, 
Portugal 

Section: History and Philosophy of Science 


XXI 



xxii 

Felipe Gomez Centro de Astrobiologia (CSIC/INTA), Instituto Nacional de 
Tecnica Aeroespacial, Torrejon de Ardoz, Madrid, Spain 

Section: Biology - General Definitions 

John Lee Grenfell German Aerospace Center (DLR), Berlin, Germany 
Section: Planetary and Exoplanetary Atmospheres 

Nader Haghighipour Institute for Astronomy, University of Hawaii- 
Manoa, Honolulu, Hawaii, HI, USA 

Section: Exoplanetary Systems 

Ravit Helled Geophysical, Atmospheric and Planetary Sciences, Tel Aviv 
University, Raymond and Beverly Sackler Faculty of Exact Sciences, 
Tel Aviv, Israel 

Section: Planetary Formation and Dynamics 

Christoph Heubeck Institut fur Geowissenschaften, Friedrich-Schiller- 
Universitat Jena, Jena, Germany 

Section: Archean Geology 

Gerda Horneck DLR German Aerospace Center, Institute of Aerospace 
Medicine, Radiation Biology, Koln, Germany 

Section: Microbiology in Space 

Emmanuelle J. Javaux Palaeobiogeology-Palaeobotany-Palaeopalynology, 
Geology Department, Universite de Liege, Liege, Belgium 

Section: Traces of Life 

Kensei Kobayashi Yokohama National University, Tokiwadai, Hodogaya-ku, 
Yokohama, Japan 

Section: Chemistry - General Definitions 

Juli Pereto Institut Cavanilles de Biodiversitat i Biologia Evolutiva, 
Universitat de Valencia, Valencia, Spain 

Section: Biochemistry 

Andrew Pohorille NASA Ames Research Center, Mountain View, CA, USA 
Section: Prebiotic Chemistry and Origins of Life 
Nikos Prantzos Institut d’Astrophysique de Paris, Paris, France 
Section: Nucleosynthesis 

Barbara Stracke Deutsches Zentrum fur Luft- und Raumfahrt (DLR), 
Institut fur Planetenforschung, Berlin, Germany 


Section Editors 


Section: Inner Solar System 



Contributors 


Jose Pascual Abad Facultad de Ciencias, Departamento de Biologia Molec¬ 
ular, Universidad Autonoma de Madrid, Cantoblanco, Madrid, Spain 

Farah Abdul-Rahman University of Massachusetts Amherst, Amherst, 
MA, USA 

Delphine Acolat Centre Francois Viete, Universite de Bretagne 
Occidentale, Quimper, France 

Angeles Aguilera Laboratorio de Extremofilos, Centro de Astrobiologia 
(INTA-CSIC), Torrejon de Ardoz, Madrid, Spain 

Marcelino Agundez Instituto de Ciencia de Materiales de Madrid, Madrid, 
Spain 

Alessandro Airo Institut fur Geologische Wissenschaften Tektonik und 
Sedimentare Geologie, Freie Universitat Berlin, Fachbereich 
Geowissenschaften, Berlin, Germany 

Francis Albarede Ecole Normale Superieure de Lyon, Lyon, France 

Conel Michael O’Donel Alexander Department of Terrestrial Magnetism, 
Carnegie Institution of Washington, NW Washington, DC, USA 

Yann Alibert Space Research and Planetary Sciences, Physics Institute, 
University of Bern, Bern, Swiss 

Abigail Allwood Jet Propulsion Laboratory, Pasadena, CA, USA 

Concepcion Alonso Universidad Autonoma de Madrid, Madrid, Spain 

Wladyslaw Altermann Department of Geology, University of Pretoria, 
Pretoria, South Africa 

Linda Amaral-Zettler Marine Biological Laboratory, Josephine Bay Paul 
Center for Comparative Molecular Biology and Evolution, Woods Hole, 
MA, USA 

Ricardo Amils Departamento de Biologia Molecular, Universidad 
Autonoma de Madrid, Madrid, Spain 

Ariel D. Anbar School of Earth & Space Exploration and Department of 
Chemistry & Biochemistry, Arizona State University, Tempe, AZ, USA 



xxiv 

Luc Andre Department of Earth Sciences, Royal Museum of Central Africa, 
Tervuren, Belgium 

Philippe Andre Laboratoire AIM, IRFU/Service d’Astrophysique, CEA 
Saclay, Gif-sur-Yvette, France 

Ralf H. Anken German Aerospace Center (DLR), Institute of Aerospace 
Medicine, Cologne, Germany 

Josefa Anton Department of Physiology, Genetics and Microbiology, 
University of Alicante, Alicante, Spain 

Nicholas Arndt ISTerre, Universite Grenoble Alpes, France 

Andrew Aubrey NASA Jet Propulsion Laboratory, Pasadena, CA, USA 

Jeffrey Bada Scripps Institution of Oceanography, La Jolla, CA, USA 

Juan P. G. Ballesta Genome Dynamics and Function, Centro de Biologia 
Molecular Severo Ochoa, Cantoblanco, Madrid, Spain 

Nadia Balucani Dipartimento di Chimica, Universita degli Studi di Perugia, 
Perugia, Italy 

Rory Barnes Astronomy Department, University of Washington, Seattle, 
WA, USA 

Maria Antonietta Barucci Observatoire de Paris, LESIA, Meudon Princi¬ 
pal, Cedex, France 

Gibor Basri Astronomy Department, MC 3411, University of California, 
Berkeley, CA, USA 

Ugo Bastolla Unidad de Bioinformatica, Centro de Biologia Molecular 
“Severo Ochoa,” CSIC-UAM, Madrid, Spain 

Fabia Ursula Battistuzzi Oakland University, Rochester, MI, USA 

Christa Baumstark-Khan German Aerospace Center (DLR), Institute of 
Aerospace Medicine, Cologne, Germany 

Andrey Bekker Department of Geology and Geophysics, Yale University, 
New Haven, CT, USA 

G. Fritz Benedict McDonald Observatory, The University of Texas, Austin, 
TX, USA 

Stefan Bengtson Department of Palaeozoology, The Swedish Museum of 
Natural History, Stockholm, Sweden 

Karim Benzerara Institut de Mineralogie et de Physique des Milieux 
Condenses, UMR 7590, CNRS, Universite Pierre et Marie Curie & Institut 
de Physique du Globe de Paris, Paris, France 

Jose Berenguer Centro de Biologia Molecular Severo Ochoa, UAM-CSIC, 
Madrid, Spain 


Contributors 



Contributors 


xxv 


Sylvain Bernard Laboratoire de Mineralogie et de Cosmochimie du 
Museum (LMCM), Paris, France 

Hugues Bersini IRIDIA, Universite Libre de Bruxelles, Brussels, Belgium 

Bruno Bezard LESIA, Observatoire de Paris, Meudon, France 

Jean-Pierre Bibring Institut d’Astrophysique Spatiale, Universite Paris 
Sud, Orsay, France 

John H. Black Department of Earth and Space Sciences, Chalmers Univer¬ 
sity of Technology, Onsala Space Observatory, Onsala, Sweden 

Donna Blackmond The Scripps Research Institute, La Jolla, CA, USA 

Jeffrey Blanchard Biology Department, University of Massachusetts 
Amherst, Amherst, MA, USA 

Laurent Boiteau Institut des Biomolecules Max Mousseron, UMR5247 
CNRS, University Montpellier-2, Montepellier Cedex, France 

Tyler Bourke Square Kilometre Array Organisation, Macclesfield, 
Cheshire, UK 

Jessica C. Bowman School of Chemistry and Biochemistry, Georgia Insti¬ 
tute of Technology, Atlanta, GA, USA 

Samuel A. Bowring Department of Earth, Atmospheric and Planetary 
Sciences, Massachusetts Institute of Technology, Building 54-1126, 
Cambridge, MA, USA 

Maud Boyet Universite Blaise Pascal, Clermont-Ferrand, France 

Andre Brack Centre de Biophysique Moleculaire CNRS, Orleans Cedex 2, 
France 

Robert Braun Square Kilometre Array Organisation, Macclesfield, 
Cheshire, UK 

Doris Breuer German Aerospace Center (DLR), Institute of Planetary 
Research, Berlin, Germany 

Carlos Briones Centro de Astrobiologia (CSIC/INTA), Consejo Superior de 
Investigaciones Cientificas, Madrid, Spain 

Gilles Bruylants Engineering of Molecular NanoSystems, Universte Libre 
de Bruxelles, Brussels, Belgium 

Sergey Bulat NRC ‘Kurchatov institute’, Petersburg Nuclear Physics Insti¬ 
tute, Leningrad Region, Gatchina, Russia 

Vincent Busigny Institut de Physique du Globe de Paris, Paris, France 

Gary R. Byerly Department of Geology & Geophysics, Louisiana State 
University, Baton Rouge, LA, USA 



xxvi 

Michel Cabane LATMOS/IPSL B102/T45-46, Universite Pierre et Marie 
Curie UPMC-Paris 6, Paris, France 

Jean Cadet Laboratoire Lesions des Acides Nucleiques, Institute 
Nanosciences et Cryogenie/CEA, Grenoble, France 

Michael P. Callahan Astrochemistry Laboratory, Code 691, NASA 
Goddard Space Flight Center, Greenbelt, MD, USA 

Jan Cami Department of Physics and Astronomy, The University of 
Western Ontario, London, ON, Canada 

SETI Institute, 189 Bernardo Avenue, Suite 100, Mountain View, CA, USA 

Ian Campbell Research School of Earth Sciences, The Australian National 
University, Canberra, ACT, Australia 

Tammy Campbell Chemistry, The Scripps Research Institute, La Jolla, 
CA, USA 

Donald E. Canfield Institute of Biology, University of Southern Denmark, 
Odense, Denmark 

Maria Luz Cardenas Unite de Bioenergetique et Ingenierie des Proteines, 
Centre National de la Recherche Scientihque, Aix-Marseille Universite, 
Marseille Cedex 20, France 

Damien Cardinal LOCEAN, Universite Pierre & Marie Curie, Paris, 
France 

Leticia Carigi Instituto de Astronomia, Universidad Nacional Autonoma de 
Mexico, Mexico, DF, Mexico 

P. Brandon Carroll California Institute of Technology, Pasadena, CA, USA 

Piergiorgio Casavecchia Dipartimento di Chimica, Universita degli Studi 
di Perugia, Perugia, Italy 

Claude Catala 1LESIA, Observatoire de Paris, Meudon, France 

Franco Cataldo Istituto Nazionale di Astrohsica - Osservatorio Astrohsico 
di Catania, Catania, Italy 

Actinium Chemical Research, Rome, Italy 

David C. Catling Department of Earth and Space Sciences, University of 
Washington, Seattle, WA, USA 

Cecilia Ceccarelli Laboratoire d’Astrophysique de Grenoble (LAOG/ 
IP AG), Universite J.Fourier de Grenoble, CNRS, Grenoble, France 

Gilles Chabrier Centre de Recherche Astrophysiue de Lyon, Ecole 
Normale Superieure de Lyon, Lyon, France 

John H. Chalmers Scripps Institute of Oceanography Geosciences 
Research Division, University of California, San Diego, La Jolla, CA, USA 


Contributors 



Contributors 


XXVII 


Gregory Chambon Faculty of Arts and Humanities, University of Nantes, 
Brest Cedex 3, France 

Steven B. Charnley Solar System Exploration Division, Code 691, 
Astrochemistry Laboratory, NASA Goddard Space Flight Center, Greenbelt, 
MD, USA 

Marc Chaussidon Institut de Physique du Globe de Paris (IPGP), Paris, 
France 

Glenn E. Ciolek New York Center for Astrobiology, Rensselaer Polytech¬ 
nic Institute, Troy, NY, USA 

Philippe Claeys Earth System Science, Vrije Universiteit Brussel, Brussels, 
Belgium 

Henderson James (Jim) Cleaves II Earth-Life Science Institute (ELSI), 
Tokyo Institute of Technology, Meguro-ku, Tokyo, Japan 

Institute for Advanced Study, Princeton, NJ, USA 

Blue Marble Space Institute of Science, Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute of Technology, Atlanta, 
GA, USA 

Alain Coc Centre de Sciences Nucleaires et de Sciences de la Matiere 
(CSNSM) CNRS/IN2P3, Universite Paris Sud 11, UMR 8609, Orsay, France 

Charles S. Cockell Geomicrobiology Research Group, PSSRI, Open 
University, Milton Keynes, UK 

Catharine A. Conley NASA Headquarters, Washington, DC, USA 

Joanna F. Corby University of Virginia, Charlottesville, VA, USA 

Martin A. Cordiner The Goddard Center for Astrobiology, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 

Athel Cornish-Bowden Unite de Bioenergetique et Ingenierie des 
Proteines, Centre National de la Recherche Scientihque, Aix-Marseille 
Universite, Marseille Cedex 20, France 

Herve Cottin Laboratoire Interuniversitaire des Systemes Atmospheriques, 
Universite Paris Est-Creteil, Creteil, France 

Athena Coustenis Laboratoire d’ Etudes Spatiales et d’ Instrumentation en 
Astrophysique (LESIA), Observatoire de Paris, CNRS, UPMC Univ. Paris 
06, Univ. Paris-Diderot, Meudon Cedex, France 

Vanessa Cox Georgia Institute of Technology, Atlanta, GA, USA 

Jacques Crovisier LESIA, Observatoire de Paris, Meudon, France 

Alfonso F. Davila SETI Institute - NASA Ames Research Center MS 245-3, 
Moffett Field, CA, USA 


Thijs de Grauuw ALMA, Vitacura, Santiago, Chile 



XXVIII 


Bradley De Gregorio Materials Science and Technology Division, U.S. 
Naval Research Laboratory, Washington, DC, USA 

Andres de la Escosura Nanoscience and Molecular Materials Research 
Group, Universidad Autonoma de Madrid, Madrid, Spain 

Rafael R. de la Haba Department of Microbiology and Parasitology, 
Faculty of Pharmacy, University of Sevilla, Sevilla, Spain 

Jean-Pierre de Vera DLR, Institut fur Planetenforschung, Berlin, Germany 

David Deamer Department of Chemistry, University of California, Santa 
Cruz, Santa Cruz, CA, USA 

Luis Delaye Departamento de Ingenieria Genetica, CINVESTAV-Irapuato, 
Irapuato, Gto, Mexico 

Rene Demets ESTEC (HSF-USL), Noordwijk, The Netherlands 

Didier Despois Laboratoire d’Astrophysique de Bordeaux, CNRS- 
Universite de Bordeaux, France 

Louis d’Hendecourt Institut d’Astrophysique Spatiale, Universite 
Paris-Sud 11, Orsay Cedex, France 

Phil Diamond Square Kilometre Array Organisation, Macclesfield, 
Cheshire, UK 

Mark A. Ditzler NASA Ames Research Center, Moffett Field, CA, USA 

Mark Dorr University of Southern Denmark, Odense M, Denmark 

Thierry Douki Laboratoire Lesions des Acides Nucleiques, Institute 
Nanosciences et Cryogenie/CEA, Grenoble, France 

Nadja Drabon Stanford University, Stanford, CA, USA 

Line Drube DLR Institute of Planetary Research, German Aerospace 
Center (DLR), Berlin-Adlershof, Germany 

Jean Duprat Centre de Sciences Nucleates et de Sciences de la Matiere 
(CSNSM), Orsay, France 

Claude D’Uston Geophysique Planetaire & Plasmas Spatiaux, Institut de 
Recherche Astrophysique et Planetologique, Toulouse, France 

Jason P. Dworkin NASA Goddard Space Flight Center, Astrochemistry 
Laboratory, Greenbelt, MD, USA 

Patrick Eggenberger Geneva Observatory, University of Geneva, Geneva, 
Switzerland 

Pascale Ehrenfreund Space Policy Institute, George Washington University, 
Washington, DC, USA 

Jennifer Eigenbrode NASA Goddard Space Flight Center, Greenbelt, 
MD, USA 



Contributors 


xxix 

Sylvia Ekstrom Observatoire Astronomique de l’Universite de Geneve, 
Faculte des Sciences, Universite de Geneve, Versoix, Switzerland 

J. Cynan Ellis-Evans UK Arctic Office, Strategic Coordination Group, 
British Antarctic Survey, Cambridge, UK 

Josef Elster Faculty of Science, Centre for Polar Ecology, University of 
South Bohemia, Ceske Budejovice, Czech Republic 

Institute of Botany, Academy of Sciences of the Czech Republic, Trebon, 
Czech Republic 

Therese Encrenaz LESIA, Observatoire de Paris - Section de Meudon, 
Meudon, France 

Cecile Engrand Centre de Sciences Nucleates et de Sciences de la Matiere 
(CSNSM), Orsay, France 

Gozen Ertem National Institutes of Health, Bethesda, MD, USA 

Alberto G. Fairen NASA Ames Research Center, Moffett Field, CA, USA 

James Farquhar Department of Geology, University of Maryland, College 
Park, MD, USA 

Victor M. Fernandez Institute of Catalysis, CSIC, Madrid, Spain 

David C. Fernandez-Remolar Centro de Astrobiologia (INTA-CSIC), 
INTA, Torrejon de Ardoz, Spain 

Fernando B. Figueiredo CITEUC, University of Coimbra, Coimbra, 
Portugal 

Ricardo Flores Instituto de Biologia Molecular y Celular de Plantas (UPV- 
CSIC), Universidad Politecnica de Valencia - Consejo Superior de 
Investigaciones Cientificas, Valencia, Spain 

Francois Forget Institut Pierre Simon Laplace, Laboratoire de 
Meteorologie Dynamique, UMR 8539, Universite Paris 6, Paris, France 

Yves Fouquet Institut Francois de Recherche pour l’Exploitation de la mer 
(IFREMER), Issy-les-Moulineaux, France 

Dionysis Foustoukos Geophysical Laboratory, Carnegie Institution of 
Washington, Washington, DC, USA 

Stephen Freeland Astrobiology Institute, University of Hawaii NASA, 
Honolulu, HI, USA 

Malcolm Fridlund Max-Planck-Institut fur Astronomie, Heidelberg, 
Germany 

Muriel Gargaud CNRS-Universite de Bordeaux, Laboratoire 

d’Astrophysique de Bordeaux, Floirac, France 

William Gamier Square Kilometre Array Organisation, Macclesfield, 
Cheshire, UK 



XXX 


Contributors 


Jose Carlos Gaspar Institute of Geosciences, University of Brasilia, 
Brasilia, DF, Brazil 

Maria Gasset Consejo Superior de Investigaciones Cientificas, Instituto 
Quimica-Fisica Rocasolano, Madrid, Spain 

Philipp Gast Asteroids and Comets, Institute of Planetary Research, 
German Aerospace Center, Berlin, Germany 

Eric Gaucher School of Biology, Georgia Institute of Technology, Atlanta, 
GA, USA 

B. Scott Gaudi Department of Astronomy, Ohio State University, 
Columbus, OH, USA 

Carlos Gershenson Instituto de Investigaciones en Matematicas Aplicadas 
y en Sistemas, Universidad Nacional Autonoma de Mexico, DF, Mexico 

Rosario Gil Institut Cavanilles de Biodiversitat i Biologia Evolutiva, 
Universitat de Valencia, Patema (Valencia), Spain 

Felipe Gomez Centro de Astrobiologia (CSIC/INTA), Instituto Nacional de 
Tecnica Aeroespacial, Torrejon de Ardoz, Madrid, Spain 

Aldo Gonzalez Centro de Biologia Molecular, CBMSO Consejo Superior 
de Investigaciones Cientificas Universidad Autonoma de Madrid, Madrid, 
Spain 

Elena Gonzalez-Toril Laboratorio de Extremofilos, Centro de 
Astrobiologia (INTA-CSIC), Torrejon de Ardoz, Madrid, Spain 

Andrew Gould Department of Astronomy, Ohio State University, Colum¬ 
bus, OH, USA 

Matthieu Gounelle Laboratoire de Mineralogie et Cosmochimie du 
Museum (LMCM) MNHN USM 0205 - CNRS UMR 7202, Museum National 
d’Histoire Naturelle, Paris, France 

Pierre-Henri Gouyon Departement Systematique et Evolution, UMR 7138 
CNRS-MNHN-UPMC-IRD, Museum National d’Histoire Naturelle, Paris 
Cedex 05, France 

Felix M. Gradstein University of Oslo, Blindem, Oslo, Norway 

Olivier Grasset University of Nantes, Nantes, France 

Jimi Green Square Kilometre Array Organisation, Macclesfield, Cheshire, 
UK 

John Lee Grenfell German Aerospace Center (DLR), Berlin, Germany 

Richard A. F. Grieve University of Western Ontario, London, ON, Canada 

Elizabeth C. Griffith University of Colorado, Boulder, CO, USA 

Roderich GroB Department of Automatic Control & Systems Engineering, 
The University of Sheffield, Sheffield, UK 



Contributors 


xxxi 


Manuel Giidel Department of Astrophysics, University of Vienna, Vienna, 
Austria 

Stephane Guillot LGCA, Universite de Grenoble, St Martin d’Heres, 
France 

Tristan Guillot Observatoire de la Cote d’Azur, Universite de Nice-Sophia 
Antipolis, CNRS, Nice, France 

Weifu Guo Carnegie Institution of Washington, Washington, DC, USA 

Nader Haghighipour Institute for Astronomy, University of Hawaii- 
Manoa, Honolulu, Hawaii, HI, USA 

Gerhard Hahn Asteroids and Comets, DLR, Institute of Planetary 
Research, Berlin, Germany 

Salman Hameed Hampshire College, Amherst, MA, USA 

Alan W. Harris DLR, Institute of Planetary Research, Berlin, Germany 

Emma Hart School of Computing, Edinburgh Napier University, 
Edinburgh, UK 

Thomas H. P. Harvey Department of Earth Sciences, University of 
Cambridge, Cambridge, UK 

Ko Hashizume Department of Earth and Space Sciences, Osaka University, 
Toyonaka, Osaka, Japan 

Ernst Hauber Deutsches Zentrum fiir Luft- und Raumfahrt (DLR) e.V., 
Institut fiir Planetenforschung, Berlin, Germany 

Rasmus Nielsen Haugaard Department of Earth and Atmospheric 
Sciences, University of Alberta, Edmonton, AB, Canada 

Robert Hazen Geophysical Laboratory, Carnegie Institution of Washington, 
Washington, DC, USA 

Jorn Helbert DLR, Institut fiir Planetenforschung, Berlin, Germany 

Ravit Helled Geophysical, Atmospheric and Planetary Sciences, Tel Aviv 
University, Raymond and Beverly Sackler Faculty of Exact Sciences, 
Tel Aviv, Israel 

Ruth Hemmersbach German Aerospace Center (DLR), Institute of 
Aerospace Medicine, Cologne, Germany 

Patrick Hennebelle Service d’Astrophysique, CEA, Saclay, Gif-sur Yvette, 
France 

Judith Herzfeld Brandeis University, Waltham, MA, USA 

Christoph Heubeck Institut fiir Geowissenschaften, Friedrich-Schiller- 
Universitat Jena, Jena, Germany 

Ake Hjalmarson Chalmers University of Technology, Gothenburg, Sweden 



xxxii 

Pentti Holtta Department of Geosciences and Geography, University of 
Helsinki, Finland and Geological Survey of Finland, Espoo, Finland 

Tori M. Hoehler Exobiology Branch, NASA Ames Research Center, 
Mountain View, CA, USA 

Paul Hoffman Department of Earth & Planetary Sciences, Harvard Univer¬ 
sity, Cambridge, MA, USA 

Harald Hoffmann DLR, Institute of Planetary Research, Berlin, Germany 

Axel Hofmann Department of Geology, University of Johannesburg, 
Auckland Park, Johannesburg, South Africa 

Michiel R. Hogerheijde Leiden Observatory, Leiden University, Leiden, 
The Netherlands 

Martin Homann Institut fur Geologische Wissenschaften, Freie Universitat 
Berlin, Berlin, Germany 

Gerda Horneck DLR German Aerospace Center, Institute of Aerospace 
Medicine, Radiation Biology, Koln, Germany 

David P. Horning Department of Molecular Biology, The Scripps Research 
Institute, La Jolla, CA, USA 

Nicholas V. Hud School of Chemistry and Biochemistry, Georgia Institute 
of Technology, Atlanta, GA, USA 

Elizabeth Humphreys ESO European Southern Observatory, Garching, 
Germany 

Susana Iglesias-Groth Instituto de Astrofisica de Canarias, La Laguna, 
Tenerife, Spain 

Heshan Grasshopper Illangkoon Department of Chemistry, University of 
Florida, Gainesville, FL, USA 

Eiichi Imai Nagaoka University of Technology, Nagaoka, Japan 

William M. Irvine University of Massachusetts, Amherst, MA, USA 

Akizumi Ishida Atmosphere and Ocean Research Institute, University of 
Tokyo, Kashiwa, Chiba, Japan 

Mathieu Isidro Square Kilometre Array Organisation, Macclesfield, 
Cheshire, UK 

Ralf Jaumann German Aerospace Center (DLR), Institute of Planetary 
Research, Berlin, Germany 

Emmanuelle J. Javaux Palaeobiogeology-Palaeobotany-Palaeopalynology, 
Geology Department, Universite de Liege, Liege, Belgium 

Michel Jebrak Departement des Sciences de la Terre et de T Atmosphere, 
Universite du Quebec a Montreal, Montreal, QC, Canada 


Contributors 



XXXIII 


Anders Johansen Lund University, Lund, Sweden 

Natasha M. Johnson NASA Goddard Space Flight Center, Greenbelt, 
MD, USA 

Takeshi Kakegawa Graduate School of Science, Tohoku University, 
Sendai, Japan 

Paul Kalas Astronomy Department, University of California, Berkeley, 
CA, USA 

Lisa Kaltenegger Cornell University, Ithaca, NY, USA 

Balz Samuel Kamber Trinity College, Dublin, Ireland 

Inge Loes ten Kate Earth Sciences, Utrecht University, Utrecht, 
The Netherlands 

Michael J. Kaufman Department of Physics and Astronomy, San Jose State 
University, San Jose, CA, USA 

Kunio Kawamura Department of Human Environmental Studies, 
Hiroshima Shudo University, Hiroshima, Japan 

Yoko Kebukawa Department of Natural History Sciences, Hokkaido 
University, Sapporo, Japan 

Laura Kelly Ecogenomics of Interactions Lab, Nancy, France 

Pierre Kervella LESIA, Observatoire de Paris, Meudon, France 

Martin F. Kessler European Space Agency (ESA), European Space 
Astronomy Centre (ESAC), Madrid, Spain 

Daisuke Kiga Tokyo Institute of Technology, Tokyo, Japan 

Eun-Kyong Kim Chemistry, The Scripps Research Institute, La Jolla, 
CA, USA 

Adrienne Kish Institut de Genetique et Microbiologie, Universite Paris-Sud 
11, Orsay Cedex, France 

Daniel Kitzmann University of Bern, Bern, Switzerland 

David Klaus University of Colorado Boulder, Boulder, CO, USA 

Thorsten Kleine Institut fiir Planetologie, Westfalische Wilhelms- 
Universitat Munster, Munster, Germany 

Kateryna Klochko Carnegie Institution of Washington, Washington, 
DC, USA 

Jorg Knollenberg Institute of Planetary Research, German Aerospace 
Center, Berlin, Germany 

Kensei Kobayashi Yokohama National University, Tokiwadai, Hodogaya-ku, 
Yokohama, Japan 



xxxiv 

Kurt O. Konhauser Department of Earth and Atmospheric Sciences, 
University of Alberta, Edmonton, AB, Canada 

Akira Kouchi Institute of Low Temperature Science, Hokkaido University, 
Kita-ku, Sapporo, Hokkaido, Japan 

Ramanarayanan Krishnamurthy Chemistry, The Scripps Research 
Institute, La Jolla, CA, USA 

Edwin C. Krupp Griffith Observatory, Los Angeles, CA, USA 

Marc Kuchner NASA Goddard Space Llight Center, Exoplanets and Stellar 
Astrophysics Laboratory, Greenbelt, MD, USA 

Ekkehard Kiihrt Institute of Planetary Research, German Aerospace 
Center, Berlin, Germany 

Jana Kviderova Institute of Botany, Academy of Sciences of the Czech 
Republic, Trebon, Czech Republic 

Sun Kwok Laculty of Science, The University of Hong Kong, Hong Kong, 
China 

Jean-Fran^ois Lambert Laboratoire de Reactivite de Surface, Universite 
Pierre et Marie Curie, Paris, France 

Doron Lancet Weizmann Institute of Science, Rehovot, Israel 

David W. Latham Harvard-Smithsonian Center for Astrophysics, 
Cambridge, MA, USA 

Amparo Latorre Institute Cavanilles for Biodiversity and Evolutionary 
Biology, Universitat de Valencia, Valencia, Spain 

Ester Lazaro Molecular Evolution Laboratory, Centro de Astrobiologia 
(CSIC-INTA), Torrejon de Ardoz, Madrid, Spain 

Antonio Lazcano Facultad de Ciencias, UNAM, Mexico, DF, Mexico 

Stephane Le Gars Centre Francis Viete, Universite de Nantes, Nantes, 
France 

Michael Lebert Biology Department, Plant Ecophysiology, Friedrich- 
Alexander-University Erlangen/Nuremberg, Erlangen, Germany 

Laura M. Lechuga Nanobiosensors and Bioanalytical Applications Group, 
Institut Catala de Nanociencia i Nanotecnologia (ICN2) CSIC and 
CIBER-BBN, Barcelona, Spain 

Guillaume Lecointre Departement Systematique et Evolution, UMR 7138 
CNRS-MNHN-UPMC-IRD, Museum National d’Histoire Naturelle, Paris 
Cedex 05, France 

Emmanuel Lellouch Laboratoire d’Etudes Spatiales et d’Instrumentation 
en Astrophysique (LESIA), Observatoire de Paris, Meudon, France 


Contributors 



Contributors 


xxxv 


Tom Lenaerts Departement d’lnformatique, Universite Libre de Bruxelles, 
Brussels, Belgium 

Kevin Lepot Laboratoire d’Oceanologie et de Geosciences, Universite de 
Lille, Villeneuve d’Ascq, France 

Hugues Leroux Unite Materiaux et Transformations (UMET), University 
Lille 1, Ronchin, Nord-Pas-de-Calais, France 

Anny-Chantal Levasseur-Regourd UPMC University of Paris 
6/LATMOS-IPSL, Paris, France 

Richard Leveille Natural Resource Sciences, McGill University, St. Anne 
de Bellevue, Quebec, Canada 

Matthew Levy Michael F. Price Center, Albert Einstein College of 
Medicine, Bronx, NY, USA 

Purificacion Lopez-Garcia Unite d’Ecologie, Systematique et Evolution, 
CNRS UMR8079 Universite Paris-Sud 11, Paris, Orsay Cedex, France 

Christophe Malaterre Institut d’Histoire et Philosophic des Sciences et 
Techniques (IHPST), Universite Paris 1-Pantheon Sorbonne, Paris, France 

Physicalism Malaterre Institut d’Histoire et Philosophic des Sciences et 
Techniques (IHPST), Universite Paris 1-Pantheon Sorbonne, Paris, France 

Irena Mamajanov School of Chemistry and Biochemistry, Georgia Insti¬ 
tute of Technology, Atlanta, GA, USA 

Rocco Mancinelli Bay Area Environmental Research Institute, 
NASA Ames Research Institute, NASA Ames Research Center, Moffett 
Field, CA, USA 

Avi M. Mandell NASA Goddard Space Flight Center, Greenbelt, MD, USA 

Susanna Manrubia Systems Biology Program, Centro Nacional de 
Biotecnologia (CSIC), Madrid, Spain 

Irma Mann Departamento de Biologia Molecular, Universidad Autonoma 
de Madrid, Madrid, Spain 

Lori Marino Emory Centre for Ethics, Emory University, Atlanta, GA, USA 

Olivier La Marie Centre National d’Etudes Spatiales DSP/EU, Paris, 
France 

Mark S. Marley NASA Ames Research Center, Moffett Field, CA, USA 

Jean-Emmanuel Martelat LST UMR5570, Universite Claude Bernard 
Lyon 1, St Martin d’Heres, Grenoble, France 

Herve Martin Laboratoire Magmas et Volcans, Universite Blaise Pascal, 
OPGC, CNRS, IRD, Clermont-Ferrand, France 



xxxvi 

Bernard Marty Institut Universitaire de France, Ecole Nationale 
Superieure de Geologie, Centre de Recherches Petrographiques et 
Geochimiques (CRPG), CNRS, Vandoeuvre les Nancy Cedex, France 

Koichiro Matsuno Nagaoka University of Technology, Nagaoka, Japan 

Thomas McCollom Laboratory for Atmospheric and Space Physics, 
University of Colorado, Boulder, CO, USA 

Francis McCubbin Institute of Meteoritics, University of New Mexico, 
Albuquerque, NM, USA 

Brett A. McGuire California Institute of Technology, Pasadena, CA, USA 

Christopher P. McKay NASA Ames Research Center, Moffett Field, 
CA, USA 

Nicola McLoughlin Department of Earth Science and Centre for 
Geobiology, University of Bergen, Bergen, Norway 

Uwe J. Meierhenrich Institut de Chimie de Nice (ICN), University Nice- 
Sophia Antipolis, Nice, France 

H. Jay Melosh Departments of Earth, Atmospheric and Planetary Sciences, 
Physics and Aerospace Engineering, Purdue University, West Lafayette, 
IN, USA 

Francesca Merlin CNRS UMR 8690 IHPST & Universite Paris 1, Paris, 
France 

Allyssa Metzger Harvard University, Cambridge, MA, USA 

Francois Mignard CNRS, Observatoire de la Cote d’Azur, University of 
Nice Sophia-Antipolis, Nice, France 

Stefanie N. Milam Astrochemistry Laboratory, NASA Goddard Space 
Flight Center, Greenbelt, MD, USA 

Thomas J. Millar Astrophysics Research Centre, School of Mathematics 
and Physics, Queen’s University Belfast, Belfast, Antrim, UK 

Vincent Minier CEA, Saclay, France 

Shin Miyakawa Ribomic Inc., Minato-ku, Tokyo, Japan 

A. M. Mloszewska Department of Earth and Atmospheric Sciences, 
University of Alberta, Edmonton, AB, Canada 

Robert Mochkovitch Institut d’Astrophysique de Paris, Paris, France 

Ralf Moeller German Aerospace Center (DLR), Institute of Aerospace 
Medicine, Cologne, Germany 

Stephen Mojzsis University of Colorado, Boulder, CO, USA 

Pierre-Alain Monnard FLinT center, Institute for Physics and Chemistry, 
University of Southern Denmark, Odense M, Denmark 


Contributors 



XXXVII 


Francisco Montero Department of Biochemistry and Molecular Biology I, 
Facultad de Ciencias Quimicas, Universidad Complutense de Madrid, 
Madrid, Spain 

Thierry Montmerle Institut d’Astrophysique de Paris, CNRS/Universite 
Paris 6, Paris, France 

Michel Morange Centre Cavailles, USR 3308 CIRPHLES, Ecole normale 
superieure, Paris Cedex 05, France 

Alessandro Morbidelli Observatoire de la Cote d’Azur, Nice, France 

David Moreira Unite d’Ecologie, Systematique et Evolution CNRS 
UMR8079, Universite Paris-Sud 11, Paris, Orsay Cedex, France 

Alvaro Moreno Departamento de Logica y Filosofia de la Ciencia, 
Universidad del Pais Vasco, San Sebastian, Spain 

Miguel Moreno Centro de Astrobiologia, CSIC, Madrid, Spain 

Harold Morowitz George Mason University, Fairfax, VA, USA 

Stefano Mottola German Aerospace Center (DLR), Institute of Planetary 
Research, Berlin, Germany 

Denis J. P. Moura Ambassade de France en Italie, Ambascia di Francia, 
Rome, Italy 

Jean-Fran^ois Moyen LMV-TL, Universite Jean-Monnet, Saint-Etienne, 
France 

Armen Y. Mulkidjanian School of Physics, University of Osnabrueck, 
Osnabrueck, Germany 

Moscow State University, Moscow, Russia 

Holger S. P. Muller I. Physikalisches Institut, Universitat zu Koln, Koln, 
Germany 

Sami Nabhan Institute of Geological Sciences, Freie Universitat Berlin, 
Berlin, Germany 

Kazumichi Nakagawa Graduate School of Human Development and 
Environment, Kobe University, Nada, Kobe, Japan 

Hiroshi Naraoka Department of Earth and Planetary Sciences, Kyushu 
University, Fukuoka, Japan 

Gopal Narayanan Five College Radio Astronomy Observatory, University 
of Massachusetts, Amherst, MA, USA 

Alicia Negronk-Mendoza Instituto de Ciencias Nucleares, Universidad 
Nacional Autonoma de Mexico, Mexico, Coyoacan, DF, Mexico 

Gerhard Neukum Planetary Sciences and Remote Sensing, Institute of 
Geological Sciences, Freie Universitat Berlin, Berlin, Germany 



XXXVIII 


Wayne L. Nicholson Space Life Sciences Laboratory, University of 
Florida, Merritt Island, FL, USA 

Space Life Sciences Laboratory, Kennedy Space Center, University of 
Florida, Gainesville, FL, USA 

Peter E. Nielsen The Panum Institute, ICMM, University of Copenhagen, 
Copenhagen, Denmark 

Nora Noffke Department of Ocean, Earth & Atmospheric Sciences, Old 
Dominion University, Norfolk, VA, USA 

Ann Nowe Vrije Universiteit Brussel, Brussels, Belgium 

Joseph Andrew Nuth III Solar System Exploration Division, NASA’s 
Goddard Space Flight Center, Greenbelt, MD, USA 

Karin I. Oberg Harvard-Smithsonian Center for Astrophysics, Cambridge, 
MA, USA 

Shohei Ohara Carnegie Institution of Washington, Geophysical Labora¬ 
tory, Washington, DC, USA 

Hiroshi Ohmoto NASA Astrobiology Institute and Department of 
Geosciences, The Pennsylvania State University, University Park, PA, USA 

Jose Olivares Esztacion Experimental del Zaidm. CSIC, Granada, Spain 

Marc Ollivier Institut d’Astrophysique Spatiale, CNRS, Universite de 
Paris-Sud, Orsay, France 

Hans Olofsson Department of Earth and Space Sciences, Chalmers Univer¬ 
sity of Technology, Gothenburg, Sweden 

Jonathan O’Neil Department of Earth and Environmental Sciences, 
University of Ottawa, Ottawa, ON, Canada 

Silvano Onofri Department of Ecological and Biological Sciences, Univer¬ 
sity of Tuscia, Viterbo, Italy 

Tullis C. Onstott Department of Geosciences, Princeton University, 
Princeton, NJ, USA 

Sijbren Otto Stratingh Institute for Chemistry, University of Groningen, 
Groningen, The Netherlands 

Corinna Panitz German Aerospace Center (DLR), Institute of Aerospace 
Medicine, Cologne, Germany 

Victor Parro Molecular Evolution Department, Centro de Astrobiologia 
(INTA-CSIC), Torrejon de Ardoz, Madrid, Spain 

Camille Partin Department of Geological Sciences, University of Manitoba, 
Winnipeg, MB, Canada 

Robert Pascal Institut des Biomolecules Max Mousseron CC1706, 
Universite de Montpellier II, Montpellier, France 



Contributors 


xxxix 


Matthew A. Pasek University of South Florida, Tampa, FL, USA 

Mercedes Moreno Paz Molecular Evolution Department, Centro de 
Astrobiologia (INTA-CSIC), Torrejon de Ardoz, Madrid, Spain 

Ernesto Pecoits Department of Earth and Atmospheric Sciences, University 
of Alberta, Edmonton, AB, Canada 

Els Peeters Department of Physics and Astronomy, The University of 
Western Ontario, London, ON, Canada 

SETI Institute, 189 Bernardo Avenue, Suite 100, Mountain View, CA, USA 

Ivanka Pelivan Institute of Planetary Research, German Aerospace Center, 
Berlin, Germany 

Juli Pereto Institut Cavanilles de Biodiversitat i Biologia Evolutiva, 
Universitat de Valencia, Valencia, Spain 

Jerome Perez Applied Mathematics Laboratory, ENSTA ParisTech, Paris 
Cedex 15, France 

Jean-Robert Petit CNRS-UJF, Laboratoire de Glaciologie et Geophysique 
de l’Environnement (LGGE), St Martin D’Heres, France 

Pascal Philippot Equipe Geobiosphere Actuelle et Primitive, Institut de 
Physique du Globe de Paris (IPGP), Paris, France 

Ray Pierrehumbert Department of the Geophysical Sciences, University of 
Chicago, Chicago, IL, USA 

Goran L. Pilbratt ESA/ESTEC/SRE-S, European Space Agency (ESA), 
Science Support Office, Noordwijk, The Netherlands 

Samanta Pino Department of Biology and Biotechnologies “Charles 
Darwin”, University of Rome “Sapienza”, Rome, Italy 

Daniele L. Pinti GEOTOP Research Center for Geochemistry and 
Geodynamics, Universite du Quebec a Montreal, Montreal, QC, Canada 

Sandra Pizzarello Department of Chemistry & Biochemistry, Arizona State 
University, Tempe, AZ, USA 

Noah Planavsky Department of Geology and Geophysics, Yale University, 
New Haven, CT, USA 

Raphael Plasson Department of Earth and Planetary Science, Harvard 
University, Cambridge, MA, USA 

Ana-Catalina Plesa German Aerospace Center (DLR), Institute of 
Planetary Research, Berlin, Germany 

Franck Poitrasson Geosciences Environnement Toulouse, CNRS, 
Toulouse, France 

Nikos Prantzos Institut d’Astrophysique de Paris, Paris, France 
Lawrence Pratt Tulane University, New Orleans, LA, USA 



xl 


Contributors 


Daniel Prieur Universite de Bretagne Occidentale (University of Western 
Britanny), Brest, France 

Institut Universitaire Europeen de la Mer (IUEM), Technopole Brest-Iroise, 
Plouzane, France 

Jose Cernicharo Quintanilla Department of Astrophysics, Laboratory of 
Molecular Astrophysics, Iorrejon de Ardoz, Madrid, Spain 

Ahmed Ragab Harvard Divinity School, Cambridge, MA, USA 

Heike Rauer German Aerospace Center (DLR), Berlin, Germany 

Francois Raulin Faculte des Sciences et Technologie, Universite Paris Est 
Creteil et Paris Diderot, LISA - UMR CNRS 7583, Creteil, France 

Florence Raulin-Cerceau Maitre de Conferences, Centre Alexandre Koyre 
(UMR 8560-CNRS/EHESS/MNHN/CSI) Museum National d’Histoire 
Naturelle, Brunoy, France 

Sean N. Raymond Laboratoire d’Astrophysique de Bordeaux, CNRS, 
Universite de Bordeaux, France 

Jacques Reisse Universite Libre de Bruxelles, Brussels, Belgium 

Anthony J. Remijan NRAO, Charlottesville, VA, USA 

Petra Rettberg German Aerospace Center (DLR), Institute of Aerospace 
Medicine, Cologne, Germany 

Alonso Ricardo Ra Pharmaceuticals, Cambridge, MA, USA 

Antonio J. Ricco NASA Ames Research Center, on Assignment from 
Stanford University, Moffett Field, CA, USA 

Wayne G. Roberge New York Center for Astrobiology, Rensselaer 
Polytechnic Institute, Troy, NY, USA 

Francois Robert Laboratoire de Mineralogie et Cosmochimie du Museum 
(LMCM), Museum National d’Histoire Naturelle, UMR 7202 CNRS, Paris 
Cedex 05, France 

Michael P. Robertson Department of Molecular Biology MB42, The 
Scripps Research Institute, La Jolla, CA, USA 

Bernd Michael Rode Institute for General, Inorganic and Theoretical 
Chemistry, Leopold-Franzens University, Universitat Innsbruck, Innsbruck, 
Austria 

Francisco Rodriguez-Valera Microbiologia, Universidad Miguel 

Hernandez, Campus San Juan, San Juan, Alicante, Spain 

Fran^oise Roques Laboratoire d’Etudes Spatiales et d’Instrumentation en 
Astrophysique (LESIA), Observatoire de Paris, Meudon, France 

Minik T. Rosing Nordic Center for Earth’s Evolution, Natural History 
Museum of Denmark, University of Copenhagen, Copenhagen, Denmark 



Contributors 


xli 

Ramon Rossello-Mora IMEDEA (CSIC-UIB), Esporles, Mallorca, 
Balearic Islands, Spain 

Daniel Rouan LESIA, Observatoire Paris-Site de Meudon, Meudon, France 

Kepa Ruiz-Mirazo Department of Logic and Philosophy of Science, FICE, 
UPV-EHU, Biophysics Research Unit (CSIC - UPV/EHU), Donostia, San 
Sebastian, Spain 

Jan W. Sadownik Stratingh Institute for Chemistry, University of 
Groningen, Groningen, The Netherlands 

Nita Sahai Department of Polymer Science, University of Akron, Akron, 
OH, USA 

Cristina Sanchez-Porro Department of Microbiology and Parasitology, 
Faculty of Pharmacy, University of Sevilla, Sevilla, Spain 

Leopoldo G. Sancho Facultad de Farmacia Departamento de Biologia 
Vegetal II, Universidad Complutense de Madrid, Madrid, Spain 

Jose Luis Sanz Departamento de Biologia Molecular, Universidad 
Autonoma de Madrid, Madrid, Spain 

Pierre Savaton Universite de Caen Basse-Normandie, Caen, France 

Kevin Schindler Lowell Observatory, Flagstaff, AZ, USA 

Karel Schulmann Ecole et Observatoire de Science de la Terre, Institute de 
Physique de Globe, Universite de Strasbourg, Strasbourg, France 

Peter Schuster Institut fur Theoretische Chemie der Universitat Wien, 
Wien, Austria 

Alan W. Schwartz Radboud University Nijmegen, Nijmegen, The 
Netherlands 

William G. Scott Department of Chemistry and Biochemistry, The Center 
for the Molecular Biology of RNA, University of California at Santa Cruz, 
Santa Cruz, CA, USA 

Burckhard Seelig Department of Biochemistry, Molecular Biology and 
Biophysics & BioTechnology Institute, University of Minnesota, St. Paul, 
MN, USA 

Antigona Segura Instituto de Ciencias Nucleares, Universidad Nacional 
Autonoma de Mexico, Mexico, DF, Mexico 

Franck Selsis Laboratoire d’Astrophysique de Bordeaux, Universite de 
Bordeaux, Floirac, France 

CNRS, LAB, Floirac, France 

Dmitry Semenov Max Planck Institute of Astronomy, Heidelberg, 
Germany 



xlii 

Silke Severmann Institute of Marine & Coastal Sciences and Department of 
Earth & Planetary Sciences, Rutgers University, New Brunswick, NJ, USA 

M. A. Shea Air Force Research Laboratory (Emeritus), Bedford, MA, USA 

Don F. Smart Air Force Research Laboratory (Emeritus), Bedford, MA, USA 

Alexander Smirnov Department of Earth and Marine Science, Dowling 
College, Oakdale, NY, USA 

Ian W. M. Smith Chemistry Laboratory, University of Cambridge, 
Cambridge, UK 

Ronald L. Snell Department of Astronomy, 517 K Lederle Graduate 
Research Center, University of Massachusetts, Amherst, MA, USA 

Frank Sohl Deutsches Zentrum fur Luft- und Raumfahrt (DLR), Institut fur 
Planetenforschung, Berlin, Germany 

Alessandro Sozzetti Istituto Nazionale di Astrofisica (INAF) - Osservatorio 
Astrofisico di Torino, Pino Torinese, Italy 

Pietro Speroni di Fenizio CISUC, Department of Informatics Engineering, 
University of Coimbra, Coimbra, Portugal 

Tilman Spohn Deutsches Zentrum fur Luft- und Raumfahrt (DLR), Institut 
fur Planetenforschung, Berlin, Germany 

Greg Springsteen Furman University, Greenville, SC, USA 

Steven W. Stahler Department of Astronomy, University of California, 
Berkeley, CA, USA 

Lucas J. Stal Department of Marine Microbiology, Royal Netherlands 
Institute of Sea Research (NIOZ), Yerseke, The Netherlands 

Vlada Stamenkovic Earth, Atmospheric and Planetary Sciences, Massachu¬ 
setts Institute of Technology (MIT), Cambridge, MA, USA 

Kenneth Mark Stedman Department of Biology, Center for Life in 
Extreme Environments, Portland State University, Portland, OR, USA 

Jennifer C. Stern Planetary Environments Laboratory, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 

Barbara Stracke Deutsches Zentrum fur Luft- und Raumfahrt (DLR), 
Institut fur Planetenforschung, Berlin, Germany 

Harald Strauss Institut fur Geologie und Palaontologie, Westfalische 
Wilhelms-Universitat Munster, Miinster, Germany 

Kenichiro Sugitani Graduate School of Environmental Studies, Nagoya 
University, Nagoya, Japan 


Contributors 



Contributors 


xliii 


Jun-Ichi Takahashi NTT Microsystem Integration Laboratories, Atsugi, 
Japan 

Olga Taran Chemistry and Chemical Biology, Harvard University, 
Cambridge, MA, USA 

Christophe Thomazo UMR CNRS 6282 Biogeosciences, Universite de 
Bourgogne, Dijon, France 

Phil Thurston Laurentian University, Sudbury, ON, Canada 

Simon Tillier Departement Systematique et Evolution, UMR 7138 CNRS- 
MNHN-UPMC-IRD, Museum National d’Histoire Naturelle, Paris, France 

Stephane Tirard Centre Francois Viete d’Histoire des Sciences et des 
Techniques EA 1161, Faculte des Sciences et des Techniques de Nantes, 
Nantes, France 

Daniela Tirsch German Aerospace Center DLR, Institute of Planetary 
Research, Berlin, Germany 

Dmitri Titov European Space Agency, Noordwijk, The Netherlands 

Marco Tomassini Information Systems Department, University of 
Lausanne, Lausanne, Switzerland 

Carmen Tornow Institute of Planetary Research, German Aerospace 
Center, Berlin, Germany 

Melissa G. Trainer NASA Goddard Space Flight Center Code 699, 
Greenbelt, MD, USA 

Pascal Tremblin CEA, Saclay, France 

Jorge L. Vago European Space Agency - ESA/ESTEC (SRE-SM), 
Noordwijk, The Netherlands 

Veronica Vaida University of Colorado, Boulder, CO, USA 

Stephan van Gasselt Planetary Sciences and Remote Sensing, Institute of 
Geological Sciences, Freie Universitat Berlin, Berlin, Germany 

Martin J. Van Kranendonk School of Biological, Earth and Environmen¬ 
tal Sciences, University of New South Wales, Australia 

Antonio Ventosa Department of Microbiology and Parasitology, Faculty of 
Pharmacy, University of Sevilla, Sevilla, Spain 

Enrique Viguera Genetics Department, Sciences Faculty, University of 
Malaga, Malaga, Spain 

Michel Viso CNES/DSP/SME, Veterinaire/DVM, Astro/Exobiology, Paris 
Cedex 1, France 



xliv 

Gunter von Kiedrowski Lehrstuhl fiir Organische Chemie I, Ruhr- 
Universitat Bochum, Bochum, NRW, Germany 

Philip von Paris Laboratoire d’Astrophysique de Bordeaux, Universite de 
Bordeaux, Floirac, France 

CNRS, LAB, Floirac, France 

Jeff Wagg Square Kilometre Array Organisation, Macclesfield, Cheshire, 
UK 

Roland J. Wagner German Aerospace Center (DLR), Institute of Planetary 
Research, Berlin, Germany 

Sara Imari Walker School of Earth and Space Exploration, Arizona State 
University, Tempe, AZ, USA 

Frances Westall Centre de Biophysique Moleculaire, CNRS, Orleans 
Cedex 2, France 

Hubert Whitechurch Ecole et Observatoire de Science de la Terre, Institute 
de Physique de Globe, Universite de Strasbourg, Strasbourg, France 

Douglas Whittet New York Center for Astrobiology, Rensselaer Polytech¬ 
nic Institute, Troy, NY, USA 

Simon Wilde Department of Applied Geology, Curtin University of 
Technology, Perth, Australia 

Ian S. Williams Research School of Earth Sciences, ANU College of 
Physical and Mathematical Sciences, Research School of Earth Sciences, 
The Australian National University, Canberra, ACT, Australia 

Loren Dean Williams School of Chemistry and Biochemistry, Georgia 
Institute of Technology, Atlanta, GA, USA 

Charles T. Wolfe Unit for History and Philosophy of Science, University of 
Sydney, Sydney, NSW, Australia 

Mark G. Wolfire Astronomy Department, University of Maryland, College 
Park, MD, USA 

Alexander Wolszczan Department of Astronomy & Astrophysics and Center 
for Exoplanets & Habitable Worlds, The Pennsylvania State University, 
University Park, PA, USA 

Paul M. Woods Astrophysics Research Centre, School of Mathematics and 
Physics, Queen’s University Belfast, Belfast, Antrim, UK 

Kosei E. Yamaguchi Geochemical Laboratory, Department of Chemistry, 
Toho University, Funabashi, Chiba, Japan 

Masamichi Yamashita Institute of Space and Astronautical Science 
(ISAS)/JAXA, Sagamihara, Kanagawa, Japan 

Bruce Yardley School of Earth and Environment, University of Leeds, 
Leeds, UK 


Contributors 



Contributors 


xlv 


Reika Yokochi Department of Geophysical Sciences, The University of 
Chicago, Chicago, IL, USA 

Department of Earth and Environmental Sciences, University of Illinois at 
Chicago, Chicago, IL, USA 

Philippe Zarka LESIA, Observatoire de Paris, CNRS, UPMC, Universite 
Paris Diderot, Meudon, France 

Annie Zavagno CNRS, LAM (Laboratoire d’Astrophysique de Marseille) 
UMR 7326, Aix Marseille Universite, Marseille, France 

Tanja Elsa Zegers Paleomagnetic Laboratory, Institute of Earth Sciences, 
Utrecht University, Utrecht, CD, The Netherlands 



Astrobiology by Discipline 


Field - Astrophysics & Astrochemistry: 
J. Cernicharo, M. Gargaud, W. Irvine, 

D. Rouan 

Section - Astrochemistry: J. Cernicharo , 
W. Irvine, F. Salama 

4-Cyano-1,3-Butadiynyl 

Absorption Spectroscopy 

Acetone 

Acetylene 

Adsorption 

Amino Radical 

Aminoacetonitrile 

Ammonium (NH3D+) 

Amorphous Solid 
Anion 

Apolar Molecule 

Argonium 

Benzene 

Bimolecular Reaction 
Binding Energy 
Butadiynyl Radical 
C3H+ 

Carbene 
Carbodiimide 
Carbon Mono sulfide 
Charge Transfer 
Chemical Bistability 
Chemisorption 

Chlorine Hydrides in the Interstellar Medium 
Circumstellar Chemistry 
Clathrate Hydrate 
CN- 

Condensation Temperature 


Cosmic Ray, Ionization Rate 
Cyanoethynyl Radical 
Cyanogen Radical 
Cyanomethanimine 
Cyanopolyyne 
Cyclopropenylidene 
Diacetylene 
Diazenylium 

Diffuse Interstellar Bands 

Dihydroxyacetone 

Dimethyl Ether 

Dust Grain 

Electron Attachment 

Electron Dissociative Recombination 

Electron Radiative Recombination 

Elemental Depletion 

Eley-Rideal Mechanism 

Ethanimine 

Ethyl Cyanide 

Ethyl Formate 

Ethylene Glycol 

Ethylene Oxide 

Ethynyl Radical 

Extended Red Emission 

Formamide 

Formyl Cation 

Fullerane 

Fullerene 

Gas-Grain Chemistry 

Glycolaldehyde 

Hydrogen Chloride 

Hydrogen Isocyanide 

Hydrogenated Amorphous Carbon 

Hydroxyl Radical 

Imidogen 


© Springer-Verlag Berlin Heidelberg 2015 
M. Gargaud et al. (eds.), Encyclopedia of Astrobiology, 
DOI 10.1007/978-3-662-44185-5 



2 


Astrobiology by Discipline 


Interstellar Chemical Processes 
Interstellar Ices 
Interstellar Molecule 
Ion-Neutral Reaction 
IRC+10216 

Isotopic Exchange Reaction 

Isotopic Fractionation (Interstellar Medium) 

Isotopolog 

Langevin Rate Coefficient 
Langmuir-Hinshelwood Mechanism 
Line Shielding 

Metal Compounds in Circumstellar Envelopes 

Methanethiol 

Methoxy Radical 

Methyl Acetate 

Methyl Formate 

Methyl Radical 

Methyl Triacetylene 

Methylene 

Methylidyne 

Methylidyne Cation 

Molecular Abundances 

Molecular Depletion 

Molecular Desorption 

Molecular Line Cooling 

Molecular Line Map 

Molecular Line Survey 

Molecules in Space 

Mutual Neutralization 

Nanodiamond 

Neutral-Neutral Reaction 

Nitrogen Sulfide 

Nucleation of Dust Grains 

Organic dust, synthesis by stars 

Organic Dust, Influence on the Origin of Life 

Phosphaethyne 

Phosphorus Monoxide 

Photochemistry 

Photodesorption 

Photodetachment 

Photodissociation 

Photoionization 

Photolysis 

Physisorption 

Polar Molecule 

Polycyclic Aromatic Hydrocarbon 
Prasad-Tarafdar Mechanism 


Predissociation 
Propyl Cyanide 
Propylene 
Propynylidyne 
Proton Transfer 

Quenched Carbonaceous Composite 

Radiative Attachment 

Radical 

Radiolysis 

Reaction Rate Coefficient 

Refractory Molecule 

Scattering 

SgrB2 

Silane 

Silicon Monosulfide 
Silicon Monoxide 
Silicon Nitride 
Sputtering 
Star Dust 

Sticking Coefficient 

Sulfur Hydrides in the Interstellar Medium 

Sulfur Monoxide 

Thioformaldehyde 

TiO 

Ti02 

Unidentified Infrared Emission Bands 
Unimolecular Reaction 
UV Absorption Bump 
Vinyl Cyanide 
VY CMa 

Water in the Universe 
Water, Formation and Photodissociation 
Water, Related Interstellar Radicals & Ions 
Water, Vibrational and Rotational Transitions 

Section - Astrophysics: General 
Definitions: D. Rouan 

Ablation 
Accretion Shock 
Activity, Magnetic 
Adaptive Optics 
Alignment of Dust Grains 
Angular Diameter 
Angular Momentum 
Aphelion 



Astrobiology by Discipline 


3 


Astrometry 

Atomic Fine Structure Cooling 
AU 

Background 
Band Pass 
Blackbody 
Bolometer 

Bolometric Magnitude 
Bremsstrahlung Radiation 
CCD 

Celestial Equator 
Center of Mass Velocity 
Chandrasekhar’s Limit 
Cirrus Cloud 

Coagulation, Interstellar Dust Grains 

Color Excess 

Color Index 

Column Density 

Continuum 

Coordinate Systems 

Coronagraphy 

Cosmogony 

Declination 

Dense Cloud 

Diffraction 

Diffuse Cloud 

Diffuse Galactic Light 

Doppler Shift 

Dust Cloud, Interstellar 

Eccentricity 

Ecliptic 

Effective Temperature 
Electromagnetic Radiation 
Electromagnetic Spectrum 
Emission Nebula 
Emissivity 
Ephemeris 
Equation of State 
Equinox 

Exozodiacal Light 

Extinction, Interstellar or Atmospheric 

Flux, Radiative 

Gas Giant Planet 

Gravitation 

Grey Body 

Heavy Element 

HII Region 


Hydrodynamic Flow 
Hydrostatic Equilibrium 
Imaging 

Impact Parameter 
Inclination (Astronomy) 
Infrared Astronomy 
Interferometry 
Interstellar Cloud 
Interstellar Dust 
Interstellar Medium 
Jeans Escape 

Johnson UBV Bandpasses 
Lagrangian Points 
Light-Year 
Limb Darkening 
Limb, Astronomical 
Line Emission 
Line of Sight 
Line Profile 
Linewidth 

Local Standard of Rest 
Luminosity 
Lyman Alpha 
Magnetic Field 
Magnitude 
Magnitude, Absolute 
Maser 

Mass Loss Rate 
Mean Free Path 
Nadir 
Noise 

Nulling Interferometry 

Occultation 

Optical Depth 

Orbital Resonance 

Parallax 

Parsec 

Photodissociation Region 

Photon 

Photosphere 

Plasma 

Polar Axis 

Precession 

Proper Motion 

Protoplanetary Nebula 

Q (Orbital Parameter) 

Radiative Processes 



4 


Astrobiology by Discipline 


Radiative Transfer 

Asymptotic Giant Branch Star 

Radio Astronomy 

Big Bang Nucleosynthesis 

Red Rectangle 

Black Hole 

Reddening, Interstellar 

CNO Cycle 

Redshift 

Cosmochemistry 

Reflection Nebula 

Diffusion 

Right Ascension 

Drake Equation 

Roche Limit 

Dwarf Star 

Rotational Velocity 

Faint Young Sun Paradox 

Semi Major Axis 

Fermi Paradox 

Semi Minor Axis 

Galactic Habitable Zone 

Shock, Interstellar 

Galaxy 

Solar Constant 

Globular Cluster 

Solar Luminosity 

Hertzsprung-Russell Diagram 

Solar Mass 

High Mass Star 

Solar Radius 

Horizontal Branch 

Spectral Line 

Initial Mass Function 

Spectrometer 

Isochrone 

Spectroscopy 

Low Mass Star 

Star Counts 

Main Sequence, Star 

Suprathermal 

Mass-Luminosity Relation 

Surface Gravity 

Metallicity 

Synchrotron Radiation 

Milky Way 

Telescope 

Neutron Star 

Thermodynamical Chemical Equilibrium 

Nova 

Time Series 

Nuclear Reaction 

Titius-Bode Law 

Nuclear Stability 

Translucent Interstellar Clouds 

Nucleosynthesis, explosive 

Turbulence, Interstellar 

Nucleosynthesis, neutrino 

Ultraviolet Radiation 

Nucleosynthesis, Stellar 

UV Radiation 

Opacity 

Vacuum Ultraviolet 

Open Cluster 

Variability, Stellar 

Planetary Nebula 

Vernal Point 

P-P Chains 

Visible Light 

Pulsar 

VLB I 

Red Dwarf 

VLT 

Red Giant 

XDR 

R-Process 

X-rays (Stellar) 

Solar Neighborhood 

Z 

Spallation Reaction 

Zenith 

Spectral Type 

S-process 

Star 

Section - Nucleosynthesis: N. Prantzos 

Stellar Evolution 

Stellar Population 

Abundances of Elements 

Stellar Pulsation 

Astero seismology 

Stellar Rotation 



Astrobiology by Discipline 


5 


Stellar Yield 

Sun (and Young Sun) 

Supernova 
Supernova Remnant 
Supernova Types 
White Dwarf 
Zero Age Main Sequence 

Section - Stars - Formation and 
Evolution: Ph. Andre 

Accretion, Stellar 
Ambipolar Diffusion 
Binary Stars, Young 
Bipolar Flow 
Birthline 
Brown Dwarf 
Convection, Stellar 
Debris Disk 
Dense Core 

Fragmentation of Interstellar Clouds 
Free-Fall Time 

Gravitational Collapse, Stellar 
Hot Core 
Hot Corino 
Infrared Excess 

Initial Mass Function, Origin of 

Interstellar Filaments 

Larson’s Law 

Lithium Absorption 

Magnetic Fields and Star Formation 

Molecular Cloud 

OB Association 

Pillars 

Pre-main-sequence Star 
Protobinary Star 
Protoplanetary Disk 
Protostars 

Protostellar Envelope 
Skumanich Law 

Spectral Classification of Embedded Stars 

Spectral Veiling of Young Stars 

Star Formation, Observations 

Star Formation, Theory 

Star Formation, Triggering 

Stellar Cluster 


Stellar Winds 
T Association 
T Tauri Star 
YY Orionis Star 


Field - Chemical Sciences: J. Cleaves 

Section - Chemistry - General 
Definitions: K. Kobayashi, K. Bartik 

Acetaldehyde 

Acetic Acid 

Acetonitrile 

Activated Nucleotide 

Adenine 

Aerosols 

Alcohol 

Aliphatic Hydrocarbon 

Alpha Rays 

Alteration 

Amide 

Amine 

Amino Acid Precursors 
Aminoisobutyric Acid 
Aminonitrile 
Amorphous Carbon 
Amphiphilicity 
Amphoteric Compounds 
Arginine 
Asparagine 
Aspartic Acid 

Asymmetric Reaction, Absolute 
Atmosphere, Organic Synthesis 
ATP 

Beta Rays 

Black Smoker, Organic Chemistry 

Carbon 

Carbonyl 

Carboxylic Acid 

Catalyst 

Circular Dichroism 

Clathrate 

Clay 

Complex Organic Molecules 
Corona Discharge 
Cosmic Ray in the Galaxy 



6 


Astrobiology by Discipline 


Cyanoacetylene 

Cysteine 

Cystine 

Cytosine 

D/L-Ratio 

D-Amino Acids 

Decarboxylation 

Diamino Acid 

Dicarboxylic Acid 

Diketopiperazine 

Disulfide Bond 

Endogenous Synthesis 

Ester 

Ethanol 

Ether 

Evolution, Chemical 

Extraterrestrial Delivery of Organic Compounds 

Extreme Ultraviolet Light 

Fischer Projection 

Formic Acid 

Fractionation 

Free Amino Acid 

Gamma Rays 

GC/MS 

Glutamic Acid 

Glutamine 

Glyceraldehyde 

Glycerol 

Glycolic Acid 

Guanine 

Halogen 

HCN Polymer 

Heme 

Heterocycle 

Histidine 

Hoogsteen Pair 

Hydrocarbons 

Hydrogen 

Hydrogen Cyanide 

Hydrogen Sulfide 

Hydrolysis 

Hydrophobicity 

Hydrothermal Reaction 

Hydrothermal Vent Origin of Life Models 

Hydroxy Acid 

Hydroxyl Group 

Hypoxanthine 

Ice 


Insoluble Organic Matter 

Ionization Constant 

Isoelectric Point 

Isoleucine 

Isovaline 

Kaolinite 

Ketose 

Kinetic Isotope Effect 

Lactic Acid 

Leucine 

Ligand 

Lysine 

Mass Spectrometry 
Methane 
Methanol 
Methionine 

Mildly Reducing Atmosphere 

Molecular Weight 

Monosaccharide 

Montmorillonite 

Non-Protein Amino Acids 

Nucleoside Phosphoimidazolide 

Oligomerization 

Oligonucleotide 

Organic Molecule 

Organometallic 

Oxygen, Atomic 

pH 

Phenylalanine 

Photochemistry, Atmospheric 

Polarized Electron 

Polarized Light and Homochirality 

Polymer 

Polynucleotide 

Polypeptide 

Polysaccharide 

Porphyrin 

Prebiotic Chemistry 

Precursor 

Proline 

Propionaldehyde 
Proteinoid Microsphere 
Proteins, Primary Structure 
Proteins, Quaternary Structure 
Proteins, Secondary Structure 
Proteins, Tertiary Structure 
Proton Irradiation 
Pyrolysis GC/MS 



Astrobiology by Discipline 


7 


Quenching 

Radiochemistry 

Refractory Organic Polymer 

Ribonucleoside 

Ribonucleotide 

Sarcosine 

Selenocysteine 

Serine 

Shock Wave 
Succinic Acid 
Sulfur 

Supercritical Fluid 

Svedberg Unit 

Synchrotron Accelerator 

Synthetic Biology 

Tautomer 

Thermolysis 

Thiol 

Tholins 

Threonine 

Thymine (T) 

Tryptophan 
Tyrosine 
Uracil (Ura) 

Urea 

Valine 

Vesicle 

Volatile 

vuv 

Water, Solvent of Life 
Watson-Crick Pairing 
Wave Number 
Wavelength 
Weak Bonds 
Wobble Pair 
XANES 

X-rays (Organic Synthesis) 
Zwitterion 


Section - Prebiotic Chemistry and 
Origins of Life: J. Cleaves, A. Pohorille 

Abiotic Photosynthesis 
Achiral 

Acid Hydrolysis 
Activation Energy 
Active Site 


Activity 

Affinity Chromatography 

Affinity Constant 

Alanine 

Aldehyde 

Aldose 

Alpha Helix 

Amino Acid 

Amino Acid N-Carboxy Anhydride 

Amino Butyric Acid 

Ammonia 

Amphiphile 

Aqueous Interfaces 

Aromatic Hydrocarbon 

Arrhenius Plot 

Autocatalysis 

Automaton, Chemical 

Borate 

Branching Ratio 
Biicherer-Bergs Synthesis 
Cahn Ingold Prelog Rules 
Carbohydrate 
Carbon Dioxide 
Carbon Monoxide 

Carbonaceous Chondrites, Organic Chemistry of 
Cell Models 

Chicken or Egg Problem 
Chirality 

Chromatographic Co-elution 

Chromatography 

Chromophore 

Combinatorial Library 

Combustion 

Composomes 

Concentration Gradients 

Covalent Bonds 

Cryostat 

Cyanamide 

Cyanogen 

Deamination 

Denaturation 

Deoxyribose 

Derivatization 

Deuterium 

Diastereomers 

Dinitrogen 

Dioxygen 

Disproportionation 



8 


Astrobiology by Discipline 


Dissolved Inorganic Carbon Equilibrium 

Membrane Potential 

DNA 

Metabolism, Prebiotic 

Double Helix 

Micelle 

Electric Discharge 

Moiety 

Electrophoresis 

Mole 

Enantiomeric Excess 

Molecular Beacon 

Enantiomers 

Molecular Recognition 

Endergonic 

mRNA Display 

Endothermic 

N-Carbamoyl-Amino Acid 

Enthalpy 

Neutral Atmosphere 

Entropy 

Nitrile 

Evolution, Molecular 

Nitrogen 

Exergonic 

Nucleic Acid Base 

Exothermic 

Nucleic Acids 

Fischer-Tropsch-Type Reaction 

Nucleon 

Flow Reactor 

Nucleoside 

Fluorescence 

Nucleotide 

Fluorometry 

Nuclide 

Fluorophore 

O/OREOS Nanosatellite 

Formaldehyde 

Oligomer 

Formose Reaction 

Oligopeptide 

Free Energy 

Origin of Life 

FRET 

Ornithine 

Furanose 

Oxidizing Atmosphere 

Gas Chromatography 

Permeability 

Genetic Code 

Phase Transition 

Globule, Nanoglobule 

Phosphine 

Glycine 

Phosphite 

Hapten 

Phosphoric Acid 

HCNO Isomers 

PIXE 

Heterotrophic Hypothesis 

PNA 

Hexamethylenetetramine 

Polyoxymethylene 

Homochirality 

Post-impact Plume 

Homolysis 

Primordial Soup 

HPLC 

p-RNA 

Hydantoin 

Protein 

Hydrogen Bond 

Protocell 

Hydrophobic Effect 

Purine Bases 

Hypercycle 

PVED 

Infrared Spectroscopy 

Pyranose 

Ion-Exchange Chromatography 

Pyrimidine Base 

Isomer 

Pyrolysis 

Isotopomer 

Pyrophosphate 

L-Amino Acids 

Pyruvate 

Ligase 

Quencher 

Lipid Bilayer 

Racemic Mixture 

Liquid Chromatography-Mass Spectrometry 

Racemization 

Liquidus 

Radiation Pressure 



Astrobiology by Discipline 


9 


Raman Spectroscopy 
Redox Potential 
Ribose 
Ribozyme 

Rice-Ramsperger-Kassel-Marcus 

RNA 

RNA Ligase 

RNA Replicase Ribozyme 
RNA World 
Rotatory Power 
Self-Assembly, Biological 
Self-Replication, Chemical 
Solidus 

Spark Discharge 
Specific Activity 
Stereochemistry 
Stereoisomers 
Steric Effect 
Strecker Synthesis 
Sublimation 
Substrate 

Surface Plasmon Resonance 

Systems Chemistry 

Template-Directed Polymerization 

Thiocyanate 

Thioester 

Trace Elements 

Transferase 

Triple Point 

Van Der Waals Forces 

Water 


Field - Earth Sciences: D. Pinti 

Section - Archean Geology: 

Ch. Heubeck 

Acasta Gneiss 
Akilia 

Amphibolite Facies 
Anorthosite 
Apex Basalt, Australia 
Apex Chert 

Archean Drilling Projects 
Archean Environmental Conditions 
Archean Eon 
Archean Mantle 


Archean Tectonics 

Banded Iron Formation 

Barberton Greenstone Belt 

Barberton Greenstone Belt, Sedimentology 

Barberton Supergroup 

Baryte 

Basalt 

Black Smoker 

Campbellrand-Malmani Platform, South Africa 
Canadian Precambrian Shield 
Carbonate on Mars 
Chert 

Continental Crust 

Continents 

Cool Early Earth 

Coonterunah Subgroup, Australia 

Craton 

Crust 

Cryosphere 
Deccan Trapps 
Diagenesis 

Diamictite/Diamicton 

Diapirism 

Dixon Island Formation, Western Australia 
Earth 

Earth, Formation and Early Evolution 
Earth, Surface Evolution 
Evaporite 

Evaporites, Archean 
Fennoscandia 
Fig Tree Group 
Fortescue Group 
Ga 

Geological Timescale 
Geothermal Gradient 
Geothermobarometers 
Gondwana 
Granite 
Greenland 
Greenschist Facies 
Greenstone Belts 
Hadean 

Huronian Glaciation 
Hydrosphere 

Hydrothermal Environments 

Igneous Rock 

Isua Supracrustal Belt 

Jack Hills (Yilgarn, Western Australia) 



10 


Astrobiology by Discipline 


Jaspilite 

Komatiite 

Laurasia 

Lithosphere, Planetary 
Ma 

Magma 

Magnetic Anomaly 
Magnetic Pole 
Magnetite 
Mantle 

Mantle Plume, Planetary 

Metamorphic Rock 

Metamorphism 

Metasediments 

Metasomatism 

Mineral 

Moho 

Moodies Group 

Moodies Group, Microbial Mats 
MORB 

Mount McRae Shale 

North Pole Dome (Pilbara, Western Australia) 

Obduction 

Oceanic Crust 

Oceans, Origin of 

Onverwacht Group 

Ophiolite 

Paleomagnetism 

Paleosols 

Pangea 

Peridotite 

Pilbara Craton 

Pillow Lava 

Plate Tectonics 

Plate, Lithospheric 

Precambrian 

Precambrian Oceans, Temperature of 

Proterozoic Eon 

Pyrite 

Quartz 

Regolith, Terrestrial 

Rock 

Rodinia 

Sagduction 

Sedimentary Rock 

Serpentine 

Serpentinization 

Shale 


Shield 

Silicate Minerals 
Snowball Earth 
Spherules 
Stratigraphy 
Subduction 
Sulfate Minerals 
Tides, Archean 

T onalite-Trondhj emite-Granodiorite 
Transvaal Supergroup, South Africa 
Trapps 
Trondhjemite 

Tumbiana Formation (Pilbara, Western 
Australia) 

Turbidite 

Volcaniclastic Sediment 
Volcano 

Warrawoona Group 
Weathering 
White Smoker 
Zircon 

Section - Early Earth Geochemistry: 

F. Albarede 

Boron Isotopes 
Carbonation 
Cerium, Anomalies of 
Chalcophile Elements 
Decay Constant 
Degassing 

Distillation, Rayleigh 
Earth, Age of 

Fischer-Tropsch Effects on Isotopic Fractionation 
Fluid Inclusions 

Fractionation, Mass Independent and Dependent 

Geochronology 

Graphite 

Half-Life 

Hydrodynamic Escape 

Isochron 

Isotope 

Isotopic Fractionation (Planetary Process) 

Isotopic Ratio 

Late Veneer 

Lithophile Elements 

Mantle, Oxidation of 



Astrobiology by Discipline 


11 


Oxygen Fugacity 
Oxygen Isotopes 
Ozone 
Phosphates 

Platinum Group Elements 
Radioactivity 
Rare Earth Elements 
Siderophile Elements 
Sulfur Isotopes 

Section - Traces of Life: E. Javaux 

Acid Maceration 

Acritarch 

Amoebae 

Archean Traces of Life 

Barberton Greenstone Belt, Traces of Early Life 

Belcher Group, Microfossils 

Biogenicity 

Biomarkers 

Biomarkers, Morphological 
B iomineralization 
Biopolymer 
Bioprecipitation 

Biosignatures, Effect of Metamorphism 

Biostabilization 

Bitumen 

Burgess Shale Biota 
Cambrian Explosion 
Cap Carbonates 

Carbon Isotopes as a Geochemical Tracer 

Carboxylic Acids, Geological Record of 

Chengjiang Biota, China 

Cyanobacteria, Diversity and Evolution of 

Dubiofossil 

Ediacaran Biota 

Ediacaran Period 

Endogenicity 

Eukaryotes, Appearance and Early Evolution of 
Exopolymers 

Fatty Acids, Geological Record of 
Fossil 

Fossilization, Process of 

Gunflint Microbiota 

Hopanes, Geological Record of 

Iron oxides, hydroxides and Oxy-hydroxides 

Isoprenoids 


Kerogen 
Microbial Mats 

Microbially Induced Sedimentary Structures 
Microfossils 

Microfossils, Analytical Techniques 
Molecular Fossils 
Prokaryotes, Origin of 
Pseudofossil 
Rio Tinto 

Shark Bay, Stromatolites of 
Steranes, Rock Record 
Stirling Range Biota 
Stirling Range, Australia 
Strelley Pool Formation 
Stromatolites 
Sulfidic Oceans 
Syngenicity 

Transition Metals and Their Isotopes 

Section - Geology and Geochemistry: 
General Definitions: D. Pinti 

Absolute and Relative Ages 

Accretion 

Alunite 

Amitsoq Gneisses 
Antarctica 

Apex Chert, Microfossils 
Asthenosphere 
Atacama Desert 
Breccia 

Bulk Silicate Earth 
Chemocline 
Chicxulub Crater 
Delta, Isotopic 
Deuterium/Hydrogen Ratio 
Devon Island 
Dharwar Craton 

Earth’s Atmosphere, Origin and Evolution of 
Ejecta 

Extinct Radionuclides 

Gabbro 

Geotherm 

Geyser 

Glaciation 

Goethite 

Great Oxygenation Event 



12 


Astrobiology by Discipline 


Gunflint Formation 
Hadean Mantle 
Hematite 

Hydrogen Isotopes 

Hydrothermal Alteration 

Impact Degassing 

Impact Melt Rock 

Impactite 

Iridium 

Iron Isotopes 

Isotope Biosignatures 

Kaapvaal Craton, South Africa 

KREEP 

KT Boundary 

Late Heavy Bombardment 

Lomagundi Carbon Isotope Excursion 

Mafic and Felsic 

Mantle Volatiles 

Mars Analogue Sites 

Mass Extinctions 

Mid-Ocean Ridges 

Monomictic Breccia 

Mud Volcano 

Natron 

Nitrogen Isotopes 
Noble Gases 

Nuvvuagittuq (Porpoise Cove) Greenstone Belt 

Ocean, Chemical Evolution of 

Olivine 

Oxygen Minimum Zone 

Oxygenation of the Earth’s Atmosphere 

Permafrost 

Polimictic Breccia 

Radiative Forcing 

Radiogenic Isotopes 

Red Beds 

Redox Zonation 

Sanukitoid 

Self-shielding Effects on Isotope Fractionation 

Shocked Quartz 

Siderite 

Silicon Isotopes 
Soda Lakes 
Stable Isotopes 
Subglacial Environments 
Suboxic 

Sudbury Impact Structure 
Suevite 


Supercontinent 

Tektite 

Theia 

Thermonatrite 

Trona 

True Polar Wander, Theory of 
Ultramafic Rocks 
Ultrastructure 
Uraninite 

Vostok, Subglacial Lake 
Water, Delivery to Earth 
Weathering Profile 

Yellowstone National Park, Natural Analogue 
Site 


Field - History and Philosophy of 
Science: S. Tirard 

Section - History and Philosophy of 
Science: S. Tirard, F. Figueirido 

Abiogenesis 

Al-Andalus, Cosmological Ideas 

al-Blrunl, Abu Rayhan 

al-TusI, Nasir al-DIn 

Animalcules 

Astrobiology 

Baly’s Experiment 

Bathybius Haeckelii 

Bernal’s Conception of Origins of Life 

Bruno, Giordano 

Buffon’s Conception of Origins of Life 

Calvin’s Conception of Origins of Life 

Cassini, Giovani Domenico 

Cellular Theory, History of 

Chance and Randomness 

Co-evolution 

Comets, History of 

Cosmic Background Radiation 

Cosmogonia: Greece 

Cosmogonia: Mesopotamia 

Cosmogonia: Roma 

Cuvier’s Conception of Origins of Life 

Darwin’s Conception of Origins of Life 

De Duve, Christian 

de Maillet’s Conception of Origins of Life 
Diderot’s Conception of Origins of Life 



Astrobiology by Discipline 


13 


Dirac, Paul 

Earth’s Atmosphere, History of the Origins 
Ecology, History of 
Enzymology: History of 
Evo-devo 

Evolution of Species, Islamic Ideas 

Fermi, Enrico 

Galilean Satellites 

Gene, Selfish 

Genetics, History of 

Geological Time Scale, History of 

Goldschmidt, Viktor Moritz 

Haeckel’s Conception of Origins of Life 

Haldane’s Conception of Origins of Life 

Halley, Edmond 

Herschel, William 

Hoyle, Fred 

Hubble, Edwin 

Huxley’s Conception on Origins of Life 
Ikhwan al-Safa 

Kant-Laplace Cosmogonic Hypothesis 
Kepler, Johannes 

Lamarck’s Conception of Origins of Life 
Lemaitre’s Theory of Expanding Universe (History) 
Life in the Solar System (History) 

Lowell, Percival 
Materialism 
Meteorites, History of 
Miller, Stanley 

Monod’s Conception on the Origins of Life 
Mythology 

Native American Cosmology and Other Worlds 
Oparin’s Conception of Origins of Life 
Origins of Life, History of 
Physicalism 

Planetary Theories and Cosmology, Islamic 
Theories 
Plank, Max 

Plate Tectonics, History of 

Plurality of Worlds 

Protoplasmic Theory of Life 

Radio Astronomy and Radio Telescopes, History of 

Reductionism 

Sagan Carl 

SETI, History of 

Spectroscopy, History of 

Spontaneous Generation, History of 

Todd, David 


Urey’s Conception of Origins of Life 

Vernadsky 

Vitalism 

Woese, Carl 

Field - Institutions and Organizations: 
W. Irvine, M. Viso 

AEB 

ASA 

ASI 

Bioastronomy (IAU Commission 51) 

BNSC 
CAB, Spain 
CNES 
CNSA 

CONAE, Argentina 

COSPAR 

CSA 

DLR, Germany 
DTU Space, Denmark 
EANA 
ECSS 

European Space Agency 

IAF 

IAU 

IKI 

ISO (Normative Organisation) 

ISRO 

ISSI 

ISSOL 

JAXA 

JPL 

NAI 

NASA 

NSO 

Roskosmos 

SSB 

UK Space Agency 

Field - Life Sciences: R. Amils 

Section - Artificial Life: H. Bersini 

Artificial Chemistries 
Artificial Life 



14 


Astrobiology by Discipline 


Biological Networks 
Cellular Automata 
Chemical Reaction Network 
Code 

Complexity 
Genetic Algorithms 
Scale Free Networks 
Self Replication 
Self-Assembly 

Section - Biochemistry: J. Pereto 

Aerobic Respiration 
Anabolism 

Anaerobic Respiration 
Anoxygenic Photosynthesis 
Antibody 
Anticodon 

Assimilative Metabolism 

ATP Synthase 

ATPase 

Autopoiesis 

Autotroph 

Autotrophy 

B acteriochlorophy 11 

Base Pair 

Bioenergetics 

Buffer 

Calvin-Benson Cycle 

Catabolism 

Cell 

Cell, Minimal 

Chlorophylls 

Chromosome 

Citric Acid Cycle 

Cloning 

Codon 

Coenzyme 

Cofactor 

Cytochromes 

Cytoplasm 

Diazotrophy 

Dissimilative Metabolism 
DNA Polymerase 
Electrochemical Potential 
Electron Acceptor 
Electron Carrier 


Electron Donor 
Electron Transport 
Embden-Meyerhof-Pamas Pathway 
Energy 

Energy Conservation 
Entner-Doudoroff Pathway 
Enzyme 
Exon 

Fermentation 

Genome, Minimal 

Gluconeogenesis 

Glycolysis 

Homeostasis 

Intron 

Life 

Metabolism 

Metabolism, Secondary 

Mitochondrion 

NADH, NADPH 

Nitrogen Cycle, Biological 

Nitrogen Fixation 

Nucleus 

Photosynthesis 

Photosynthesis, Oxygenic 

Photosynthetic Pigments 

Phototroph 

Primer 

Prion 

Respiration 

Restriction Enzyme 

RNA Polymerase 

Rubisco 

Symbiosis 

Transcription 

Transduction 

Transformation 

Translation 

Wobble Hypothesis (Genetics) 

Section - Biology - General Definitions: 
F. Gomez 

Abiotic 

Acidophile 

Aerobe 

Algae 

Anaerobe 



Astrobiology by Discipline 


15 


Biofilm 

Carbon Cycle, Biological 
Carbon Source 
Cell Wall 

Colonization, Biological 

Cryptoendolithic 

Cyanobacteria 

Deep Biosphere 

Deep-Sea Microbiology 

Deep-Subsurface Microbiology 

Dormant State 

Ecological Niche 

Ecosystem 

Endogenous 

Endolithic 

Energy Sources 

Environment 

Europa Analogues 

Exogenous 

Extreme Environment 

Extremophiles 

Habitat 

Halophile 

Halotolerance 

Heterotroph 

Hot Spring Microbiology 
Hot Vent Microbiology 
Hypersaline Environment 
Hyperthermophile 
Intelligence 

Intelligence, Evolution of 

Magnetosome 

Magnetotactic Bacteria 

Mars Analogues 

Mesophile 

Metabolic Diversity 

Microorganism 

Nitrification 

Organelle 

Osmolite 

Oxidation 

Oxygenase 

Peptidoglycan 

Periplasm 

Piezophile 

Plankton 

Proteobacteria 

Proton Motive Force 


Proton Pump 
Psychrophile 
Reducing Agent 
Reduction 
Sulfate Reducers 
Sulfur Cycle 
Terrestrial Analog 
Thermophile 
Yeast 


Section - Genetics and Evolution: 
C. Briones 

Adaptation 

Amplification (Genetics) 

Aptamer 

Aptasensor 

Biodiversity 

Bioinformatics 

Cell Membrane 

Cenancestor 

Combinatorial Nucleic Acid Library 

Common Ancestor 

Conjugation 

DNA Sequencing 

Domain (Taxonomy) 

Endosymbiosis 
Error Rate 

Evolution, Biological 

Evolution, In Vitro 

Fidelity 

Fitness 

Gene 

Gene Expression 

Genetic Map 

Genetics 

Genome 

Genomics 

Genotype 

Homology 

Hybridization 

Last Universal Common Ancestor 

Lateral Gene Transfer 

Metagenome 

Metatranscriptome 

Metavirome 

Molecular Clock 



16 


Astrobiology by Discipline 


Monophyletic 

Chemoautotroph 

Mutagen 

Chemolithoautotroph 

Mutagenesis 

Chemolithotroph 

Mutant 

Chemoorganotroph 

Mutation 

Chemotaxis 

Natural Selection 

Chemotroph 

Operon 

Chloroplast 

Orthologous Gene 

Compatible Solute 

Paralogous Gene 

Crenarchaeota 

Phenetics 

Denitrification 

Phenotype 

Eukarya 

Phylogenetic Tree 

Euryarchaeota 

Phylogeny 

Fungi 

Phylotype 

Gaia Hypothesis 

Phylum 

Genus 

Plasmid 

Geomicrobiology 

Polymerase Chain Reaction 

Glove Box 

Proteome, Proteomics 

Gram-negative Bacteria 

Quasispecies 

Gram-Positive Bacteria 

Recombination 

Green Bacteria 

Replication (Genetics) 

Hydrogenosomes 

Ribosome 

Iron 

Selection 

Iron Cycle 

Sequence 

Korarchaeota 

Sequence Analysis 

Lithotroph 

Splicing 

Macronutrient 

Systems Biology 

Membrane 

Template 

Methanogens 

Virion 

Methanotroph 

Viroid 

Micronutrients 

Virology 

Motility 

Virus 

Multicellular Organisms 
Nanoarchaeota 

Nucleoid 

Section - Life in Extreme Environments: 

Osmotic Pressure 

R. Amils 

Outer Membrane 

Oxic 

Alkaliphile 

Peroxisome 

Anoxic 

Photoautotroph 

Antibiotic 

Pili 

Archaea 

Planetary Ecosynthesis 

Bacteria 

Ploidy 

Bacterirhodopsin 

Prokaryote 

Biogeochemical Cycles 

Protists 

Biosensor 

Protoplast 

Biosphere 

Quorum Sensing 

Biotope 

Species 

Carboxysomes, Structure and Function 

Species (Prokaryote) 



Astrobiology by Discipline 


17 


Taq Polymerase 
Taxonomy 
Transport, Biological 
Unicellular Organisms 
Water Activity 
Xerophile 


Section - Microbiology in Space: 

G. Horneck 

Aerobiology 
Apollo Mission 
Arrhenius Svante 
Biostack 

Cosmic Rays in the Heliosphere 

Desiccation 

DNA Damage 

DNA Repair 

Endospore 

Epilithic 

Gravitational Biology 

Hypolithic 

HZE Particle 

Ionizing Radiation, Biological Effects 
Lichens 

Linear Energy Transfer 

Lithopanspermia 

MEED 

Microgravity 

Ozone Layer 

Photobiology 

Planetary and Space Simulation Facilities 

Radiation Biology 

Radiation Dose 

Solar Particle Events 

Solar UV Radiation, Biological Effects 

Space Biology 

Space Environment 

Space Vacuum Effects 

Spallation Zone 

Spore 

Sporulation 

Survival 

UV Climate 

UV Radiation Dose 

UV Radiation, Biological Effects 


Field - Planetary Sciences and 
Exoplanets: T. Spohn 

Section - Exoplanetary Systems: 

N. Haghighipour 

51 Pegasi B 
Alpha Centauri Bb 
Astrometric Orbit 
Astrometric Planets 
B ary center 
Beta Pictoris b 
Circumbinary Planet 
Circumprimary Planet 
CoRoT 7b 

Direct-Imaging, Planets 

Eclipse 

Eta-Earth 

Exomoon 

Exoplanet, Detection and Characterization 
Exoplanets, Discovery 

Exoplanets, Modeling Giant Planets’ Atmospheres 
Fomalhaut b 
Gamma Cephei 

GJ 667C: First System with Multiple Super¬ 
earths in Habitable Zone 
Gliese 581, The Most Highly Debated Habitable 
System 

Habitable Zone Around Binary Star Systems 

Habitable Zone in Binary Stars Systems 

Habitable Zone in Multi-star Systems 

HARPS 

HATNet 

HD 189733b 

HD 209458b 

HIRES 

Hot Jupiters 

Hot Neptunes 

HR 8799: The First Directly Imaged Multi-planet 
System 
Kepler 10 

Kepler 11: Multiple Transiting Planet System 
Kepler 16b: First Circumbinary Planet 
Kepler 186f: First Earth-sized Planet in Habitable 
Zone 

Kepler 37b: A Moon-sized Planet 

Kepler 47: First Multi-circumbinary Planet System 



18 


Astrobiology by Discipline 


Kepler 9: First Transiting System Confirmed by 
TTV 

Keplerian Orbits 

Light Travel Time Effect 

Microlensing Follow-Up Network 

Microlensing Observations in Astrophysics 

Microlensing Planets 

Mini-Neptunes 

Ocean Planet 

OGLE-2005-BLG-390Lb 

OGLE-2006-BLG-109Lb,c 

Optical Gravitational Lensing Experiment 

Periastron 

Period 

Phase, Orbital 

Planet Detection: Transit Timing Variation 
Planet detection; Eclipse Timing Variation 
Planets in Binary Star Systems 
Probing Lensing Anomalies Network 
Pulsar Planets 
Radial Velocity 
Radial-Velocity Planets 
Rossiter-McLaughlin Effect 
SETI 

Spectroscopic Orbit 

Super-Earths 

Transit 

Transiting Planets 
TrES 


Section - Inner Solar System: A. Airo, 
B. Stracke 

6 Hebe 
Achondrite 
Active Asteroid 
Albedo Feature 
ALH 84001 
Amazonian 
Annefrank 
Apollo Asteroid 
Apophis Asteroid 
Aquifer (Mars) 

Arachnoid 

Areology 

Asteroid 


Asteroid Belt, Main 

Carbonaceous Chondrite 

Carbonate, Extraterrestrial 

C-Asteroid 

Catena, Catenae 

Cavus, Cavi 

Ceres 

Chaotic Region 
Chasma, Chasmata 
Chassignites 
Chassigny 
Chondrite 
Chondrule 
Chronostratigraphy 
C02 Ice Cap (Mars) 

C02 Ice Clouds (Mars) 
Concretions (Mars) 

Core, Planetary 
Corona, Coronae 
Cosmic Spherules 
Crater lakes (Mars) 

Crater, Impact 
Dark Streaks (Mars) 

Deimos 

Dichotomy, Planetary 

Differentiation, Planetary 

Dust Devils 

Dwarf Planet 

Dynamo, Planetary 

Eros Asteroid 

Facula, Faculae 

Fossa, Fossae 

Fumarole 

Fusion Crust 

Gaspra 

Gegenschein 

Gullies 

Habitability on Mars 

Heat Flow, Planetary 

Heat Transfer, Planetary 

Hesperian 

Hygiea 

Ida 

Impact Basin 

Interior Structure, Planetary 
Interplanetary Dust Particle 
Jarosite 



Astrobiology by Discipline 


19 


JU3 

Juno 

Labyrinthus, Labyrinthi 
Lacus 

Landing Site 
Landslide (Mars) 

Lava Tubes 
Lenticula, Lenticulae 
Linea, Lineae 
Lingula, Lingulae 
Lutetia 

Macula, Maculae 
Magnetic Field, Planetary 
Mare, Maria 
Mars 

Mars Stratigraphy 
Mathilde 
Mensa/Mensae 
Mercury 

Meridiani (Mars) 

Meteor 
Meteoroid 
Mons, Montes 
Moon, Origin of 
Moon, The 
Nakhla 
Nakhlites 
Nanoparticle 
Near-Earth Objects 
Nitrates on Mars 
Noachian 

Obliquity and Obliquity Variations 

Oceanus, Oceani 

Olympus Mons 

Opaline Silica on Mars 

Outflow Channels 

Pallas 

Palus, Paludes 
Panspermia 
Patera, Paterae 
Perchlorates on Mars 
Phobos 

Phosphates on Mars 

Phyllosilicates, Extraterrestrial 

Planet 

Planitia 

Planum 


Plume 

Polar Caps (Mars) 

Polar Layered Deposits (Mars) 
Poynting-Robertson Drag 
Primordial Heat 
Psyche 

Radioactive Heating 
Regio 

Regolith, Planetary 
Rheology, Planetary Interior 
Rille 

Rima, Rimae 
Rotation Planet 
RQ36 

Rupes, Rupes 
Satellite or Moon 
Selenology 

Serpentinization (Mars) 

Shergottites 

Shergotty 

Slope Lineae, Recurrent 
Slope streaks (Mars) 

Small Solar System Body 

SNC Meteorites 

Sol 

Solar System, Inner 
Solid-State Greenhouse Effect 
Space Weathering 
Stagnant Lid Convection 
Steins 

Sulcus, Sulci 

Sulfates, Extraterrestrial 

Terra, Terrae 

Terrestrial Planet 

Tessera, Tesserae 

Tharsis 

Tholus 

Tides, Planetary 
Toutatis 

Valles Marineris 
Valley Networks 
Vallis, Valles 
Vastitas, Vastitates 
Venus 

Venus Clouds 

Vesta 

Zeolites 



20 


Astrobiology by Discipline 


Section - Outer Solar System: 
Th. Encrenaz 

Ariel 

CAIs 

Callisto 

Cassini 

Cassini Division 
Centaurs (Asteroids) 

Charon 

Chiron 

Comet 

Comet (Nucleus) 

Comet Borrelly 

Comet Encke 

Comet Giacobini-Zinner 

Comet Hale-Bopp 

Comet Halley 

Comet Hartley 2 

Comet Hyakutake 

Comet Me Naught 

Comet Shoemaker-Levy 9 

Comet Shower 

Comet Tempel 1 

Comet Wild 2 

Cryovolcanism 

Daughter Molecule, Comet 

Dione 

Enceladus 

Europa 

Galileo Galilei 

Ganymede 

GEMs 

Giant Planets 
Huygens 
Iapetus 
Io 

Itokawa Asteroid 

Jupiter 

Kuiper Belt 

Lightcurve 

Magnetosphere 

Meteorite, Allende 

Meteorite, Murchison 

Meteorite, Orgueil 

Meteorites 

Micrometeorites 


Mimas 

Miranda 

Neptune 

Nereid 

Oberon 

Oort Cloud 

Organic Refractory Matter 
Parent Body 
Parent Molecule, Comet 
Phoebe 

Planetary Rings 

Pluto 

Quaoar 

Rhea 

Saturn 

Sedna 

Solar System 

Solar System, Outer 

System Solar Formation, Chronology of 

Tethys 

Titan 

Titania 

Trans-Neptunian Object 
Triton 

Trojans (Asteroids) 

UltraCarbonaceous Antarctic Micrometeorites 

Umbriel 

Uranus 

Water in the Solar System 
Zodiacal Light 


Section - Planetary and Exoplanetary 
Atmospheres: J.L. Grenfell 

Absorption Cross Section 
Adiabatic Processes 
Albedo 
AOGCM 

Atmosphere, Escape 
Atmosphere, Model ID 
Atmosphere, Structure 
Atmosphere, Temperature Inversion 
Atmospheric Habitability 
Bioindicator 

Biomarkers Atmospheric, Evolution Over Geo¬ 
logical Time 



Astrobiology by Discipline 


21 


Biomarkers, Spectral 
Clouds 

Earth-like Atmosphere 
Exoplanetary Atmospheric Retrieval 
False Negative 
False Positive 
GCM 

Greenhouse Effect 

Grey Gas Model 

Habitability of the Solar System 

Habitability, Effect of Eccentricity 

Habitability, Effects of Stellar Irradiation 

Habitable Planet, Characterization 

Habitable Zone 

Habitable Zone, Effect of Tidal Locking 
Hadley Cells 
Latent Heat 
Mie Scattering 

Non-Grey Gas Model: Real Gas Atmospheres 

Raman Scattering 

Rayleigh Scattering 

Scale Height 

Stratosphere 

Troposphere 

Section - Planetary Formation and 
Dynamics: /. Alibert, R. Helled 

Apsidal Angle 

Atmosphere, Primitive Envelope 
Cassini State 

Coagulation in Planetary Disks 
Condensation Sequence 

Core Accretion, Model for Giant Planet 

Formation 
Corotation Torque 

Critical Core Mass (Giant Planet Formation) 
Disk Instability, Model for Giant Planet 

Formation 
Dynamical Friction 
Dynamical Instability 
Ejection, Hyperbolic 
Escape Velocity 
Feeding Zone 

Formation of Planetesimals - the Building Blocks 
of Planets 


Gas Drag 
Giant Impact 

Gravitational Collapse, Planetary 
Gravitational Focusing 
Hill Radius/Sphere 
Hill/Lagrange Stability 
Impact, Hit and Run 
Isolation Mass 
Kozai Mechanism 
Laplace Resonance 
Late-stage Accretion 
Libration 

Lindblad Resonance 

Magnetic Fields and Planetary Systems 
Formation 

Mean Motion Resonance 
Meter-Size Catastrophe 
Nice Model 
Oligarchic Growth 
Orbit 

Orbital Period 

Photoevaporation of Protoplanetary Disks 

Planet Formation 

Planet V Hypothesis 

Planetary Embryo 

Planetary Evolution 

Planetary Migration 

Planetesimals 

Protoplanetary Disk Dead Zone 
Protoplanetary Disk Instability 
Protoplanetary Disk Midplane 
Protoplanetary Disk of Second Generation 
Protoplanetary Disk, Chemistry 
Protosolar Nebula, Minimum Mass 
Proto-sun Composition 
Q (Tidal Quality Factor) 

Q (Toomre Parameter) 

Q* (Specific Energy to Destroy an Object) 
Radial Drift 

Runaway Gas Accretion 
Runaway Growth 
Secular Dynamics 
Secular Resonance 
Shepherding 
Snow Line 
Solar Nebula 

Turbulence (Planetary Disks) 



22 


Astrobiology by Discipline 


Viscosity 
Viscous Stirring 
Vortex, Vortices 

Field - Space Missions, Ground 
Facilities and Planetary Protection: 
M. Viso 

Section - Planetary Protection: M. Viso 

Aerobic Mesophilic Bacterial Spores 

Aseptic Process 

Assay 

Biobarrier 

Bioburden 

Bioburden Controlled Environment 
Bioburden Reduction 
Biodiversity (Planetary Protection) 

Biohazard Assessment Protocol 
Biological Efficacy 
Biological Indicator 
Biological Safety Level 
Clean Room 
Cleanliness 

Coleman-Sagan Equation 

Contamination, Probability 

Depyrogenation 

DHMR 

Disinfection 

D-Value 

Encapsulated Bioburden 
Exposed Surface Bioburden 
Hard Landing 
Heat Shock 
HEPA Filters 
Impact, Probability 
Inactivation 
Mated Bioburden 
Organic Material Inventory 
Outer Space Treaty 
Parametric Release 
Pasteurization 
Perennial Heat Source 
Planetary Protection 
Planetary Protection Category 
Quarantine 

Sample Receiving Facility 


Special Region (Mars) 

Sporicide 

Sterile 

Sterility Assurance Level 
Sterilization 

Terminal Sterilization Process 
Z-Value 

Section - Space Missions and Ground 
Facilities: M. Viso 

67P/Churyumov-Gerasimenko 

ALMA 

Beagle 2 

Biopan 

Cassini-Huygens Space Mission 
Cheops 

COMET (Experiment) 

CoRoT Satellite 
Deep Impact 
EPOXI Mission 
ERA 

EURECA 

Exobiologie Experiment 

ExoMars 

Expose 

Exposure Facilities 
Foton Capsule, Spacecraft 
Gaia Mission 
Galileo Mission 
Giotto Spacecraft 
Hayabusa Mission 
Herschel Mission 
Hipparcos 
HST 

Huygens Probe 

Infrared Astronomical Satellite 
Infrared Space Observatory 
International Space Station 
JUICE Mission 
JWST 

Kepler Mission 

Large Millimeter Telescope 

Long Duration Exposure Facility 

Mars 2020 

Mars Express 

Mars Global Surveyor 

Mars Odyssey 



Astrobiology by Discipline 


23 


Mars Orbiter Mission 

Mars Pathfinder 

Mars Reconnaissance Orbiter 

Mars Sample Return Mission 

Mars Science Laboratory 

MER, Spirit and Opportunity (Mars) 

Odin 

Philae Lander 
Phobos-Grunt 
Phoenix 

Pioneer Spacecraft 
PLATO 2.0 Satellite 
Rosetta Spacecraft 
SIM 

Spitzer Space Telescope 
Square Kilometre Array 
Stardust Mission 
STONE 


Submillimeter Wave Astronomy Satellite 
TESS 

TPF/Darwin 
Ulysses Mission 
Vega 1 and 2 Spacecraft 
Viking 

Voyager, Spacecraft 

WASP 

Yinghuo-1 

Field - Data Tables: M. Gargaud 

Astronomical Data 
Chemical and Biological Data 
Chronological History of Life on Earth 
General Data 
Geological Data 



A 


AAN Abiogenic Photosynthesis 

► Aminoacetonitrile ► Abiotic Photosynthesis 


Abiogenesis 

Stephane Tirard 

Centre Francis Viete d’Histoire des 
Sciences et des Techniques EA 1161, Faculte 
des Sciences et des Techniques de Nantes, 
Nantes, France 

Definition 

Thomas Huxley (1825-1895) used the term abio¬ 
genesis in an important text published in 1870. 
He strictly made the difference between sponta¬ 
neous generation, which he did not accept, and 
the possibility of the evolution of matter from 
inert to living, without any influence of life. 

Since the end of the nineteenth century, 
evolutive abiogenesis means increasing complexity 
and evolution of matter from inert to living state in 
the abiotic context of evolution of primitive Earth. 

See Also 

► Darwin’s Conception of the Origins of Life 

► Huxley’s Conception on Origins of Life 

► Origin of Life 

© Springer-Verlag Berlin Heidelberg 2015 
M. Gargaud et al. (eds.), Encyclopedia of Astrobiology, 
DOI 10.1007/978-3-662-44185-5 


Abiotic 

David C. Fernandez-Remolar 

Centro de Astrobiologia (INTA-CSIC), INTA, 

Torrejon de Ardoz, Spain 

Definition 

Abiotic refers to the physical and chemical pro¬ 
cesses that take place in natural environments but 
are driven by mechanisms that do not involve any 
biological activity. Although major physical and 
chemical cycles on Earth can hardly escape the 
activity of the biosphere, some processes do not 
depend on biological activities. For example, this 
is the case of the formation of hydrothermal 
deposits that are based on redox, volatile fugac- 
ity, and high thermal conditions. Some abiotic 
processes are involved in the production of sur¬ 
face oxidants through photochemical reactions in 
planet atmospheres as has been proposed to 
explain the presence of perchlorates on Mars. 
Paradoxically, different abiotic pathways 
(thermal, radiolytic, or photochemical) create 
the chemical disequilibrium which is strictly nec¬ 
essary to fuel physical and chemical cycles on 







26 


Abiotic Photosynthesis 


planets depleted of life. Some abiotic pathways 
have likely been essential to originate the 
primary biochemical machinery that drove the 
emergence of life on Earth. In this sense, most 
abiotic processes support the production of the 
compounds and chemical disequilibrium essen¬ 
tial for a region of the universe to become 
habitable. 


See Also 

► Hydrothermal Environments 

► Origin of Life 

► Photochemistry 

► Prebiotic Chemistry 


Abiotic Photosynthesis 

Armen Y. Mulkidjanian 

School of Physics, University of Osnabrueck, 

Osnabrueck, Germany 

Moscow State University, Moscow, Russia 

Keywords 

Bacterial photosynthesis; Carbon fixation; Pho¬ 
tochemistry; Semiconductors; Anoxic geother¬ 
mal fields 


Synonyms 

Abiogenic photosynthesis; Prebiotic 
photosynthesis 


Definition 

Abiotic or abiogenic photosynthesis is the syn¬ 
thesis of organic compounds with the aid of radi¬ 
ant energy and various inorganic or organic 
catalysts. 


History 

In September 1912, Benjamin Moore suggested 
at a discussion on the origin of life, held by the 
joint sections of Zoology and Physiology of the 
British Association for the Advancement of Sci¬ 
ence, that “the first step towards the origin of life 
must have been the synthesis of organic matter 
from inorganic by the agency of inorganic col¬ 
loids acting as transformers or catalysts for radi¬ 
ant solar energy” (Moore and Webster 1913). 

Overview 

In spite of Haldane’s well-known idea that UV 
light may have served as a driving force for 
formation of the first viruslike organisms 
(Haldane 1929), the idea of directly driving abio- 
genesis by solar energy had not won much sup¬ 
port at that time, despite the fact that the Sun is by 
far the most powerful energy source on Earth. 
The limited acceptance of the idea was partly 
due to the low quantum yield of abiotic photo¬ 
synthetic reactions and the poor reproducibility 
of experimental results. Abiotic photoproduction 
of hydrogen, in the presence of ions of divalent 
iron, has been observed (Mauzerall et al. 1993). It 
has been shown atmospheric photochemistry can 
produce aldehydes from CO (Bar-Nun and Chang 
1983). Only in the 1980s, were robust procedures 
of producing colloidal nanoparticles of 
photoactive semiconductors, such as zinc sulfide 
(ZnS) or cadmium sulfide (CdS), developed 
(Henglein 1984). These particles (see Fig. 1), 
due to their high surface-to-volume ratio, pro¬ 
vided experimental systems in which the photo¬ 
reduction of C0 2 to diverse organic compounds 
could be studied. The photoreduction proceeded 
with high and reproducible quantum yield (up to 
80 % for C0 2 reduction to formate at the surface 
of colloidal ZnS particles (Henglein 1984)). 
Recent studies have demonstrated high-yielding 
ZnS- and MnS-mediated photosynthesis under 
simulated primeval conditions (Zhang 
et al. 2004, 2007; Guzman and Martin 2009). In 
the modem oceans, ZnS and MnS are found at the 
sites of geothermal activity, where minute 




Abiotic Photosynthesis 


27 



Abiotic Photosynthesis, Fig. 1 Abiogenic photosyn¬ 
thesis on the primordial Earth. Left panel’, light-induced 
reactions in a ZnS particle combined with an energy 
diagram. The absorption of a UV quantum by a minute 
crystal of ZnS, an n -type semiconductor, leads to the 
separation of electric charges and to the transition of the 
excited electrons into the conducting zone. The electrons 
can migrate inside the crystal until they are trapped at the 


surface, where they can be picked up by appropriate 
acceptors, e.g., molecules of C0 2 . The residual electron 
vacancies (holes) are initially reduced by the S 2- ions of 
the crystal, which then eventually can be replenished by 
external electron donors, e.g., H 2 S (cf with the mechanism 
of anoxygenic photosynthesis). Right panel : the precipi¬ 
tation of ZnS particles (gray dots ) around a Hadean con¬ 
tinental hot spring (Figure from Mulkidjanian 2009) 


particles of these minerals continuously precipi¬ 
tate around hot, deep-sea hydrothermal vents; 
thereby, particles of ZnS and MnS, slowly pre¬ 
cipitating sulfides, make rings around black 
throats of such vents that are covered by promptly 
precipited particles of FeS (Tivey 2007). On the 
primordial Earth, hot metal-enriched geothermal 
fluids and vapor may have discharged to the sur¬ 
face of the first continents, so that particles of ZnS 
and MnS could have precipitated within regions 
exposed to solar radiation (Mulkidjanian 2009). 
These sulfide minerals could have been present in 
shallow waters (Guzman and Martin 2009) and 
should have precipitated around continental ther¬ 
mal springs (Mulkidjanian 2009). Since Zn 2+ 
ions are much more volatile than Fe 2+ ions, the 
vapor of continental geothermal systems would 
be particularly enriched in ZnS (Mulkidjanian 
et al. 2012). On the primordial Earth, ZnS could 
not be oxidized by atmospheric oxygen, so that 
photosynthesizing and habitable rings may have 
persisted around terrestrial thermal springs and 


fumaroles. The development of the first life forms 
within photosynthesizing, ZnS-containing pre¬ 
cipitates at such anoxic geothermal fields, where 
Zn 2+ ions would be continuously released as 
by-products of abiogenic photosynthesis, might 
explain cellular enrichments in Zn 2+ , the equilib¬ 
rium concentration of which in the primordial 
ocean should have been extremely low 
(Mulkidjanian and Galperin 2009; Mulkidjanian 
et al. 2012). Several proteins shared by all extant 
organisms and believed to form the core of the 
last universal common ancestor (LUCA) are par¬ 
ticularly enriched in Zn and Mn; this may also 
support the notion of a role for abiogenic photo¬ 
synthesis in the earliest stages of evolution 
(Mulkidjanian and Galperin 2009; Mulkidjanian 
et al. 2012). Since these ubiquitous proteins are 
depleted in iron, it remains to be established 
whether and to what extent iron (II), the predom¬ 
inant transition metal in geothermal exhalations, 
was involved in abiogenic photosynthesis. It has 
also been shown that titanium dioxide particles 







28 


Ablation 


can drive photo synthetic organic chemistry 
inside cell membrane-like vesicles (Summers 
et al. 2009). Titanium dioxide (both rutile and 
anatase) particles could have been formed by 
precipitation or released (directly or from alter¬ 
ation of other titanium minerals) by weathering. 
This energy transduction could have provided 
pathways to new compounds in a prebiotic sys¬ 
tem or support early biochemical reactions. 


See Also 

► Anoxygenic Photosynthesis 

► Black Smoker 

► Carbon Dioxide 

► Charge Transfer 

► Earth’s Atmosphere, Origin and Evolution of 

► Electron Acceptor 

► Electron Donor 

► Energy Sources 

► Extreme Ultraviolet Light 

► Formic Acid 

► Haldane’s Conception of Origins of Life 

► Hot Spring Microbiology 

► Hydrothermal Vent Origin of Life Models 

► Iron 

► LUCA 

► Origin of Life 

► Photochemistry 

► Photosynthesis 

► Transition Metals and Their Isotopes 

► UV Radiation 

► White Smoker 

References and Further Reading 

Guzman MI, Martin ST (2009) Prebiotic metabolism: 
production by mineral photoelectrochemistry of 
alpha-ketocarboxylic acids in the reductive tricarbox¬ 
ylic acid cycle. Astrobiology 9(9):833—842 

Haldane JBS (1929) The origin of life. Rationalist annual. 
Watts & Co, London, pp 3-10 

Henglein A (1984) Catalysis of photochemical reactions 
by colloidal semiconductors. Pure Appl Chem 
56(9): 1215-1224 

Mauzerall D, Borowska Z, Zielinski I (1993) Photo and 
thermal reactions of ferrous hydroxide. Orig Life 
EvolBiosph 23(2): 105-114 


Moore B, Webster TA (1913) Synthesis by sunlight 
in relationship to the origin of life. Synthesis of 
formaldehyde from carbon dioxide and water by 
inorganic colloids acting as transformers 
of light energy. Proc R Soc Lond B Biol Sci 
87:163-176 

Mulkidjanian AY (2009) On the origin of life in the Zinc 
world: 1. Photosynthetic, porous edifices built of 
hydrothermally precipitated zinc sulfide (ZnS) as cra¬ 
dles of life on Earth. Biol Direct 4:26 

Mulkidjanian AY, Galperin MY (2009) On the 
origin of life in the Zinc world. 2. Validation of 
the hypothesis on the photo synthesizing zinc 
sulfide edifices as cradles of life on Earth. Biol 
Direct 4:27 

Mulkidjanian AY, Bychkov AY, Dibrova DV, Galperin 
MY, Koonin EV (2012) Origin of first cells at terres¬ 
trial, anoxic geothermal fields. Proc Natl Acad Sci 
USA 109:E821-E830 

Summers DP, Noveron J, Basa RCB (2009) Energy trans¬ 
duction inside of amphiphilic vesicles: encapsulation 
of photochemically active semiconducting particles. 
Orig Life Evol Biosph 39:127-140 

Tivey MK (2007) Generation of seafloor hydrothermal 
vent fluids and associated mineral deposits. Oceanog¬ 
raphy 20(l):50-65 

Zhang XV, Martin ST, Friend CM, Schoonen MAA, Hol¬ 
land HD (2004) Mineral-assisted pathways in prebiotic 
synthesis: photoelectrochemical reduction of carbon 
(+IV) by manganese sulfide. J Am Chem Soc 
126(36): 11247-11253 

Zhang XV, Ellery SP, Friend CM, Holland HD, Michel 
FM, Schoonen MAA, Martin ST (2007) Photodriven 
reduction and oxidation reactions on colloidal 
semiconductor particles: implications for prebiotic 
synthesis. J Photochem Photobiol A Chem 185(2-3): 
301-311 


Ablation 

Daniel Rouan 

LESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 


Definition 

Ablation is the erosion of the surface of a solid 
object in a flow (e.g., during the entrance of an 
object into the atmosphere) through some physi¬ 
cal process, such as formation of a ► fusion crust, 
vaporization, or friction. 




Absorption Spectroscopy 


29 


Absolute and Relative Ages 

Daniele L. Pinti 

GEOTOP Research Center for Geochemistry and 
Geodynamics, Universite du Quebec a Montreal, 
Montreal, QC, Canada 

Definition 

In ► geochronology, the absolute age of a rock is 
the age obtained from the measurement of spon¬ 
taneous decay of radioactive nuclides contained 
in the rocks or its constituent minerals. It differs 
from the relative age. This latter is the age of a 
rock obtained from time and space relations 
between rock formations, giving only qualitative 
or semiquantitative information on the period 
when the rock formed. 


See Also 

► Earth, Age of 

► Geochronology 

► Radioactivity 


Absorption Cross Section 

Lisa Kaltenegger 

Cornell University, Ithaca, NY, USA 

Keywords 

Absorption 

Definition 

When a parallel, monochromatic beam of light 
traveling in some specific direction encounters a 
medium of finite extent, a certain amount of the 
flux will be absorbed and a certain amount will be 


scattered into other angles. The rate at which 
energy is taken out of the beam by absorption 
and scattering can be characterized in terms of 
coefficients with dimensions of area, which are 
known as cross sections. The term absorption 
cross section is often used to include both the 
portion due to scattering and that due to true 
absorption (loss of the photon into another form 
of energy, such as heat). For atmospheric gases, 
this total absorption cross section is defined by 
the Beer’s law expression: 

I = Io exp (—(777/) 

where 7 0 and 7 are the incident and transmitted 
light intensities, respectively, o is the absorption 
cross section (cm 2 molecule -1 ), n is the molecu¬ 
lar density, and / is the pathlength in cm. 


Absorption Spectroscopy 

Steven B. Charnley 

Solar System Exploration Division, Code 
691, Astrochemistry Laboratory, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 

Definition 

In absorption ► spectroscopy, the spectral fea¬ 
tures of interest appear in absorption with respect 
to a background continuous spectrum. In the 
interstellar medium, the background continuum 
may be supplied by a radiation source, such as a 
star, located behind the region of interest. The 
absorbing material may be either in the gas or 
the solid phase (e.g., interstellar dust or ices). 
Solid state features are much broader than atomic 
or molecular absorptions and are consequently 
more difficult to assign to a specific carrier. 
Much of the solar (Fraunhofer) spectrum is seen 
in absorption, as the outer cooler layers of the 
solar atmosphere absorb radiation from the 
deeper photosphere. Spectral lines in planetary 
atmospheres are typically seen in absorption, 






30 


Abundances of Elements 


against the continuous thermal spectrum from the 
planetary or satellite surface. 


History 

The first person to notice a number of dark fea¬ 
tures in the solar spectrum was the English chem¬ 
ist William Wollaston in 1802. This absorption 
spectrum was first systematically investigated by 
Joseph von Fraunhofer, starting in 1814, and the 
spectral features are now known as Fraunhofer 
lines. 


See Also 

► Spectroscopy 


Abundances of Elements 

Nikos Prantzos 

Institut d’Astrophysique de Paris, Paris, France 

Keywords 

Chemical composition; Nucleosynthesis; 
Nuclide 


Definition 

The relative amount (or fraction) of a given 
nuclide in a sample of matter is called the abun¬ 
dance of that nuclide. It can be expressed either in 
absolute terms (i.e., with respect to the total 
amount of matter in the sample) or in relative 
terms (with respect to the amount of some key 
element, e.g., the most abundant one, in the sam¬ 
ple). Similarities and differences in the elemental 
and isotopic composition of ► stars and galaxies 


are key ingredients for understanding their origin 
and evolution. 

Overview 

The composition of remote objects (the Sun, 
► stars, interstellar gas, and galaxies) is deter¬ 
mined through spectroscopy, which usually 
allows the determination of elemental abun¬ 
dances; in rare cases, particularly for interstellar 
clouds, some isotopic abundances may be deter¬ 
mined in those objects. For Earth, lunar, and 
meteoritic samples, nuclear mass spectroscopy 
allows precise determination of most isotopic 
abundances; this is also the case for cosmic 
rays, albeit only for the most abundant nuclides 
at present. Hydrogen (H) being the most abun¬ 
dant element in the Universe, spectroscopists 
express the abundance of element i as the number 
ratio of its nuclei with respect to those of H: 
nj = Nj 1N H , and they use a scale where 
lo g(N H ) = 12. In the meteoritics community, 
the silicon scale of lo g(N Si ) = 6 is used. Theore¬ 
ticians use the mass fraction X t = N t A t / YJXj Ay, 
where Aj is the mass number of nuclide /; obvi¬ 
ously, XX = 1 • Conversion of mass fractions to 
abundances by number requires use of the quan¬ 
tity Yj = X Mi called the mole fraction (notice 
that XX ^ 1). 

According to our current understanding, the 
material of the proto-solar nebula had a remark¬ 
ably homogeneous composition, as a result of 
high temperatures (which caused the melting of 
nearly all the dust grains) and thorough mixing. 
This composition characterizes the present-day 
surface layers of the Sun, which remain unaf¬ 
fected by nuclear reactions occurring in the 
solar interior (with a few exceptions, e.g., the 
fragile D and Li). Furthermore, after various 
physicochemical effects are taken into account, 
it appears that the elemental composition of the 
Earth and meteorites matches extremely well 
with the solar photospheric composition. The 
composition of stars in the Milky Way presents 
both striking similarities and considerable 




Abundances of Elements 


31 


CO 


in 


CD 

O 

c 

CO 

■o 


_Q 

< 


O) 

o 



0 10 20 30 40 50 60 70 80 90 


Z (Element) 


Abundances of Elements, Fig. 1 Solar system abundances (by number) of the 92 chemical elements, in a logarithmic 
scale where log(N) = 6 for Silicon (from a compilation in Lodders 2003) 


differences with the solar composition. The uni¬ 
versal predominance of H (90 % by number, but 
~70 % by mass) and He (9 % by number, but 
~25 % by mass) and the relative abundances of 
“metals” (to astronomers, elements heavier than 
He) is the most important similarity. On the other 
hand, the fraction of metals {metallicity , about 
1.5 % in the Sun) appears to vary considerably 
within the solar neighborhood (where the oldest 
stars have a metallicity of 0.1 solar), across the 
Milky Way disk (with young stars in the inner 
Galaxy having three times more metals than the 
Sun), or in the galactic halo (with stellar 
metallicities ranging from 0.1 to 0.00001 solar). 
These variations in composition reflect the his¬ 
tory of “chemical evolution” of the Milky Way 
(Fig. 1). 


See Also 

► Nucleosynthesis, Neutrino 

► Nucleosynthesis, Explosive 

► Primordial Nucleosynthesis 

► S-process 

► Star 


References and Further Reading 

Asplund M, Grevesse N, Sauval AJ, Scott P (2009) The 
chemical composition of the sun. Ann Rev Astron 
Astrophys 47:481-522 

Lodders K (2003) Solar system abundances and conden¬ 
sation temperatures of the elements. Astrophys 
J 591:1220-1247 









32 


1989 AC 


1989 AC 

► Toutatis 


Acasta Gneiss 

Samuel A. Bowring 

Department of Earth, Atmospheric and Planetary 
Sciences, Massachusetts Institute of Technology, 
Building 54-1126, Cambridge, MA, USA 

Keywords 

Geochronology; Oldest rocks; Zircon 

Definition 

The Acasta Gneisses are the oldest known rocks 
on the surface of the Earth. They are exposed in 
northern Canada, north of Great Slave Lake, east 
of Great Bear Lake with the approximate position 
of 65° 10' N and 115° 30' W. They have a com¬ 
position close to granitic and are interpreted to 
have formed, at least in part, from even older 
rocks that may be as old as 4.2 Ga. 

Overview 

The Acasta Gneisses are the oldest dated rocks on 
Earth. They are exposed in northwestern Canada 
(65° 10' N and 115° 30' W) along the western 
margin of the Archean Slave craton (>2.5 Ga), in 
the core of a north-trending fold in the foreland of 
the Wopmay orogen, a 2.02-1.84 Ga-old oro- 
genic belt. The Acasta Gneisses range in age 
from 4.03 Ga to ca. 3.6 Ga with distinct groupings 
at 4.03-3.94 Ga, 3.74-3.72 Ga, and 
3.66-3.58 Ga. Rocks from these three distinct 
groups are compositionally diverse and range 
from ► granite to quartz diorite to tonalite. 
Rocks have been deformed several times 
resulting in well-developed foliations (planar 


fabric present in metamorphic rocks and pro¬ 
duced by reorientation of minerals). Lens-shaped 
boudins (cylinder-like structures making up a 
layer in a deformed rock) of serpentinized ultra- 
mafic rocks, up to several hundred meters long, 
occur throughout the gneisses. No ca. 4.0-3.6 Ga 
metasedimentary rocks have been discovered 
although sparse outcrops of locally tightly folded 
quartzite, iron formation, and pelite are found 
in the older gneisses. Weakly deformed, ca. 
3.6 Ga-old granitic dikes cut many outcrops. 
During the 1.88 Ga Calderian orogeny to the 
west, sheets of 1.9-2.5 Ga-old rocks were thrust 
over the western edge of the Slave craton, 
resulting in a set of north-trending folds and 
metamorphism of underlying Archean rocks. 
Ar-Ar biotite and U-Pb apatite dates record com¬ 
plex reheating during this event at ca. 1.77 Ga. 

The protoliths of the Acasta Gneiss range 
from granite to tonalite/diorite in composition. 
Their U-Pb zircon dates indicate that the older 
igneous crystallization ages are 4.03-3.96 Ga. 
Many zircons from all rock types contain older 
cores with the oldest at 4.06 and 4.2 Ga, which is 
consistent with the involvement of even older 
crust in their generation by partial melting or 
assimilation. In general, the geochemistry of the 
Acasta Gneisses is not different from other 
Archean and younger rocks: they are on average 
enriched in light rare earth elements with variable 
depletion in heavy rare earth elements, features 
that are thought to reflect the presence of garnet in 
the source area. ► Radiogenic isotope systemat- 
ics in whole rocks (Sm-Nd) and zircon (Lu-Hf) 
are also consistent with the involvement of older 
► continental crust. Many of the rocks have zir¬ 
cons with thin overgrowths likely related to meta¬ 
morphism at ca 3.65 Ga, 3.6 Ga, and 3.4 Ga. 

The formation and preservation of ► conti¬ 
nental crust early in Earth’s history is of broad 
interest to Earth scientists because the oldest con¬ 
tinental crust provides a record of magma forma¬ 
tion and the role of water in generating granitic 
magmas over 4 billion years ago. The ca. 4 Ga 
granitoids are very similar to those formed much 
later in Earth’s history by plate-tectonic pro¬ 
cesses. No evidence of the late heavy bombard¬ 
ment is preserved in the Acasta Gneisses. 





Accretion Shock 


33 


See Also 

► Canadian Precambrian Shield 

► Continental Crust 

► Earth, Formation and Early Evolution 

► Geochronology 

► Granite 


References and Further Reading 

Bowring SA, Housh TB (1995) The Earth’s early evolu¬ 
tion. Science 269:1535-1540 

Bowring SA, Williams IS (1999) Priscoan (4.00-4.03 Ga) 
orthogneisses from northwestern Canada. Contrib 
Mineral Petrol 134:3-16 

Bowring SA, Housh TB, Isachsen CE (1990) The Acasta 
gneisses: remnant of Earth’s early crust. Origin of the 
earth. Oxford University Press, New York 

Iizuka T, Horie K, Komiya T, Maruyama S, Hirata T, 
Hidaka T, Windley BF (2006) 4.2 Ga zircon 
xenocryst in an Acasta gneiss from northwestern Can¬ 
ada: evidence for early continental crust. Geology 
34:245-248 

Iizuka T, Komiya T, Ueno Y, Katayama I, Uehara Y, 
Maruyama S, Hirata T, Johnson SP, Dunkley DJ 
(2007) Geology and zircon geochronology of the 
Acasta Gneiss Complex, northwestern Canada: new 
constraints on its tectonothermal history. Precambrian 
Res 153:179-208 


Accretion 

Daniele L. Pinti 

GEOTOP Research Center for Geochemistry and 
Geodynamics, Universite du Quebec a Montreal, 
Montreal, QC, Canada 

Definition 

In planetary sciences, accretion is the complex 
process of formation of a planet, either rocky or 
gaseous, from the disk of dust and gas around a 
protostar. In geology, accretion is a process by 
which rocks and sediments are added to a tectonic 
plate (plate accretion) or a landmass (landmass 
accretion). When subduction of an oceanic plate 


under a continental plate occurs, plate accretion is 
the process of scraping oceanic floor sediments 
against the continental plate which form a prism 
of material called accretionary wedge. Landmass 
accretion is the process of adding sediments 
(alluvium) to a coastline or a riverbank, increas¬ 
ing land area surface. 


See Also 

► Magnetic Fields and Planetary Systems 
Formation 

► Planet Formation 

► Plate Tectonics 


Accretion Shock 

Steven B. Charnley 

Solar System Exploration Division, Code 
691, Astrochemistry Laboratory, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 

Definition 

Generally, an accretion shock is a shock wave 
occurring at the surface of a compact object or 
dense region that is accreting matter supersoni¬ 
cally from its environment. In the context of 
astrobiology, an accretion shock is normally 
understood to mean the shock wave present at 
the surface of the protosolar nebula or the 
corresponding nebula surrounding a ► protostar, 
as it accretes interstellar matter from the sur¬ 
rounding molecular cloud. 


See Also 

► Protoplanetary Disk 

► Protosolar Nebula, Minimum Mass 

► Protostars 

► Shock, Interstellar 





34 


Accretion, Stellar 


Accretion, Stellar 

Steven W. Stahler 

Department of Astronomy, University of 
California, Berkeley, CA, USA 

Definition 

Stellar accretion refers to the inflow of ambient gas 
onto the surface of a star. During the process of star 
formation, accretion builds up the object to its final 
mass. The infalling gas is the interior portion of a 

► dense core, a small ► molecular cloud that col¬ 
lapses under the influence of its own gravity. The 
object being built up in this manner is a protostar 
and represents the first phase of stellar evolution. 
Some infalling gas impacts the protostar directly. 
Much of the gas, however, has sufficient angular 
momentum that it goes into orbit around the young 
star. The accreting gas thus creates a circumstellar 
disk. Matter spirals in through the disk onto the 
surface of the protostar. The remaining part of the 
disk eventually gives rise to planets. 

See Also 

► Dense Core 

► Free-Fall Time 

► Gravitational Collapse, Stellar 

► Molecular Cloud 

► Protoplanetary Disk 

► Protostars 

► Protostellar Envelope 

► Star Formation, Theory 


Acetaldehyde 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Synonyms 

Acetic aldehyde; Ethanal 


Definition 

Acetaldehyde is an organic compound with 
the chemical formula CH 3 CHO 


H —C—C 
H ^ 

It is the smallest aldehyde after formaldehyde. It 
is a colorless liquid at room temperature with an 
irritating odor. It can be obtained by the oxidation 
of ► ethanol or by the reduction of ► acetic acid. 
When we drink alcohol, the ethanol is oxidized to 
acetaldehyde, by alcohol dehydrogenase, which 
is then oxidized to acetic acid by aldehyde dehy¬ 
drogenase in the liver. It can be formed easily 
from gas mixtures containing methane by ultra¬ 
violet light and electric discharges, among others. 
It reacts with hydrogen cyanide and ammonia to 
give 2-aminopropionitrile, which gives ► alanine 
(amino acid) after hydrolysis. It has been detected 
in extracts from carbonaceous chondrites. Melt¬ 
ing point: —123.5 °C, boiling point: —20.2 °C, 
density: 0.788 g cm “ 3 . 


See Also 

► Acetic Acid 

► Alanine 

► Aldehyde 

► Chondrite 

► Formaldehyde 


Acetic Acid 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 


Synonyms 

Ethanoic acid 






Acetonitrile 


35 


Definition 

Acetic acid is a ► carboxylic acid with the chem- 

H O 

I // 

ical formula CH 3 COOH H — C—C 

I \ 

H °- H 

It is a colorless liquid at room temperature with 
an irritating odor. Pure anhydrous acetic acid is 
sometimes called glacial acetic acid. It can be 
obtained by oxidation of ► acetaldehyde, which 
occurs in human liver catalyzed by the enzyme 
aldehyde dehydrogenase, or by the hydrolysis of 
acetonitrile. It is easily formed in chemical evolu¬ 
tion experiments, e.g., it was found among the 
products of spark discharge experiment in a gas 
mixture of methane, ammonia, hydrogen, and 
water by S. L. Miller in 1953. It has been found in 
extracts from carbonaceous ► chondrites and has 
also been identified in ► molecular clouds. Melting 
point: 16.6 °C, boiling point: 117.8 °C, density: 
1.0492 g cm -3 , acidity constant (pAT a ): 4.76. 

See Also 

► Acetaldehyde 

► Aldehyde 

► Carboxylic Acid 

► Chondrite 

► Miller, Stanley 

► Molecular Cloud 


Acetic Aldehyde 

► Acetaldehyde 


Acetone 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 

Synonyms 

Propanone 


Definition 

The organic compound acetone (CH 3 COCH 3 ) is 
the simplest example of a ketone. Under standard 
conditions, it is a colorless, flammable liquid. 
Acetone is naturally produced by normal meta¬ 
bolic processes in the human body. Since it is 
miscible with water, it serves as an important 
laboratory solvent. Rotational transitions in both 
the ground vibrational state and in the first 
excited torsional state have been detected by 
radio astronomers in ► molecular clouds. 


History 

Although detection of acetone in a molecular 
cloud toward the center of our ► Milky Way gal¬ 
axy was reported by radio astronomers in 1987, 
secure confirmation of its presence in interstellar 
clouds was not achieved until some 15 years later. 

See Also 

► Molecular Cloud 

► Molecules in Space 

► Milky Way 

References and Further Reading 

Friedel DN, Snyder LE, Remijan AJ, Turner BE 
(2005) Detection of acetone toward the orion-KL hot 
core. Astrophys J 632:L95-L98 


Acetonitrile 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Synonyms 

CH 3 CN; Cyanomethane; Methyl cyanide 






36 


Acetylene 


Definition 


Definition 


Acetonitrile is the simplest organic ► nitrile 
with the chemical formula CH 3 CN 


H 


H 


\ 

.\ C-C = N. It is a colorless liquid at 

"1 

H 


room temperature with an ether-like odor. It can 
be obtained by dehydration of acetamide or by 
hydrogenation of a mixture of carbon monoxide 
and ammonia. It gives ► acetic acid and ammo¬ 
nia after hydrolysis and gives ethylamine after 
reduction. Acetonitrile itself is only slightly 
toxic but gives extremely toxic ► hydrogen cya¬ 
nide by metabolism in the body. It is detected in 
► molecular clouds as an interstellar molecule and 
also found in cometary comas. When aminated on 
the methyl group, aminoacetonitrile is produced, 
which is an important precursor of ► glycine. It is 
completely miscible with water and often used as 
an eluant in high-performance liquid chromatogra¬ 
phy (HPLC), with melting point, —45.7 °C; boiling 
point, 82 °C; and density, 0.786 g cm -3 . 


See Also 

► Acetic Acid 

► Comet 

► Glycine 

► Hydrogen Cyanide 

► Molecular Cloud 

► Nitrile 


Acetylene 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 


Acetylene is the simplest alkyne (hydrocarbons 
that have a triple bond between two carbon 
atoms, with the formula C n H 2n - 2 )- Under stan¬ 
dard conditions in the laboratory, it is a colorless 
but unstable gas. Because of its symmetry, linear 
of the form HCCH, it lacks a permanent electric 
dipole moment and hence has no allowed pure 
rotational transitions, making it undetectable at 
millimeter wavelengths. Astronomers have 
observed its vibrational transitions in the infra¬ 
red, in both ► molecular clouds and in the enve¬ 
lopes of evolved stars. It is an important link in 
the chemistry of heavier carbon chain molecules 
and related species in these regions. Acetylene is 
also found as a minor component in the atmo¬ 
spheres of gas giants like the planet ► Jupiter, in 
the atmosphere of Saturn’s satellite ► Titan, and 
in ► comets. 


History 

Acetylene was discovered in 1836 by Edmund 
Davy and then rediscovered in 1860 by French 
chemist Marcellin Berthelot, who coined the 
name “acetylene.” It was first observed in the 
interstellar medium by Lacy et al. (1989) and in 
► Comet Hyakutake and ► Comet Hale-Bopp 
(Brooke et al. 1996). 


See Also 

► Comet 

► Comet Hale-Bopp 

► Comet Hyakutake 

► Molecular Cloud 

► Molecules in Space 

► Stellar Evolution 

References and Further Reading 


Synonyms 

Ethyne, HCCH 


Brooke TY, Tokunaga AT, Weaver HA, Crovisier J, 
Bockelee-Morvan D, Crisp D (1996) Detection of 
acetylene in the infrared spectrum of comet 
Hyakutake. Nature 383:606-608 




Acid Hydrolysis 


37 


Hartquist TW, Williams DA (1995) The chemically con¬ 
trolled cosmos. Cambridge University Press, 
Cambridge 

Lacy JH, Evans NJ II, Achtermann JM, Bruce DE, Arens 
JF, Carr JS (1989) Discovery of interstellar acetylene. 
Astrophys J 342:L43-L46 


Achiral 

Robert Hazen 

Geophysical Laboratory, Carnegie Institution of 
Washington, Washington, DC, USA 

Synonyms 

Mirror symmetric 

Definition 

The term “achiral” is applied to any object - in 
astrobiology most commonly a molecule, a 
two-dimensional crystal surface, or a three- 
dimensional crystal structure - that is invariant 
(i.e., superimposable) with its mirror image. 
Achiral objects possess a plane of symmetry, 
either a mirror or a glide plane symmetry 
operator. Common achiral objects include a 
soccer ball, a pencil, and the letter “X,” in con¬ 
trast with chiral objects such as a snail shell, 
your left hand, and the letter “R.” Common 
achiral molecules are H 2 0, CH 4 , and NH 3 in 
contrast with such chiral biomolecular species 
as alanine and ribose. In chemistry, achiral should 
not be confused with racemic, although in neither 
case is the optical rotation of polarized light 
affected. 


See Also 

► Chirality 

► Enantiomeric Excess 

► Homochirality 

► Racemic Mixture 

► Stereoisomers 


Achondrite 

Frank Sohl and Tilman Spohn 

Deutsches Zentmm fur Luft- und Raumfahrt (DLR), 

Institut fiir Planetenforschung, Berlin, Germany 

Definition 

Achondrites are differentiated stony ► meteorites 
and constitute a minority among the stony meteor¬ 
ites. The term literally means “without ► chon- 
drules” and therefore underlines the main 
difference with ► chondrites. Achondrites are 
igneous ► rocks or ► breccias of igneous 
rock fragments and thus their parent body has 
experienced partial melting and recrystallization. 
The class of achondrites includes the primitive 
achondrites (e.g., ureilites) and achondrites in gen¬ 
eral (e.g., aubrites, eucrites, howardites, diogenites, 
Martian meteorites, and lunar meteorites). 

See Also 

► Breccia 

► Chondrite 

► Chondrule 

► Meteorites 

► Rock 


Acicular Ironstone 

► Goethite 


Acid Hydrolysis 

Mark Dorr 

University of Southern Denmark, Odense M, 
Denmark 

Definition 

Hydrolysis (Greek: udoop [hydor] = “water” and 
'kxxiiq [lysis] = “solution”) is a chemical reaction 







38 


Acid Maceration 


in which a compound is cleaved by water. If a 
proton-donating compound (Bronsted acid) 
catalyzes the reaction, it is called “acid hydroly¬ 
sis.” Formally one part of the cleaved reaction 
product receives a proton (H + ), the other a 
hydroxyl (OH - ) moiety of a water molecule. 
Hydrolysis can also be catalyzed by a base. The 
reverse reaction is called a “condensation 
reaction.” 


Acid Maceration 

Emmanuelle J. Javaux 
Palaeobiogeology-Palaeobotany- 
Palaeopalynology, Geology Department, 
Universite de Liege, Liege, Belgium 

Definition 

Acid maceration is a technique used to extract 
organic-walled ► microfossils or kerogen from 
rock. A rock sample is cleaned to remove 
external contamination and cmshed into 
small pieces. About 25 mg is macerated in 
chlorhydric acid solution (HC1) to remove 
carbonate minerals, rinsed with distilled water, 
and then macerated in fluorhydric acid solution 
(HF) to remove silicate minerals. A following step 
of boiling the macerate in hot HC1 removes fluo¬ 
rides formed during the previous acid step. This 
protocol may vary according to the nature of the 
rock, of the fossils, and of their degree of preserva¬ 
tion. After neutralization of the final macerate with 
distilled water, the residue is filtered on sieves of 
desired size fractions, then mounted on microscopic 
slides or kept in vials for other analyses. 


See Also 

► Acritarch 

► Biomarkers, Morphological 

► Fossil 

► Kerogen 


Acidophile 

Felipe Gomez 

Centro de Astrobiologia (CSIC/INTA), 

Instituto Nacional de Tecnica Aeroespacial, 
Torrejon de Ardoz, Madrid, Spain 

Keywords 

Archaea; Chemolithoautotroph; Eukaryote; Iron 
cycle; Prokaryote; Sulfur cycle 

Definition 

Acidophiles are ► microorganisms that thrive 
under acidic conditions, usually at very low pH 
(<3). Natural niches where acidophiles can be 
found are volcanic areas (Yellowstone), hydro- 
thermal sources, deep-sea vents, metal mining 
activities (Iron Mountain, Rio Tinto), or in the 
stomachs of animals. Acidophilic organisms can 
be found in the different domains of the tree of 
life (► Archaea, Bacteria, and ► Eukarya). 

Overview 

The best characterized acidophiles belong mainly 
to Bacteria and Archaea domains (Madigan and 
Martinko 2005). These microorganisms normally 
are associated to sulfuric pools, acid mine drain¬ 
age, or hydrothermal sources, that is, environ¬ 
ments where sulfur compounds are present. The 
origin of extreme acidic conditions is related with 
the ► oxidation of reduced sulfur compounds 
which determines the strong relationship between 
acidophiles and sulfur chemistry. But also some 
eukaryotes as the green algae Dunaliella 
acidophila and the red algae Cyanidium 
caldarium (both organisms can live below pH 
1.5) and some fungi are acidophiles. Surprisingly, 
eukaryotic microbes are the principal contribu¬ 
tors of biomass in some low-pH environments as 
► Rio Tinto, a Spanish river which has a pH of 
around 2 and contains much higher 





Acidophile 


39 


concentrations of heavy metals than are typically 
found in fresh waters (Lopez-Archilla 
et al. 2001). Some interesting results from Rio 
Tinto are related with evolutionary distances 
between acidophilic species that occur in the 
river and their neutrophilic relatives. Authors 
reported some results that offer insight into adap¬ 
tation to an extremely acidic environment. Adap¬ 
tations associated with the transition from a 
neutral to an acidic environment must occur rel¬ 
atively rapidly when measured on evolutionary 
timescales (Amaral-Zettler et al. 2002). Authors 
detected clones from the Rio Tinto that are 
closely related to neutrophilic species such as 
Chlamydomonas noctigama , Chlorella 

minutissima , and Colpidium campylum. From 
microscopic observations, rotifers were also 
identified as inhabitants of Rio Tinto, as well as 
heliozoans and other types of amoeba. 

Acidophiles belonging to different orders of 
the archaeal domain have been identified, such as 
Sulfolobales (a particular order in the 
Crenarchaeota branch) and some facultative 
anaerobic thermoacidophilic microorganisms as 
Acidianus brierleyi and A. infernus and other 
thermophilic as Metallosphaera sedula , all of 
them related with metal mobilization in natural 
environments and mining processes, 
Thermoplasmatales (order included in 
Euryarchaeota branch), and some others groups 
as nanoorganisms associated to Iron Mountain 
Mine and called ARMAN (Archaeal Richmond 
Mine Acidophilic Nanoorganisms). The 
ARMAN group is composed by three different 
lineages deeply branched in the Euryarchaeota 
subgroup. 

Acidophiles belonging to the bacterial domain 
are the phylum Acidobacteria, the order Aciditio- 
bacillales of ► Proteobacteria, the genus 
Acidithiobacillus and Leptospirillum, and some 
other related microorganisms as Acetobacter 
aceti , a bacterium that belongs to the Acetobacter 
genus of Proteobacteria that produces acetic acid 
(vinegar) from the oxidation of ethanol. 

Studies of mechanisms used for adaptation at 
low pH by acidophiles reported interesting results 
about efficient apparatus for pumping protons out 
of the intracellular space as a way of maintaining 


cytoplasm at or near neutral pH (Kelch 
et al. 2007). Therefore, intracellular proteins are 
not forced to develop acid stability through evolu¬ 
tion. However, some acidophiles, as Acetobacter 
aceti , have an acidified cytoplasm. In the case of 
acidophiles with acidic cytoplasm, all proteins are 
forced to evolve acid stability. Acetobacter has 
become as a good model for studying acid stability 
mechanisms. Several authors have studied pro¬ 
teins adapted to low pH and revealed that in 
acid-stable proteins there is an overabundance of 
acidic residues which minimizes low-pH destabi¬ 
lization induced by a buildup of positive charge. 
The relocation of acid-sensitive salt bridges to 
regions with important functions in the unfolding 
process is a very specialized case of acid stability 
for some proteins of acidophiles. But some others 
mechanisms for protein stabilization in acid con¬ 
ditions have been reported. 

Applications 

Acidophiles have industrial applications as in 
biomining and bioremediation. Among the 
methods used for acid mine drainage treatment, 
there are several which involve also metal- 
immobilizing bacteria as a way for metal seques¬ 
tering. An important biotechnological application 
of acidophiles is the process known as bioleaching 
for metal extraction and exploitation of extremely 
low-grade ores. Not only bacteria but also fungi 
have been used in related projects (Mohapatra 
et al. 2007; Botuyan et al. 1996). Projects include 
nickel extraction with A. ferrooxidans and Asper¬ 
gillus sp. fungi (Mohapatra et al. 2007) and sulfur 
removal from coal with Acidithiobacillus sp. or 
naturally present population bacteria on fossil 
fuels as coal (Gomez et al. 1997). 

See Also 

► Autotroph 

► Autotrophy 

► Biodiversity 

► Chemoautotroph 

► Chemolithoautotroph 



40 


Acritarch 


► Chemolithotroph 

► Deep-Sea Microbiology 

► Early Archean 

► Eukarya 

► Eukaryote 

► Euryarchaeota 

► Extremophiles 

► Hot Spring Microbiology 

► Hot Vent Microbiology 

► Hydrothermal Environments 

► Iron Cycle 

► Microorganism 

► Oxidation 

► Prokaryote 

► Proteobacteria 

► Pyrite 

► Rio Tinto 

► Sulfur Cycle 

► Yellowstone National Park, Natural Analogue 
Site 

References and Further Reading 

Amaral Zettler LA, Gomez F, Zettler E, Keenan BG, 
Amils R, Sogin ML (2002) Microbiology: eukaryotic 
diversity in Spain’s River of Fire. Nature 417:137. 
doi: 10.1038/417137a 

Botuyan MV, Toy-Palmer A, Chung J, Blake RC 2nd, 
Beroza P, Case DA, Dyson HJ (1996) NMR solution 
structure of Cu(I) rusticyanin from Thiobacillus 
ferrooxidans: structural basis for the extreme acid sta¬ 
bility and redox potential. J Mol Biol 263(5):752-767. 
doi: 10.1006/jmbi. 1996.0613. PMID 8947573 

Gomez F, Amils R, Marin I (1997) Microbial ecology 
studies for the desulfurization of Spanish coals. Fuel 
Process Technol 52(1-3): 183-189 

Kelch BA, Eagen KP, Erciyas FP, Humphris EL, 
Thomason AR, Mitsuiki S, Agard DA (2007) Struc¬ 
tural and mechanistic exploration of acid resistance: 
kinetic stability facilitates evolution of extremophilic 
behavior. J Mol Biol 368(3):870-883. doi: 10.1016/j. 
jmb.2007.02.032. PMID 17382344 

Lopez-Archilla AI, Marin I, Amils R (2001) Microbial 
community composition and ecology of an acidic 
aquatic environment: the Tinto River. Spain Microb 
Ecol 41:20-35. doi:10.1007/s002480000044 

Madigan M, Martinko J (eds) (2005) Brock biology of 
microorganisms, 11th edn. Prentice Hall, Upper Sad¬ 
dle River. ISBN 0-13-144329-1 

Mohapatra S, Bohidar S, Pradhan N, Kar RN, Sukla LB 
(2007) Microbial extraction of nickel from Sukinda 
chromite overburden by Acidithiobacillus 
ferrooxidans and Aspergillus strains. Hydrometallurgy 
85:1-8 


Acritarch 

Emmanuelle J. Javaux 
Palaeobiogeology-Palaeobotany- 
Palaeopalynology, Geology Department, 
Universite de Liege, Liege, Belgium 

Keywords 

Organic-walled microfossils 

Definition 

An acritarch is a microscopic organic-walled hol¬ 
low vesicle with an unknown biological affinity. 
The term comes from two Greek words: “acritos” 
(unknown) and “arche” (origin). Acritarchs are 
found in marine sediments from most of the geo¬ 
logical timescale, from the Archean to the pre¬ 
sent, but were more abundant and diversified in 
the Proterozoic and the Paleozoic. Their diversity 
decreased in the Mesozoic. 

Overview 

The term “acritarch” was coined by Evitt (1963) 
to define any organic-walled ► microfossils that 
cannot be assigned to a known biological group. 
The acritarchs form a polyphyletic artificial 
group that may represent many different types 
of organisms, from bacteria to unicellular 
(protists) or multicellular eukaryotes (e.g., 
fungi, algae, animal eggs). Their size ranges 
from a few microns to a few millimeters, 
although most are microscopic. They are classed 
into several artificial morphogroups based on the 
morphology and presence and type of ornamen¬ 
tation of the vesicle. Filamentous organic-walled 
microfossils of unknown biological affinities are 
not included among acritarchs. In the Paleozoic, 
most acritarchs are assumed to represent cysts of 
marine planktonic algae (phytoplankton). 
Acritarchs are very useful to date and correlate 
marine sedimentary rocks (biostratigraphy), 




Activated Nucleotide 


41 



Acritarch, Fig. 1 Two acritarchs from the 
Mesoproterozoic (1.65 Ga Ruyang Group, China). Left, a 
spiny acritarch (acanthomorph); right, a smooth-walled 
acritarch (sphaeromorph) (Photograph: E Javaux) 

especially in the late Proterozoic and the Paleo¬ 
zoic, to reconstruct paleoenvironments, and to 
assess the thermal maturity of the organic matter 
(paleothermometer) and their potential as a source 
of hydrocarbon. Moreover, the detailed study of 
acritarch morphology, wall ultrastructure, and 
microchemistry gives precious information on the 
early evolution of eukaryotes in the Precambrian. 

The oldest acritarchs known so far have 
smooth walls (sphaeromorphs) and are preserved 
in 3.2 Ga fine-grained detritic rocks deposited in 
tidal shallow marine waters (Mesoarchean). The 
oldest ornamented acritarchs (with concentric 
striations) are 1.9 Ga and interpreted as probable 
eukaryotes. The oldest spiny acritarchs 
(acanthomorphs) are unambiguously eukaryotic 
and 1.65 Ga. Acritarchs can be preserved as flat¬ 
tened vesicles in fine-grained detritic sediments 
(shales, siltstones) or in three dimensions by 
permineralization (partial or complete replace¬ 
ment by minerals) in cherts or phosphorites. 
They are studied in thin sections or extracted 
from the rock by ► acid maceration, depending 
on their state of preservation (Fig. 1). 

See Also 

► Acid Maceration 

► Eukaryotes, Appearance and Early 
Evolution of 


► Fossilization, Process of 

► Microfossils 

► Proterozoic Eon 

References and Further Reading 

Butterfield NJ, Knoll AH, Swett N (1994) Paleobiology of 
the Neoproterozoic Svanbergfjellet formation Spits¬ 
bergen. Fossils Strata 34:1-84 

Evitt WR (1963) A discussion and proposals concerning 
fossil dinoflagellates, hystrichospheres and acritarchs. 
Proc Natl Acad Sci U S A 49:158-164 

Grey K, Willman S (2009) Taphonomy of Ediacaran 
acritarchs from Australia: significance for taxonomy 
and bio stratigraphy. Palaios 24:239-256 

Javaux EJ, Knoll AH, Walter MR (2001) Morphological 
and ecological complexity in early eukaryotic ecosys¬ 
tems. Nature 412:66-69 

Javaux EJ, Marshall CP, Bekker A (2010) Organic-walled 
microfossils in 3.2-billion-year-old shallow-marine 
siliciclastic deposits. Nature 463:934-938 

Knoll AH, Javaux EJ, Hewitt D, Cohen P (2006) Eukary¬ 
otic organisms in Proterozoic oceans. Phil Trans R Soc 
B 36:1023-1038 

Servais T (1996) Some considerations on acritarch classi¬ 
fication. Rev Palaeobot Palynol 93:9-22 

Strother PK (1996) Acritarchs. In: Jansonius J, McGregor 
DC (eds) Palynology: principles and applications, 
vol 1. American Association of Stratigraphic Palynol- 
ogists Foundation, Tulsa, pp 81-106 


Acrylonitrile 

► Vinyl Cyanide 


Activated Nucleotide 

Kunio Kawamura 

Department of Human Environmental Studies, 
Hiroshima Shudo University, Hiroshima, Japan 

Keywords 

Chemical evolution; Nucleotide; Oligonucleo¬ 
tide; RNA 






42 


Activated Nucleotide 


Synonyms 

Nucleoside 5'-monophosphorimidazolide 

Definition 

An activated nucleotide is a nucleoside 
5'-monophosphate possessing a leaving group, 
such as imidazole, which provides sufficient energy 
to form higher oligonucleotides. The activation of 
nucleoside 5'-monophosphates by N-P bond forma¬ 
tion between the phosphate group and a base (such 
as an amino acid or an imidazole) seems to be 
essential for the abiotic formation of RNA oligo¬ 
mers. In contrast, DNA oligomers are less readily 
formed from activated deoxynucleotides. 

Overview 

The synthesis of ► RNA molecules may have 
been an essential step for the emergence of life¬ 
like systems on the primitive Earth. In modern 
organisms, polymerization of RNA monomers 
only proceeds because thermodynamics and 
kinetics allow for biochemical polymerization 
in organisms. In modem biology, nucleoside 
5'-triphosphate monomers are used to form 
RNA polymers. This is thermodynamically 
favorable, since nucleoside 5'-triphosphates pos¬ 
sess high-energy phosphate groups. These by 
themselves are rather kinetically slow to react in 
solution; however, their polymerization becomes 
kinetically favorable due to the involvement of 
biological catalysts, RNA polymerases. In addi¬ 
tion, biological nucleotide polymerization is usu¬ 
ally conducted on a DNA template; in the 
absence of an RNA polymerase or a template, 
the polymerization of 5'-triphosphate does not 
proceed. 

RNA polymers are also formed in biology 
from nucleoside 5'-diphosphate in the presence 
of polynucleotide phosphorylase without a DNA 
template. This is an exception, although this does 
show that the polymerization of nucleoside 
5'-diphosphates is also thermodynamically 
possible. 


As mentioned above, the polymerization of 
nucleotide 5'-triphosphates does not proceed in 
the absence of an enzyme and a polynucleotide 
template. Since enzymes are fairly complicated 
biological catalysts, and since the first nucleic 
acids must have predated the first nucleic acid 
templates, primitive pathways to form RNA 
polymers without an enzyme and a template mol¬ 
ecule have been investigated under simulated 
Earth conditions. The activation of nucleoside 
5'-monophosphates is essential thermodynami¬ 
cally, since the nucleoside 5'-monophosphate 
does not possess sufficient energy to form 
phosphodiester bonding. These monomers also 
have the experimental benefit of reacting quite 
rapidly under laboratory conditions. Further¬ 
more, the activation should have occurred from 
plausible precursors under primitive Earth 
conditions. Investigations by Orgel and 
coworkers have shown that the nucleoside 
5'-monophosphate monomers, that is, nucleoside 
5'-monophosphoimidazolides and related com¬ 
pounds, can be considered as candidate primitive 
activated nucleotide monomers, as they can be 
formed under plausible primitive Earth condi¬ 
tions (Lohrmann and Orgel 1973; Orgel and 
Lohrmann 1974; Lohrmann 1977; Huang and 
Ferris 2006). RNA oligomers up to 50 nucleotide 
units can be formed from the activated nucleotide 
monomers in the presence of a metal ion catalyst, 
a clay mineral catalyst, or a polynucleotide tem¬ 
plate. In contrast, DNA oligomers do not form 
readily from the activated nucleotides. 

See Also 

► Nucleoside 

► Nucleoside Phosphoimidazolide 

► Oligonucleotide 

► RNA 

► RNA World 

References and Further Reading 

Huang W, Ferris JP (2006) One-step, regioselective syn¬ 
thesis of up to 50-mers of RNA oligomers by mont- 
morillonite catalysis. J Am Chem Soc 128:8914-8919 



Active Asteroid 


43 


Lohrmann R (1977) Formation of nucleoside S'-phosphor- 
amidates under potentially prebiological conditions. 
J Mol Evol 10:137-154 

Lohrmann R, Orgel LE (1973) Prebiotic activation 
processes. Nature 244:418-420 
Orgel LE, Lohrmann R (1974) Prebiotic chemistry and 
nucleic acid replication. Acc Chem Res 7:368-377 


Activation Energy 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Synonyms 

E a 

Definition 

In chemical kinetics, the activation energy 
(abbreviated E a ) is the energy barrier which 
must be overcome for a sufficient number of 
reactant molecules to acquire enough kinetic 
energy for a reaction to occur appreciably. The 
activation energy can generally be achieved by 
supplying energy, for example, in the form of 
heat, to the system or through the intervention 
of a catalyst. The Arrhenius equation gives the 
temperature dependence of the rate constant k : E a 
is obtained from the slope of a plot of In k versus 
1/r, where T is the absolute temperature in Kel¬ 
vin. The activation energy is usually measured in 
kJ/mol. 

E a is related to the rate ( k ) via the equation 
E a = —RT ln(k/A) 


where A is a constant called the frequency or 
pre-exponential factor, usually given in units of 
s" 1 , and R is the universal gas constant. 

See Also 

► Arrhenius Plot 


Active Asteroid 

Gerhard Hahn 

Asteroids and Comets, DLR, Institute of 
Planetary Research, Berlin, Germany 

Synonyms 

Dual status objects; Mainbelt comet 

Definition 

Objects in typical asteroidal orbits, e.g., located 
in the main asteroid belt, showing typical come¬ 
tary activity, such as tails or comae, either tem¬ 
porarily or sporadically. The possible origin of 
this “cometary” activity may either be intrinsi¬ 
cally comet-like, e.g., outgassing, or triggered 
externally, e.g., by impact events, collisions, 
etc. Such objects are not confined to the asteroid 
belt, but exist also in the NEO population, and 
among Centaurs. A comprehensive recent review 
can be found in Jewitt (2012). 


History 

The first observation of such an object was the 
Centaur asteroid (2060) Chiron = 95P, which 
was found in 1988-1989 to show unusual bright¬ 
ening that could be related to comet-like activity 
exhibiting a coma. A member of the NEO 
group that was observed as both an asteroid and 
as a comet is (4015) Wilson-Harrington = 107P. 





44 


Active Site 


Mainbelt asteroid (7968) Elst-Pizarro = 133P 
shows repeated activity, most likely caused by 
sublimation of water ice. 

Most recent related finding is the detection of 
water vapor on dwarf planet Ceres = asteroid 
(1) Ceres. 

See Also 

► Asteroid Belt, Main 

► Centaurs (Asteroids) 

► Comets, History of 

► Near-Earth Objects 


References and Further Readings 

Jewitt D (2012) The active asteroids. Astron J 143:66 
(14 pp) 

Kiippers M, O’Rourke L, Bockelee-Morvan D, Zakharov V, 
Lee S, von Almen P, Carry B, Teyssier D, Marston A, 
Muller T, Crovisier J, Barucci MA, Moreno R (2014) 
Localized sources of water vapour on the dwarf planet 
(1) Ceres. Nature 505:525-527 

List of Dual status object at the MPC: http://www. 
minorplanetcenter.net/iau/lists/DualStatus.html. Last 
accessed 5 May 2014 


Active Site 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 


Definition 

In catalysis, an active site is the specific location 
on the surface of a catalyst where reactions take 


place. For example, in surface chemistry, this 
could be a specific set of surface sites, and in 
biochemistry, it is a particular surface or cleft of 
a protein ► enzyme or ► ribozyme surface where 
catalysis occurs. In protein enzymes, the active 
site is generally a pocket or cleft with specific 
amino acid side chains presented in particular 
orientations that bind a ► substrate and facilitate 
catalysis. Cofactors facilitating catalysis may 
also be bound in the active site. 


See Also 

► Catalyst 

► Cofactor 

► Enzyme 

► Ribozyme 

► Substrate 


Activity 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Definition 

In chemistry, the activity of a species is a measure 
of its effective concentration, as distinct from its 
concentration. This is by convention usually 
presented as a unitless value. Activity can be 
affected by factors such as pressure, temperature, 
and the presence of other solutes. The difference 
in value between concentration and activity is due 
to the fact that molecules in solution often display 





Activity, Magnetic 


45 


nonideal behavior due to molecular interactions. 
In the gas phase, activity is called fugacity. 

See Also 

► Oxygen Fugacity 


Activity, Magnetic 

Thierry Montmerle 

Institut d’Astrophysique de Paris, CNRS/ 
Universite Paris 6, Paris, France 

Keywords 

Chromosphere; Corona; Doppler-Zeeman imag¬ 
ing; Dynamo effect; Flares; Magnetic fields; UV 
radiation; X-rays 

Synonyms 

Variability (magnetic) 


Definition 

Magnetic activity is a characteristic of low-mass 
stars, with the Sun as a prototype. Its most spec¬ 
tacular observational manifestation is in the form 
of stellar flares that can be seen in the optical, UV, 
and X-ray domains. These flares correspond to 
the release of magnetic energy itself temporarily 
built up as a result of movements of the outer 
layers of these stars, which are convective 
(“dynamo” effect). During flares, the stellar lumi¬ 
nosity is enhanced by a factor which depends on 
the energy domain, but which is maximum in 
X-rays (amplification by a factor of up to 10 or 
more). The whole phenomenon typically lasts a 
few hours and may be described by a rapid 
heating phase (minutes to tens of minutes), 
followed by a long cooling phase (a few hours). 


History 

The Sun is the first known celestial X-ray source. 
It was discovered by rocket observations in 1949 
by a group of physicists in New Mexico, USA 
(Friedmann et al. 1951). Since EUV photons and 
X-rays cannot penetrate the Earth’s atmosphere, 
studies continued using high-altitude balloons 
and finally satellites (14 launched in the world 
between 1957 and 2006). The first solar X-ray 
images were obtained on the Sky lab space station 
(1973-1979), establishing the link between 
X-rays and ► magnetic fields. The Sun is now 
continuously monitored by satellites on various 
orbits, some of which are heliosynchronous, like 
the recently launched NASA’s Solar Dynamics 
Explorer. Following the progress in solar X-ray 
imaging, the X-ray emission from individual 
stars was discovered by the Einstein satellite 
(1978-1981), already showing “solar-type activ¬ 
ity” (flares), hence magnetic in origin. X-ray sat¬ 
ellites currently in operation (NASA’s Chandra 
and ESA’s XMM-Newton) have detected hun¬ 
dreds of thousands of stars with evidence for 
magnetic activity. 

Overview 
Solar Activity 

The prototype of a “magnetically active star” is 
the Sun, for which high-resolution images show, 
at all wavelengths, numerous localized “active 
regions” (the largest ones seen as sunspots in 
the visible domain). The solar magnetic activity 
is best seen at “hot” temperatures (10 5 -10 7 K), 
i.e., in the EUV and X-ray domains. The 
corresponding regions of the Sun’s atmosphere 
are, respectively, called the “chromosphere” and 
the “corona.” Magnetic activity is also seen in the 
visible domain, which corresponds to the “pho¬ 
tosphere” (the surface of the Sun as we see it with 
the naked eye). A closer view shows that the solar 
surface is constantly in motion: this is due to the 
phenomenon of convection , which is the result of 
energy transport from the interior of the Sun. 
Figure 1 shows the optically visible Sun in its 
ultraquiet epoch of Spring 2009, and Fig. 2 




46 


Activity, Magnetic 



Activity, Magnetic, Fig. 1 The Sun in visible light, 
during its ultraquiet period of Spring 2009. Note the two 
minuscule black “spots”: they are the silhouettes of the 
Space Shuttle servicing the International Space Station 
(Photograph NASA/T. Legaut) 



Activity, Magnetic, Fig. 3 The Sun in X-rays, as seen 
by the Japanese Hinode satellite. Active regions are again 
tightly linked with magnetic loops. Here the brightest 
regions reach a temperature of several ~10 7 K (JAXA) 



Activity, Magnetic, Fig. 2 The Sun in visible/EUV 
light, having regained its activity in early 2010. The hot 
gas is confined by closed magnetic loops in many places, 
in particular here at the upper left sector of the limb (color 
coded: bright regions are the hottest, ~10 6 K). There are 
also open magnetic field structures, which let the hot gas 
escape in the form of the solar wind (Solar Dynamics 
Observatory, NASA) 


shows for comparison the optical/EUV Sun, 
which regained activity a few months later. 
These structures evolve with time: on long-time 
scales such as days, weeks (star spots, promi¬ 
nences), but more spectacularly on timescales of 
hours (flares, such as the one seen on the solar 
limb of Fig. 2). Solar flares reveal material being 
heated in a few tens of minutes and confined by 
large magnetic loops; subsequently, the material 
cools, decays, and eventually flows back to the 
photosphere after a few hours. The magnetic field 
is created via the so-called dynamo effect, 
resulting from the macroscopic movement of 
electrically charged convective gas. As shown 
in Fig. 3, the contrast between “active” regions 
and “quiet” regions is stronger at X-ray energies. 
This turns out to be a crucial factor for studying 
stellar magnetic activity. 

Stellar Magnetic Activity 

The so-called stellar magnetic activity is a char¬ 
acteristic of all “solar-type stars” (by extension 
from the Sun: relatively cool stars with tempera¬ 
tures between 3,000 and 10,000 K and masses 
between ~0.1 M© (1M0 = 1 solar mass) and 
~2 MQ; for comparison, the surface temperature 








Activity, Magnetic 


47 


of the Sun is ^6,000 K). These stars have con¬ 
vective outer layers and generate their own mag¬ 
netic field by the dynamo effect like the Sun. The 
crucial observational difference between these 
stars and the Sun is that they cannot be resolved; 
in other words, they appear as points in any imag¬ 
ing device. However, one can reconstitute to 
some degree the stellar surfaces by using their 
rotation , which modulates the signal: since active 
regions (such as spots) are cooler, hence darker 
than the surrounding surface, their emission is 
Doppler shifted when the spots appear to move 
toward, then away from, the observer, as the star 
rotates. In favorable cases, it is possible to go one 
step further, by using the Zeeman effect. This is a 
physical phenomenon in which, under the influ¬ 
ence of magnetic fields, specific spectral lines are 
slightly split into three components, sensitive to 
polarization, and which are also Doppler shifted 
as a result of stellar rotation. Using sophisticated 
deconvolution methods, one can then reconstruct 
not only the location and size of active regions 
but also the topology of their associated magnetic 
fields. Figure 4 shows such a reconstruction in the 
case of a young solar-type star. 



Activity, Magnetic, Fig. 4 Image reconstruction of the 
active regions and magnetic field topology of the young 
star SU Aur, observed via Zeeman-Doppler imaging 
(At Wikipedia: P. Petit, Observatoire Midi-Pyrenees) 


A broader view of stellar magnetic activity is 
provided by X-rays. In particular, the generally 
large field of view of X-ray telescopes allows the 
simultaneous study of all the stars present in the 
field, especially if they belong to a cluster. This is 
the case for young, pre-main sequence stars 
(“► T Tauri” stars): as shown as an example in 
Fig. 5, over 2,000 stars can be observed simulta¬ 
neously in the Orion star formation region 
(associated with its famous nebula M42). Long 
duration observations (several days) reveal the 
occurrence of ubiquitous X-ray flares, most very 
similar to solar flares, and a few being of much 
longer duration and extreme temperatures (up to 
10 8 K). 

Basic Methodology 

Solar and stellar magnetic activities are observed 
primarily from space. The latest solar satellite, 
NASA’s SDO ( Solar Dynamics Observatory ), 
launched in 11 February 2010, transmits high- 
resolution full-disk optical/EUV images at the 
unprecedented rate of 1 image per second 
(Fig. 2). Meanwhile, ESA/NASA’s SOHO 
(Solar and Heliospheric Observatory ), launched 
in December 1995, continues to provide data on 
the Sun’s activity and solar wind in the same 
domain, covering to this date more than one full 
solar magnetic cycle of 11 years. The Sun is also 
imaged in X-rays (Fig. 3), in particular by a series 
of Japanese-led satellites ( Yohkoh , now Hinode 
since 2006), providing the best comparison set 
for stellar magnetic activity studies. Stars are 
observed using X-ray satellites (NASA’s 
Chandra and ESA’s XMM-Newton , both 
launched in 1999 and still in operation) that 
have both a large field of view (a fraction of a 
square degree) and high spatial resolution. In the 
case of Chandra , the spatial resolution is compa¬ 
rable with that of the best ground-based tele¬ 
scopes (0.2"), allowing astronomers to resolve 
compact stellar clusters like those found in star¬ 
forming regions. In addition to imaging, X-ray 
satellites also have spectral capabilities, allowing 
measurement of densities, temperatures, and 
composition of the X-ray emitting plasma, and 




48 


Activity, Magnetic 



Activity, Magnetic, Fig. 5 The Orion Nebula seen in 
X-rays. Left : near-IR image of the Orion Nebula cluster, 
which contains ~2,000 stars (ESO/VLT/ISAAC). Right'. 
X-ray image of the same cluster, obtained with the 
Chandra satellite (NASA). An excellent, one-to-one 

their dependence with time (for instance, flares 
and associated coronal emission). 

Key Research Findings 

The vast majority of “solar-like stars” show evi¬ 
dence for magnetic activity, and observations 
show that X-rays are an excellent proxy to com¬ 
pare with solar magnetic activity. However, the 
level of activity is very different depending on 
stellar type. This level is generally measured by 
the ratio of the energy output in X-rays (the X-ray 
luminosity L x ) to the total energy output (the 
bolometric luminosity L bo j). For the Sun, L x / 
L b oi ~1(T 7 , with a variable amplitude of a factor 
~10 over magnetic cycles. In contrast, fully con¬ 
vective stars, like “emission-line” stars, late-type 
cool stars, and very young T Tauri stars, have L x / 
L bo i reaching ^10 -3 . This limiting factor is due to 
“saturation,” i.e., when active regions 
cover essentially all the stellar surface, as 
opposed to 5 % for the Sun. For the youngest 
► T Tauri stars (ages less than a few million 
years), the magnetic activity is altered by another 


correspondence holds between the stars visible on the 
left and the point X-ray sources visible on the right. 
A long exposure of this region shows ubiquitous flares 
from all the low-mass stars (From Montmerle et al. 2006) 

phenomenon, which is the accretion of material 
from a circumstellar, protoplanetary disk, along 
large-scale magnetic field lines connecting the 
star and the disk. This phenomenon is seen as 
“soft” X-ray (<1 keV) emission due to a shock 
when the accreted material falls onto the stellar 
surface, superimposed on the “hard” (>1 keV) 
coronal emission. 


Applications 

For present-day human environment, the solar 
magnetic activity is strongly related to the notion 
of “space weather,” i.e., the interaction of the 
solar wind with the Earth’s magnetic field. For 
astrobiology, X-rays from the young Sun (and 
from young stars in general) may have had an 
important influence, via ionization of atoms and 
molecules, on early planetary atmospheres. More 
generally, the study of solar and stellar magnetic 
activity is related to fundamental plasma physics: 
low-density plasmas in the corona and (in the 
case of young stars) interaction with a circum¬ 
stellar disk and high-density plasmas in motion, 





Adaptation 


49 


leading to the generation of magnetic fields in 
outer convective zones (dynamo effect). Theoret¬ 
ical developments are now based on sophisticated 
numerical 3D simulations. 

Future Directions 

From an astronomical point of view, the similar¬ 
ities between solar and stellar magnetic activity 
allow two different approaches to the same prob¬ 
lem, i.e., the origin of stellar magnetic fields: 

(1) considering the “Sun as a star,” where prox¬ 
imity allows detailed, localized studies, and 

(2) considering “stars as Suns,” allowing statisti¬ 
cal approaches on magnetic activity properties as 
a function of ► spectral type (mass, age, evolu¬ 
tionary status) for thousands of stars, in particular 
for young stars at the stage of planet formation. 

See Also 

► Faint Young Sun Paradox 

► Magnetic Field 

► Sun (and Young Sun) 

► X-Rays (Stellar) 

References and Further Reading 

Charles P, Seward FD (2010) Exploring the x-ray uni¬ 
verse. Cambridge University Press, Cambridge 
Feigelson ED, Montmerle T (1999) High-energy pro¬ 
cesses in young stellar objects. Annu Rev Astron 
Astrophys 37:363 

Friedmann H, Lichtman S, Byram E (1951) Photon coun¬ 
ter measurements of solar x-rays and extreme ultravi¬ 
olet light. Phys Rev 83:1025 

Giidel M (2007) The sun in time: activity and environ¬ 
ment. Living Rev Sol Phys 4(3): 1-137, http:// 
solarphysics.livingreviews.org/Articles/lrsp-2007-3/ 
Giidel M, Naze Y (2009) X-ray spectroscopy of stars. 

Astron Astrophys Rev 17:309 
Lanza AF (2009) Stellar coronal magnetic fields and star- 
planet interaction. Astron Astrophys 505:339 
Montmerle T et al (2006) From suns to life: a chronolog¬ 
ical approach to the history of life on earth 3 solar 
system formation and early evolution: the first 100 mil¬ 
lion years. Earth Moon Planet 98:39-95 


Adaptation 

Susanna Manrubia 

Systems Biology Program, Centro Nacional de 
Biotecnologia (CSIC), Madrid, Spain 

Keywords 

Ecosystem; Environmental change; Genetic 
change; Mutation; Phenotype; Selection 

Definition 

Adaptation is a dynamical process whereby 
populations become better suited to their habitat. It 
is promoted by ► environmental changes, be they 
abiotic (e.g., climatic change) or biotic (e.g., the 
appearance of a new trait in a predator or the extinc¬ 
tion of a competitor ► species). Adaptation is the 
outcome of ► natural selection acting on heritable 
variation and leading to a change in the genetic 
makeup of a population. It may involve changes in 
any ► phenotypic trait, among others, in morphol¬ 
ogy, physiology, dispersal, defense and attack mech¬ 
anisms, development and growth, reproduction, 
behavioral patterns, and ecological interactions. 

Overview 

Adaptation has been an ongoing process ever 
since the emergence of the first self-replicating 
molecules. Populations of replicating entities 
generate continuous variability chiefly due to 
► mutations and (in the case of organisms) to 
the migration of ► genes and other mobile geno¬ 
mic sequences. Adaptation is a gradual process 
that occurs over many generations as the off¬ 
spring (i.e., the genes) of individuals best suited 
to the current habitat become increasingly abun¬ 
dant. Under environmental changes, species can 
react in three different ways. In case of slow 
change, they (1) perform habitat tracking if the 




50 


Adaptive Optics 


change is exogenous (i.e., the population shifts 
with the ► environment to maintain the charac¬ 
teristics of its habitat) or (2) undergo genetic 
change. Only in the latter case are they truly 
adapting. If changes are too sudden, species can¬ 
not adapt and (3) become extinct. Even if the 
abiotic environment remains constant, the steady 
generation of mutants within a population com¬ 
pels related species to change. The appearance of 
teeth and claws in predators forces a simulta¬ 
neous improvement in defense organs 
(as skeletons) to escape extinction. This sustained 
competition is called the Red Queen effect (Van 
Valen 1973; Stenseth and Maynard Smith 1984). 

Many adaptive changes in the history of life are 
gradual and involve a significant number of sequen¬ 
tial modifications, as the evolution of tetrapod limbs 
from the fins of precursor fish. Some changes (the 
invention of lungs, of vascular systems in terrestrial 
plants, or of organs for flight) permitted organisms 
to colonize new ecological niches (Gould 1993). 
Certain major transitions in evolution (Maynard 
Smith and Szathmary 1995) are probably not the 
result of adaptation, but of contingency. Such might 
be the case for the appearance of eukaryotic cells or 
of multicellular organisms. 

Since natural selection acts on the phenotype 
as a whole, it is impossible to simultaneously 
improve all its traits in the same degree (Mayr 
1982). Also, traits that were once the result of 
adaptation may turn to be disadvantageous when 
the habitat changes. Hereditary hemochromatosis 
causes an excessive absorption of iron that accumu¬ 
lates in human body tissues. This disease is more 
common among Europeans: it protects against bac¬ 
terial infections and probably became frequent at 
the time of the Black Death (Moalem and Prince 
2006). This is an example of the many currently 
nonadaptive traits that were permitted to thrive at 
some point of time in the history of a species. 

See Also 

► Colonization, Biological 

► Environment 

► Evolution, Biological 

► Evolution, Molecular 


► Gene 

► Mutation 

► Natural Selection 

► Phenotype 

► Species 

References and Further Reading 

Gould SJ (ed) (1993) The book of life: an illustrated 
history of the evolution of life on Earth. WW Norton, 
New York 

Maynard Smith J, Szathmary E (1995) The major transi¬ 
tions in evolution. Oxford University Press, New York 

Mayr E (1982) The growth of biological thought: diver¬ 
sity, evolution and inheritance. Belknap Press of Har¬ 
vard University Press, Cambridge 

Moalem S, Prince J (2006) Survival of the sickest. Harper 
Collins, New York 

Rose MR, Lauder GV (eds) (1996) Adaptation. Academic, 
San Diego 

Stenseth NC, Maynard Smith J (1984) Coevolution in 
ecosystems: red queen evolution or stasis? Evolution 
38:870-880 

Van Valen L (1973) A new evolutionary law. Evol Ther 
1:1-30 


Adaptive Optics 

Daniel Rouan 

LESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 

Definition 

Adaptive optics is a technique, used while 
performing visible or infrared imaging from a 
ground-based telescope, that improves the 
image quality that is otherwise degraded by the 
atmospheric turbulence. The wave-front distor¬ 
tions, measured on the studied object or a nearby 
star, are compensated by deforming a small, thin 
mirror at a speed higher than turbulence (1 kHz 
typically) (Fig. 1). The deformable mirror is con¬ 
jugated to the pupil of the telescope. The use of 
this technique is mandatory in any method, such 
as coronagraphy, that aims at a direct imaging of 
exoplanets. Adaptive optics should not be con¬ 
fused with active optics that corrects the large 




Adenosine Triphosphate 


51 


Light from 



Adaptive Optics, Fig. 1 Cartoon describing the princi¬ 
ple of adaptive optics: the wave front deformed by atmo¬ 
spheric turbulence is corrected thanks to a deformable 
mirror that produces an inverse deformation several hun¬ 
dred times per second, after a device called a wave-front 
sensor has measured the residual distortion. A real-time 
computer is used to analyze the residuals and to define the 
proper surface to give to the mirror. The final improved 
image is obtained on a camera 

primary telescope mirror deformed under grav¬ 
ity, and which is applied at a much lower fre¬ 
quency (0.1 Hz). 

See Also 

► Coronagraphy 

► Imaging 

► Telescope 


Adenine 

Shin Miyakawa 

Ribomic Inc., Minato-ku, Tokyo, Japan 

Definition 

Adenine (C 5 H 5 N 5 ), with molecular weight 
135.13, is one of the four nucleic acid bases 


found in ► DNA and ► RNA. Via Watson- 
Crick base pairing in double-stranded ► DNA 
and ► RNA, adenine forms two hydrogen bonds 
with ► thymine (T) and ► uracil (U), respec¬ 
tively. It is hydrolyzed to give ► hypoxanthine. 
The half-life to hydrolysis in aqueous solution at 
pH 7 is 1 year at 100 °C and 6 x 10 5 years at 
0 °C. It has a UV absorption maximum at 260 nm. 
It has been found in the ► Murchison meteorite 
and can be synthesized in HCN polymerizations, 
► Fischer-Tropsch-type reaction, and electric 
discharges acting on gas mixtures such as NH 3 - 
CH 4 -C 2 H 6 -H 2 0. 


See Also 

► DNA 

► Fischer-Tropsch-Type Reaction 

► HCN Polymer 

► Hydrogen Cyanide 

► Hypoxanthine 

► Meteorite, Murchison 

► Nucleic Acid Base 

► RNA 

► Thymine (T) 

► Uracil (Ura) 


Adenosine S'-Triphosphatase 

► ATPase 


Adenosine Triphosphatase 

► ATPase 


Adenosine Triphosphate 

► ATP 













52 


Adiabatic Processes 


Adiabatic Processes 

Lisa Kaltenegger 

Cornell University, Ithaca, NY, USA 


Definition 

A process affecting a parcel of matter is said to 
be adiabatic if it occurs without addition or 
loss of heat from the parcel. No exchange of 
heat means that temperature changes in the 
parcel must be due to changes in pressure 
alone. In planetary atmospheres, the adiabatic 
lapse rate is the change in air temperature 
with changing height, resulting from 
pressure change. The so-called dry adiabatic 
lapse rate has the slope d(ln T)/d(ln p) = R/c p , 
where T is temperature, p is pressure, R is the 
specific gas constant (which depends on the mean 
molecular weight of the mixture), and c p is the 
specific heat at constant pressure. For 
Earth’s atmosphere, the value R/c p corresponds 
to about 2/7. Adiabatic processes are called 
isentropic, i.e., they leave entropy unchanged, 
provided that the changes in state of the 
system are slow enough that the system 
remains close to thermodynamic equilibrium at 
all times. 


See Also 

► Atmosphere, Model ID 

► Atmosphere, Structure 

► Atmosphere, Temperature Inversion 

► Exoplanets, Modeling Giant Planets’ 
Atmospheres 

► Grey Gas Model 

► Non-Grey Gas Model: Real Gas 
Atmospheres 


Adsorption 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 

Definition 

Adsorption is the accumulation of molecules 
from the gas phase, or more generally from any 
fluid (adsorption operates in liquids as well as 
gases), onto a solid surface, e.g., of an ► inter¬ 
stellar dust grain. The molecules may be bound 
by physical (van der Waals), electrostatic, or 
chemical (e.g., hydrogen bonding) forces. 

See Also 

► Interstellar Dust 


AEB 

Michel Viso 

CNES/DSP/SME, Veterinaire/DVM, Astro/ 
Exobiology, Paris Cedex 1, France 

Synonyms 

Agenda Espacial Brasileira; Brazilian space 
agency 

Definition 

Numerous committees since 1961 have been 
charged with space activities in Brazil. In Febru¬ 
ary 1994, the Brazilian Space Agency was 
established within the Department of Science 






Aerobic Mesophilic Bacterial Spores 


53 


and Technology. The agency is partnering with 
four institutes in charge of specific missions: the 
National Institute for Space Research (INPE) in 
charge of developing satellites and products for 
civilian use, the Institute of Aeronautics and 
Space in charge of developing planes and the 
launch vehicles, and two launching bases in 
Alcantara and Barriera do Inferno. The space 
agency is developing numerous cooperation 
with Europe, Japan, China and the United States. 

For further information: http://www.aeb.gov.br/ 


Aerobe 

Felipe Gomez 

Centro de Astrobiologia (CSIC/INTA), Instituto 
Nacional de Tecnica Aeroespacial, Torrejon de 
Ardoz, Madrid, Spain 


Definition 

Aerobes are organisms that can tolerate or require 
the presence of (strict aerobe in this case) oxygen. 
Oxygen is an extremely strong oxidant and 
produces very reactive radicals, which react 
with amino acids or nucleic acids inactivating the 
functional sites of enzymes or producing 
lethal mutations. Practically, all animals are 
aerobes; most fungi and many prokaryotes 
can survive in the presence of oxygen. To do so, 
aerobic organisms require the presence of 
detoxification activities, like catalases and peroxi¬ 
dases. Among aerobes there are different kinds of 
organisms: obligate aerobes, which require oxy¬ 
gen for growth and use oxygen as final ► electron 
acceptor in the ► respiration process; facultative 
aerobes, which can use oxygen or not, to obtain 
energy; microaerophiles, which require low levels 
of oxygen; and aerotolerants, which are not 
affected by the presence of oxygen. 


See Also 

► Aerobic Respiration 

► DNA Damage 

► Electron Acceptor 

► Respiration 


Aerobic Mesophilic Bacterial Spores 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 

Definition 

“Spores” or more precisely “bacterial endo- 
spores” are resistant dormant bodies produced 
by some ► microorganisms (Gram-positive bac¬ 
teria) upon exposure to stressful environmental 
conditions. Aerobic microorganisms grow while 
exposed to oxygen, while mesophilic microor¬ 
ganisms grow on nutrient-rich media at tempera¬ 
tures comfortable for humans (roughly between 
15 °C and 40 °C). Spores are capable of surviving 
extreme environmental conditions in a dormant 
state and proliferating when introduced into a 
hospitable environment. This particular type of 
spores is commonly used in ► planetary protec¬ 
tion as reference microorganisms for the qualifi¬ 
cation of ► bioburden reduction processes. 
Numbering the spores per unit of surface is also 
used as a proxy when measuring the relative clean¬ 
liness of spacecraft components and systems. 

See Also 

► Aerobe 

► Bacteria 

► Bioburden 

► Spore 

► Survival 





54 


Aerobic Respiration 


Aerobic Respiration 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 

Synonym 

Oxygen respiration 

Definition 

Aerobic ► respiration is a respiration in which 
dioxygen (0 2 ) serves as the terminal ► electron 
acceptor of an electron transport chain. 

See Also 

► Anaerobic Respiration 

► Electron Acceptor 

► Respiration 


Aerobiology 

Rocco Mancinelli 

Bay Area Environmental Research Institute, 
NASA Ames Research Institute, NASA Ames 
Research Center, Moffett Field, CA, USA 

Keywords 

Biology, of the atmosphere; Microorganisms, in 
the atmosphere; Pollen; Spores 

Definition 

Aerobiology is the study of the occurrence, 
movement, and dispersal of living or once-living 
material through the atmosphere. 


Overview 

The atmosphere presents a series of challenges 
for life, from radiation to ► desiccation. The 
absolute amount of solar radiation and the pro¬ 
portional contribution of ultraviolet-B and 
ultraviolet-C radiation increase with altitude, 
both of which are particularly hazardous to bio¬ 
molecules. The low temperature and pressure at 
29 km above the surface of the Earth are similar 
to those on ► Mars and create problems due to 
freezing and desiccation. Finally, the lack of 
nutrient availability in the atmosphere creates an 
additional challenge for life. 

The ► survival of airborne microbes should 
not be confused with growth and division while 
airborne. In fact, one of the critical questions that 
has yet to be answered unequivocally is, “do 
microbes metabolize and divide while airborne?” 
If they do, then the atmosphere may be consid¬ 
ered a true habitat rather than just a place where 
they are transient interlopers. 

Given the hostility of the environment, Earth’s 
atmosphere just above the surface contains a 
variety of airborne microorganisms that are 
thought to originate from the soil, lakes, oceans, 
animals, plants, as well as any process causing 

► aerosols or dust. The numbers of viable air¬ 
borne microbes recovered from the atmosphere 
vary seasonally with the highest numbers 
obtained during the summer and fall and the 
lowest in the winter. The distances that airborne 
organisms may travel range from a few kilome¬ 
ters to thousands of kilometers. There is a statis¬ 
tically significant positive correlation between 
the total number of viable ► bacteria isolated 
from urban air and the concentration of 
suspended particulate matter in the air. The 
organisms may be protected from drying by 
adsorbed water on the surfaces of these 
suspended particles. 

Studies of the biology of the upper tropo¬ 
sphere and lower stratosphere (5-20 km) date 
back to the late 1800s using balloons. But these 
studies are few in number and not well controlled. 
The organisms collected included fungi and 

► spore-forming bacteria. Later studies reported 
a larger variety of nonspore-forming microbes, 





Aerosols 


55 


especially a variety of pigmented bacteria. How¬ 
ever, the composition and prevalence of microor¬ 
ganisms in the middle to upper troposphere 
(8-15 km altitude) and their role in aerosol- 
cloud precipitation interactions are unresolved. 
Using meteorological rockets, fungi and 
pigmented bacteria have been isolated from as 
high as 77 km, the highest altitude from which 
microbes have been isolated. These studies, how¬ 
ever, all used culturing methods to determine 
microbial counts. It has been estimated that 
those methods allow studying only between 
0.1 % and 10 % of the total microbial biota in 
any given environment. Therefore, it is specu¬ 
lated that a number of microbes may exist in the 
upper atmosphere that we do not have the ability 
to culture and go unnoticed and uncounted. More 
recently, however, studies using molecular 
microbiology techniques, microscopy, and con¬ 
ventional culturing have shown that bacterial 
cells outnumber fungal cells in the upper 
troposphere. 

See Also 

► Aerosols 

► Bacteria 

► Desiccation 

► Extreme Environment 

► Mars 

► Solar UV Radiation, Biological Effects 

► Spore 

► Survival 


References and Further Reading 

DeLeon-Rodriguez N, Latham TL, Rodriguea LM, 
Barasexh JM, Anderson BE, Beyersdorf AJ, Ziemba 
LD, Bergon M, Nenes A, Konstantinidis KT 
(2013) Microbiome of the upper troposphere: species 
composition and prevalence, effects of tropical storms, 
and atmospheric implications. Proc Natl Acad Sci U S 
A 110:2575-2580 

Homeck G, Klaus D, Mancinelli RL (2010) Space micro¬ 
biology. Mol Microbiol Rev 74:121-156 

Lacey ME, West JS (2007) The air spora - a manual for 
catching and identifying airborne biological particles. 
XV. Springer, Dordrecht 


Mandrioli P, Caneva G, Sabbioni C (eds) (2003) Cultural 
heritage and aerobiology - methods and measurement 
techniques for biodeterioration monitoring. Kluwer, 
the Netherlands, 245 pp 

Aeronautics and Space Agency of 

FFG 

► ASA 


Aerosols 

Franqois Raulin 

Faculte des Sciences et Technologie, Universite 
Paris Est Creteil et Paris Diderot, LISA - UMR 
CNRS 7583, Creteil, France 

Synonyms 

Atmospheric dusts; Atmospheric particles; Haze 
particles 

Definition 

Aerosols are small liquid or solid particles in 
suspension in a gas. Solid smoke particles from 
the burning of vegetation, dust formed by wind 
erosion of soil, or liquid droplets produced by the 
ocean waves are examples of aerosols. 

Aerosols are present in many planetary envi¬ 
ronments, for example, in the atmospheres of 
Mars, the giant planets, and ► Titan, and they 
were probably present in the primitive atmo¬ 
sphere of the Earth, much as they are presently. 
Atmospheric aerosols can play an important role 
in climate, producing an antigreenhouse effect, 
like the haze in Titan’s atmosphere. Atmospheric 
photochemistry in several extraterrestrial envi¬ 
ronments, like Titan, produces organic aerosols 
which are similar to laboratory-synthesized 
► tholins, which can produce a complex set of 
prebiotic chemicals when reacted with water. 





56 


Affinity Chromatography 


See Also 

► Atmosphere, Structure 

► Carbon 

► Cassini 

► Cassini-Huygens Space Mission 

► Clouds 

► Flux, Radiative 

► Hydrocarbons 

► Jupiter 

► Methane 

► Refractory Molecule 

► Saturn 

► Tholins 

► Titan 


Affinity Chromatography 

Mark Dorr 

University of Southern Denmark, Odense M, 
Denmark 


Definition 

Affinity ► chromatography is a (bio-) chemical 
separation method based on highly specific 
molecular interactions (affinity) such as between 
antigens and antibodies, ► enzymes and ► sub¬ 
strates, or receptors and ligands. The stationary 
phase is commonly composed of beads of a gel 
(e.g., agarose gel) with a covalently bound ligand 
(e.g., an ► antibody). Affinity chromatography is 
one of the most powerful separation methods, as 
it combines the size fractionation capability of 
gel permeation chromatography with specific, 
reversible interactions of molecules. 


History 

The method was introduced by Cuatrecasas, 
Wilchek, and Anfinsen in 1968 (Cuatrecasas 
et al. 1968). Pedro Cuatrecasas and Meir Wilchek 
were jointly rewarded the Wolf Prize in Medicine 
1987 for this discovery. 


See Also 

► Antibody 

► Chromatography 

► Enzyme 

► HPLC 

► Substrate 

References and Further Reading 

Cuatrecasas P, Wilchek M, Anfinsen CB (1968) Selective 
enzyme purification by affinity chromatography. Proc 
Natl Acad Sci U S A 61:636-643. doi:10.1073/ 
pnas.61.2.636 


Affinity Constant 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, 

NJ, USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Synonyms 

Association constant; Binding constant 

Definition 

In chemistry and biochemistry, the affinity con¬ 
stant is the reciprocal of the dissociation constant, 
where both are equilibrium constants describing 
the strength of binding between a catalyst such as 
an ► enzyme or ► ribozyme and its ► substrate. 
A K m value is a specific example of an affinity 
constant in enzymatic reactions. For example, the 
equilibrium for the formation of an enzyme- 
substrate ( ES ) complex between an enzyme ( E ) 
and a substrate ( S ), 





Akilia 


57 


Ex+Sy<r+E x Sy, ( 1 ) 

can be represented as 

K = \E x S y \ 

where [E], [5], and [ES] are the concentrations of 
enzyme, substrate, and the enzyme-substrate 
complex, respectively, and v and y represent 
their stoichiometric coefficients. 

The affinity constant, also known as the 
Michaelis constant, has units of per molar 
(M -1 ) or 1/mole. Affinity constants can vary sig¬ 
nificantly with solution conditions (e.g., temper¬ 
ature, pH, and ionic strength). 

This equilibrium is also the ratio of the rate of 
association (k ass ) and rate of dissociation (£ diss ). 
Two different enzyme-substrate complexes may 
have the same affinity constants, but one could 
have a high k ass and & diss , while the other may 
have a low k ass and & diss . 

See Also 

► Enzyme 

► Ribozyme 

► Substrate 


AFGL 915, IRAS 06176-1036 

► Red Rectangle 


AGB 

► Asymptotic Giant Branch Star 


Age Measurement 

► Geochronology 


Agenda Espadal Brasileira 

► AEB 

Agentur fiir Luft- und Raumfahrt der 
FFG 

► ASA 

Agenzia Spaziale Italiana 

► ASI 


AIB 

► Aminoisobutyric Acid 


Akilia 

Minik T. Rosing 

Nordic Center for Earth’s Evolution, Natural 
History Museum of Denmark, University of 
Copenhagen, Copenhagen, Denmark 

Definition 

Akilia is the name of a small island (-2.3 km by 
1.4 km) south of the town of Nuuk on the SW 
coast of ►Greenland (63.933°N, 51.667°W). 
The Akilia sequence of rocks has its name from 
this island, but they occur throughout the 
Eoarchean of West Greenland. The Akilia 
sequence consists mainly of granitic gneiss and 
includes some of the oldest rocks on Earth. The 
largest member of this group of rocks is the 
ca. 3.8 Ga-old ► Isua supracrustal belt composed 
of metamorphosed pillow basalts, clastic, and 
chemical sediments that constitute the oldest 
known supracrustal sequence. Fractionated C, 
N, and S isotopic compositions of materials of 












58 


Al-Andalus, Cosmological Ideas 


probable sedimentary origin are thought to be 
biogenic and to provide the oldest record of life 
on Earth. 


See Also 

► Earth, Formation and Early Evolution 

► Greenland 

► Isua Supracrustal Belt 


Al-Andalus, Cosmological Ideas 

Ahmed Ragab 

Harvard Divinity School, Cambridge, MA, USA 

Keywords 

Islam; Islamic astronomy; Andalus; Iberia; Medi¬ 
eval; Ibn Tufayl; Ibn Rush; Averroes; al-Bitruji; 
Arzachel; al-Zarqall; Ibn Slna 

Overview 

Ibn Tufayl’s (Abubacer; d. 1185) main engage¬ 
ment with planetary theories was centered on his 
rejection of Ptolemaic eccentrics and epicycles as 
they contradicted the basic principles of Aristo¬ 
telian physics. Ptolemy’s eccentrics and epicy¬ 
cles implied two main violations of the classical 
principles of natural philosophy. On one hand, 
the eccentric meant that planets moved around a 
center different from the Earth. On the other 
hand, epicycles meant that planets moved west 
to east in their epicycles while moving east to 
west around the eccentric, therefore introducing 
double movement, which contradicted the single 
simple movement explained in works of natural 
philosophy. While Ptolemy’s model came close 
to solving the observational variation in 


movement, it violated significant principles of 
Aristotelian physics. Objecting to the Ptolemaic 
model required the production of different geo¬ 
metrical solutions that would allow for singular 
movement around the Earth and would explain 
the observations. Ibn Tufayl claimed to have 
arrived at a solution and promised to write it in 
a separate book but apparently never had the time 
to do so. Yet, Ibn Tufayl’s student, al-Bitruji, 
credited his master by providing the basis for 
the former’s solution. 

Ibn Tufayl’s objections had their roots in the 
works of Ibn Slna, who inspired much of Ibn 
Tufayl’s works, including his most famous 
novella “Philosophus Autodidactus.” Ibn Slna 
also rejected Ptolemy’s model and claimed to 
have arrived at a solution, but after much effort 
he decided not to share it with any of his students 
and not to write it. Ibn Slna’s student, al-Juzjanl, 
composed a solution for this problem in a letter 
addressed to his master. However, JuzjanI’s solu¬ 
tion was not sufficient. 

Ibn Tufayl’s more prominent student, Ibn 
Rushd (Averroes; d. 1198), wrote an epitome to 
Ptolemy’s Almagest and acquired much of his 
fame because of his detailed commentaries on 
Aristotle. In his commentaries on Aristotle’s 
metaphysics and De Caelo, Ibn Rushd criticized 
the Ptolemaic model and considered it to be 
unnatural. He explained that Aristotle and the 
ancients had arrived at perfect solutions for the 
celestial movement that escaped Ptolemy and 
that these solutions should be rediscovered. 
While he claimed to have worked on these solu¬ 
tions in his youth, Ibn Rushd left the task unfin¬ 
ished to his successors. 

Ibn Tufayl’s other student, al-Bitruji (d. 1204), 
who seemed to have worked entirely indepen¬ 
dently from Ibn Rushd without either of the two 
being aware of the other, was a more proficient 
astronomer and produced a model in which he 
attempted to address his master’s objections. 
BitrujI maintained a homocentric universe in cor¬ 
respondence with natural philosophy, eliminating 
eccentrics and epicycles; he developed the notion 




Alanine 


59 


of rotating poles that was mentioned by Aristotle 
in De Caelo, even wondering why Ptolemy did 
not propose such a solution. Both Ibn Rushd and 
al-Bitrujl accepted this polar movement, which 
was developed by Theon of Alexandria into spiral 
movement. 

In addition to such cosmological discussions, 
the Toledan Tables, predicting the positions of 
the Sun, Moon, and planets, represented a more 
important contribution of Andalusian astrono¬ 
mers in fields of practical and computational 
astronomy. About a dozen astronomers in 
Toledo, the most prominent of whom was the 
astronomer and instrument-maker al-Zarqall 
(Arzachel; d. 1087), and which included both 
Muslims and Jews, undertook different mathe¬ 
matical and astronomic calculations that resulted 
most prominently in the tables. Al-Zarqall had an 
important theoretical contribution in relation to 
trepidation (a medieval theory related to the pre¬ 
cession of the equinoxes), and he also improved 
Ptolemy’s calculations of the length of the 
Mediterranean. 


References and Further Reading 

Carmody FJ (1952) The planetary theory of Ibn Rushd. 
Osiris 10:556-586 

Goldstein RB (1972) Theory and observation in medieval 
astronomy. Isis 63(1):39—47 

Ibn Tufayl, Abu Bakr Muhammad, Abu’l Walid Muham¬ 
mad Ibn Rushd (1999) Two Andalusian Philosophers. 
Translated by Jim Colville. Kegan Paul International, 
New York 

Langermann Y T (1997) Arabic cosmology. Early Sci 
Med 2(2): 185-213 

Nasr SH, Leaman O (1996) History of Islamic Philosophy, 
Routledge History of World Philosophies. Routledge, 
London 

Sabra AI (1998) Configuring the universe: aporetic, prob¬ 
lem solving, and kinematic modeling as themes of 
arabic astronomy. Perspect Sci 6(3):288-330 

Sabra AI (1984) The Andalusian revolt against ptolemaic 
astronomy: averroes and Al-Bitruji. Transform Tradit 
Sci 133-53 

Saliba G (1994) Early arabic critique of ptolemaic cos¬ 
mology: a ninth-century text on the motion of celestial 
spheres. J Hist Astron 25:115 


Saliba G (2002) Greek astronomy and the medieval arabic 
tradition the medieval islamic astronomers were not 
merely translators. They may also have played a key 
role in the copemican revolution. Am Sci 360-367 


Alanine 

Jeffrey Bada 

Scripps Institution of Oceanography, La Jolla, 
CA, USA 


Definition 


Alanine is one of the 20 a-amino acids found in 
coded proteins with the formula C 3 H 7 N0 2 and 


the structure 



H 

i 

C—N 


ho' I 
ch 3 


H 

/ 

\ 

H 


The oc-carbon of alanine is chiral so there are 
two optical isomers (► enantiomers), 1- and 
d-alanine. Alanine appears to be one of the first 
and is the second most common amino acids in 
terrestrial proteins. It was the first ► amino acid 
synthesized in the laboratory, by Adolph Strecker 
in 1850, who reacted acetaldehyde with hydrogen 
cyanide and ammonia in aqueous solution. It is 
also readily produced in ► spark-discharge 
experiments from a reduced gas mixture of meth¬ 
ane, ammonia, and hydrogen and has been found 
in carbonaceous chondrites. Alanine is known to 
stabilize helical structures in proteins. 


See Also 

► Amino Acid 

► Chirality 

► Enantiomers 

► Spark Discharge 

► Strecker Synthesis 




60 


Albedo 


Albedo 

Mark S. Marley 

NASA Ames Research Center, Moffett Field, 
CA, USA 

Keywords 

Clouds; Equilibrium temperature; Planet; 
Spectroscopy 

Synonyms 

Reflectivity 


Definition 

Albedo is a unitless measure of the reflectivity of 
an object. Albedo can range between zero and 
one. Several different types of albedos have been 
defined, and it is important to appreciate their 
unique characteristics. 


History 

Albedo is derived from the Latin “albus” or 
“white.” The term was first applied to optics 
by Johann Heinrich Lambert (who gave his 
name to the Lambert disk) in his text Photometria 
in 1760. 


Overview 

From a planet-wide perspective, the albedo of 
most importance is the Bond albedo, A, the ratio 
of incident energy reflected into all angles by a 
planet to the total incident energy received from 
its star. The Bond albedo appears in the equation 
for the equilibrium temperature of a rapidly rotat¬ 
ing planet T eq , with radius R receiving an incident 
flux F, 


4nR 2 aT* q = (l-A)nR 2 F, (1) 

which equates the energy thermally radiated by 
the planet (left side) to the stellar (solar) energy 
absorbed. The Bond albedo is frequently (as in 
Eq. 1) computed by integrating the total reflec¬ 
tivity of a planet over the incident flux from the 
parent star and thus depends both on the reflec¬ 
tivity spectrum and the spectral type of the star. 
A planet that efficiently scatters in the blue and 
absorbs in the red portion of the spectrum will 
thus have a higher integrated Bond albedo when 
illuminated by a blue star than by a red star, since 
a greater proportion of the incident light is 
scattered away in the former case. However, the 
Bond albedo can be defined as a function of 
wavelength, A(X), e.g., Irvine et al. (1968), and 
is then usually termed the spherical albedo. 

The geometric albedo is defined as the ratio of a 
planet’s reflectivity measured at zero phase angle 
(opposition) to that of a Lambert disk (which has 
the same apparent brightness at all viewing angles) 
of the same radius. The geometric albedo is a 
function of wavelength and, because it is measured 
at opposition (when the phase angle </) = 0), does 
not require information on the dependence of scat¬ 
tering with phase. For a perfectly reflecting Lam¬ 
bert sphere, the geometric albedo is two-thirds and 
for a semi-infinite purely ► Rayleigh scattering 
atmosphere it is three-fourths. Both such idealized, 
perfectly scattering objects would have a Bond 
albedo of 1, but the latter atmosphere sends more 
light directly back to the observer at zero phase 
angle and thus has a higher geometric albedo. The 
geometric albedo is a fixed quantity for a given 
planet, so the computation of the geometric albedo 
does not depend on the type of incident flux. Other 
types of albedos have been defined. Great care 
thus must always be exercised to be certain that 
the correct albedo is being discussed. 


See Also 

► Atmosphere, Structure 

► Clouds 

► Rayleigh Scattering 




al-BTrunl, Abu Rayhan 


61 


References and Further Reading 

Cahoy K, Marley M, Fortney J (2010) Exoplanet albedo 
spectra and colors as a function of planet phase, sepa¬ 
ration, and metallicity. Astrophys J 724:189-214 
de Pater I, Lissauer J (2010) Planetary sciences, 2nd edn. 

Cambridge University Press, Cambridge 
Hanel RA, Conrath BJ, Jennings DE, Samuelson RE (1992) 
Exploration of the Solar System by Infrared Remote 
Sensing. Cambridge University Press, Cambridge 
Irvine WM, Simon T, Menzel DH, Pikoos C, Young AT 
(1968) Multicolor photometric photometry of the 
brighter planets, III. Astron J 73:807-828 
Seager S (2010) Exoplanet atmospheres. Princeton Uni¬ 
versity Press, Princeton 


Albedo Feature 

Daniela Tirsch 

German Aerospace Center DLR, Institute of 
Planetary Research, Berlin, Germany 

Synonym 

Regio 


Definition 

A geographic area on the surface of a ► planet or 
satellite that is distinguished from adjacent ter¬ 
rains by a difference in brightness or ► albedo. 

Classical albedo features have been identified 
with Earth-based telescopes, while no detailed mor¬ 
phology could be resolved. Time-varying albedo 
features can be due to seasonal changes, for exam¬ 
ple, due to frost covers or due to the redistribution of 
bright dust or dark sand sheets by aeolian activity. 
Thanks to high-resolution imagery on board of space 
probes, albedo feature nomenclatures are increas¬ 
ingly replaced with detailed feature descriptions. 

See Also 

► Albedo 

► Planet 

► Regio 


al-BIrunl, Abu Rayhan 

Ahmed Ragab 1 and Allyssa Metzger 2 
harvard Divinity School, Cambridge, MA, USA 
2 Harvard University, Cambridge, MA, USA 

Keywords 

Islam; Islamic astronomy; Avicenna; Medieval; 
India; Zij; Astrology; Calendar; Chronology 

Overview 

Abu Rayhan al-BIrunl (d. 1048) was a Persian 
scholar of mathematics, astronomy, astrology, 
and geography, among other disciplines. 
Although he changed patrons frequently, he pro¬ 
duced his most important works in the Ghaznavid 
court. 

Educated in the dominant Greco-Islamic 
scholarship, Blrunl was interested in comparing 
different scientific traditions. His “Chronology of 
Ancient Nations” was a detailed exposition of 
calendars and chronologies used by different 
nations, including Arabs, Greeks, Persians, 
Jews, and Syriacs, among others. The Chronol¬ 
ogy was unprecedented in its comparative 
approach and its careful examination of different 
chronological systems. It also included detailed 
descriptions of these nations’ different religious 
feasts. 

While accompanying the Ghaznavid sultan 
Mahmud (r. 998-1002) in India, Blrunl came in 
contact with Indian scholars and composed a 
significant volume where he addressed Indian 
religious beliefs and rituals, Indian sciences 
including astronomy and cosmology, and Indian 
chronology and calendars, which were missing 
from his Chronology. Blrunl’s work was the first 
to discuss “foreign” nations and histories in 
non-polemical fashion with the stated goal of 
understanding different scientific and belief tra¬ 
ditions. His work in India included transmitting 
Ptolemy’s Almagest and other books of Greco- 
Islamic sciences to Indian scholars. Blrunl’s 





62 


Alcohol 


comparative view was based on his stated belief 
that sciences are universal and they speak to 
universal laws of nature, only in different lan¬ 
guages and using different models. Comparison 
of scientific theories, and of calendars and chro¬ 
nologies, was meant to explain the different 
approaches to a single universal truth. 

Biruni’s most influential text in the Islamic 
context was his al-Qanun al-Masudi (The 
Mas‘udic Canon), an 11-volume book in which 
he developed algebraic solutions of third-degree 
equations and distinguished between the motions 
of precession and the solar apogee. While the 
Canon was primarily based on Ptolemy’s Alma¬ 
gest , it was also an attempt at incorporating ele¬ 
ments of Indian and Persian astronomy in the 
dominant Greco-Islamic tradition. Biruni was 
aware of some difficulties in the Ptolemaic plan¬ 
etary theory. However, contrary to his contempo¬ 
raries, BIrunI’s objections did not only stem from 
Ptolemaic violations of the principles of classical 
natural philosophy, as Avicenna’s (d. 1037) 
objections were, but were based on contradic¬ 
tions between the Ptolemaic system and BIrunI’s 
own observations. BIrunI’s correspondence with 
Avicenna showed some of BIrunI’s skepticism 
and doubts on Aristotelian natural philosophy. 

While working as a court astrologer, BIrunI 
composed his TafhTm on astrology, which he 
started with lengthy discussions of geometry 
and astronomy, with one quarter of the book for 
the actual discussion of judicial astrology. He 
argued that a well-trained astrologer, worthy of 
the name, must be proficient in all these 
sciences. As part of his systematic observations, 
BIrunI was interested in astronomical 
instruments - he wrote five books on instruments, 
including a lengthy one on the astrolabe. He also 
described a coordinated viewing of the 
lunar eclipse on 24 May 997 with Abu al-Wafa’ 
al-Buzjani (d. 998 CE) - from Khwarazm 
and from Baghdad - to better calculate 
coordinates of major Islamic cities. Some of 
BIrunI’s minor works discuss astronomical- 
mathematical concepts such as chords (Istikhraj 
al-awtar), “shadows” or tangents (Ifrad 
al-maqal), and planetary transits (Tamhld 
al-mustaqarr). 


References and Further Reading 

Bag AK (1975) Al-Biruni on Indian arithmetic. Indian 
J Hist Sci 10(2): 174-184 

Berggren JL (1985) The origins of Al-BlrunI‘S “Method of 
the Zijes” in the theory of sundials. Centaums 28(1): 1-16 

Hartner W, Mathias S (1963) Al-Biruni and the theory of 
the solar apogee (an example of originality in Arabic 
science). In: Scientific change. London: Heinemann, 

p206-218 

Langermann YT (1997) Arabic cosmology. Early Sci Med 
2:185-213 

Pines S (1964) The semantic distinction between the terms 
astronomy and astrology according to Al-Biruni. Isis 
55(3):343-349 

Rosenthal F (1976) Al-Biruni between Greece and India. 
Paper presented at the Biruni symposium 

Saliba G (1994) Early arabic critique of ptolemaic cos¬ 
mology: a ninth-century text on the motion of celestial 
spheres. J Hist Astron 25:115 

Saliba G (1995) A history of arabic astronomy: planetary 
theories during the golden age of Islam. NYU Press, 
New York 

Saliba G (2002) Greek astronomy and the medieval arabic 
tradition the medieval Islamic astronomers were not 
merely translators. They may also have played a key 
role in the copernican revolution. Am Sci 90:360-367 


Alcohol 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Definition 

An alcohol is an organic compound containing a 
hydroxyl (-OH) group. In the IUPAC nomencla¬ 
ture system, the suffix “-ol” is used in the name of 
each alcohol. The simplest alcohol is ► methanol 
(methyl alcohol, CH 3 OH), and the most com¬ 
monly encountered alcohol is ► ethanol (ethyl 
alcohol, C 2 H 5 OH) which is contained in alco¬ 
holic beverages. Alcohols with three or more 
carbons have isomers: Propyl alcohol has two 
isomers, which are propan-l-ol 
(CH 3 CH 2 CH 2 OH) and propan-2-ol (CH 3 CH 
(OH)CH 2 ). Many low-molecular-weight alco¬ 
hols, such as ethanol and propan-2-ol, are used 
as disinfectants, since they diffuse easily through 




Aldose 


63 


cell membranes and denaturize proteins. Com¬ 
pounds whose hydroxyl group is connected to 
benzene ring are referred to as phenols. 

See Also 

► Ethanol 

► Methanol 


Aldehyde 

John H. Chalmers 

Scripps Institute of Oceanography Geosciences 
Research Division, University of California, San 
Diego, La Jolla, CA, USA 

Definition 

Aldehydes are organic compounds containing the 
RCHO functional group where R can be hydro¬ 
gen or another carbon-containing moiety. Alde¬ 
hydes are named after the corresponding 
carboxylic acids by dropping the -ic or -oic suffix 
and adding -aldehyde or -al (e.g., acetic acid 
► acetaldehyde, ethanoic acid —> ethanal), or if 
derived from acyclic aliphatic hydrocarbons, by 
dropping the final e and adding -al (e.g., propane 
—> propanal). Formyl derivatives of ring com¬ 
pounds may be called carbaldehydes as in 
cyclopentanecarbaldehyde. See the IUPAC rules 
for more complex cases. 

Aldehydes can be reduced to alcohols or oxi¬ 
dized to carboxylic acids and undergo a variety of 
addition and condensation reactions, for example, 
addition of cyanide in the cyanohydrin synthesis, or 
condensation with another aldehyde in a benzoin 
reaction or condensation with the carbon adjacent 
to an aldehyde or ketone in the aldol reaction. 

History 

The name may be derived from the phrase 
“► alcohol dehydrogenatum.” 


See Also 

► Acetaldehyde 

► Aldose 

► Amino Acid Precursors 

► Carboxylic Acid 

► Formaldehyde 

► Formose Reaction 

► Glyceraldehyde 

► Propanal 

► Propionaldehyde 


Aldose 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 


Definition 

An aldose is a ► monosaccharide where one end 
of the molecule is sp 2 hybridized and thus pre¬ 
sents as a CHO or ► aldehyde group. These are 
typically reactive ends of the molecules 
which may be involved in redox or addition 
reactions. Examples of biologically important 
aldoses include ► ribose and glucose. 
► Glycolaldehyde is the simplest aldose. One of 
the most important aldoses is ribose, which 
plays key roles as part of the pentose 
phosphate cycle in the form of ribose 5-phosphate 
as well as the backbone sugar element of 
ribonucleic acid (RNA). Another aldose deriva¬ 
tive of ribose, 2-deoxyribose, plays the same role 
in DNA. 





64 


Algae 


See Also 

► Aldehyde 

► Carbohydrate 

► Glycolaldehyde 

► Monosaccharide 

► Ribose 


Algae 

Linda Amaral-Zettler 

Marine Biological Laboratory, Josephine Bay 
Paul Center for Comparative Molecular Biology 
and Evolution, Woods Hole, MA, USA 

Keywords 

Brown algae; Coccolithophorids; Diatoms; Dino- 
flagellates; Euglenoids; Golden algae; Green 
algae; Phytoplankton; Red algae; Seaweeds 

Synonyms 

Photosynthetic eukaryotes; Protists with 
chloroplasts 


Definition 

The algae are an eclectic grouping of photosyn¬ 
thetic eukaryotes that ranges from microscopic 
picoeukaryotes (~1 pm) (Courties et al. 1994) to 
macroscopic multicellular seaweeds (50 m) (Sze 
2003). Algae are phylogenetically and morpho¬ 
logically diverse, occur in benthic and planktonic 
forms, and can be free living, symbiotic, preda¬ 
tory, or parasitic. They inhabit diverse environ¬ 
ments including several extreme environments of 
astrobiological interest, such as desert varnish, 
permafrost, and highly acidic Mars analog envi¬ 
ronments (Seckbach 2007). Green algae have 
unicellular members that share common ancestry 
with land plants (Charales). Eukaryotic algae 


along with cyanobacteria dominate global oce¬ 
anic primary production. 

History 

The term “blue-green algae” is a colloquial term 
and refers to cyanobacteria that are members of 
the domain Bacteria. This term is seldom used in 
current literature but is still frequently encoun¬ 
tered in popular articles and other media. 

Overview 

Algae are differentiated by various means, 
including phylogenetic affiliation, photo synthetic 
pigment type, and morphological features includ¬ 
ing: the number of flagella, external ornamenta¬ 
tion (e.g., scales, frustules), subcellular 
ultrastructure, and colony-forming abilities. 
They are polyphyletic and possess representa¬ 
tives in several major lineages of the Eukarya 
including alveolates (e.g., dinoflagellates), 
chlorarachniophytes (e.g., Chlorarachnion ), 
cryptomonads, euglenids, glaucophytes (e.g., 
Cyanophora ), haptophytes (e.g., Emiliania 
huxleyi ), red algae (Rhodophyta), stramenopiles 
(e.g., diatoms, brown algae), and Viridiplantae 
(e.g., Chlorophyta). 

Newer taxonomic classifications based on 
molecular phylogenetic methods employing 
multigene approaches place representatives 
from these lineages into higher taxonomic level 
groupings called supergroups (Keeling 
et al. 2005). These six major supergroups are 
the “Plantae,” “Chromalveolata,” “Rhizaria,” 
“Excavata,” “Amoebozoa,” and 

“Opisthokonta” - the first four of these contain 
algal representatives. Plantae (also referred to as 
the Archaeplastida (Adi et al. 2005)) include the 
red algae, green algae, and streptophytes; 
Chromalveolata include alveolates and 
stramenopiles; Excavata include euglenids; 
Rhizaria include chlorarachniophytes that group 
within the Cercozoa. A note of caution is that the 
resilience of these supergroups has been called 
into question (Parfrey et al. 2006; Yoon 




ALH 84001 


65 


et al. 2008), so it is important to take this into 
consideration when using these terms. Of these 
six major supergroups, only the Opisthokonta 
appear to be strongly supported in robust phylo¬ 
genetic analyses. 

In addition to chlorophyll a, algae are further 
distinguished on the basis of other types of pho¬ 
tosynthetic pigments they possess. Alveolates, 
cryptomonads, haptophytes, and stramenopiles 
also contain chlorophyll c, while chlorarach- 
niophytes, euglenids, Viridiplantae, and 
cryptomonads contain chlorophyll b. Other 
accessory pigments, such as phycobilins, further 
distinguish cryptomonads, glaucophytes, and red 
algae. 

A feature that all algae share is the ability to 
photosynthesize. There is strong evidence that 
this characteristic was the result of a single endo- 
symbiotic event that occurred between a cyano¬ 
bacterium and an ancestor of the glaucophytes, 
red algae, and green algae (including plants) 
(Keeling 2010). The uptake of both green and 
red algae by other eukaryotes has occurred mul¬ 
tiple times in what is referred to as “secondary 
symbioses.” In some dinoflagellates, tertiary 
symbioses can occur via plastid replacement. 
Plastids are also sometimes stolen and used by 
their host for brief periods of time by sea slugs, 
dinoflagellates, as well as other protists, such as 
ciliates and foraminifera - this process is called 
kleptoplasty. 

See Also 

► Eukarya 


References and Further Reading 

Adi SM et al (2005) The new higher level classification of 
eukaryotes with emphasis on the taxonomy of protists. 
J Eukaryot Microbiol 52(5):399—451 
Courties C et al (1994) Smallest eukaryotic organism. 
Nature 370(6487):255-255 

Keeling PJ (2010) The endosymbiont origin, diversifica¬ 
tion and fate of plastids. Phil Trans R Soc 
B 365:729-748 

Keeling PJ et al (2005) The tree of eukaryotes. Trends 
Ecol Evol 20(12):670-676 


Parfrey LW et al (2006) Evaluating support for the current 
classification of eukaryotic diversity. PLoS Genet 
2(12):e220 

Seckbach J (ed) (2007) Algae and cyanobacteria in 
extreme environments. Springer, Dordrecht, p 811 

Sze P (2003) A biology of the algae, 4th edn. McGraw- 
Hill, Boston 

Yoon HS et al (2008) Broadly sampled multigene trees of 
eukaryotes. BMC Evol Biol 8(1): 14 


Internet Resources 

The Tree of Life Project: http://tolweb.org/ 
AlgaeBase: http://www.algaebase.org/ 


ALH 84001 

Jean-Pierre de Vera 

DLR, Institut fur Planetenforschung, Berlin, 
Germany 


Synonyms 

Allan Hills 84001 


Definition 

ALH 84001 (abbreviation of Allan Hills 84001) is 
a 1.93 kg ► meteorite found in 1984 on the Allan 
Hills ice field, Antarctica (Victoria Land), by US 
meteorite searchers. ALH 84001 has been classi¬ 
fied as ► achondrite and is thought to be from 

► Mars. It mainly consists of coarse-grained 
cataclastic orthpyroxene-rich material and 
among the ► SNC meteorites defines the class 
of SNC-orthopyroxenites. In 1996, NASA scien¬ 
tists announced that the meteorite might contain 

► fossils of Martian microorganisms, a view that 
has been widely criticized. Radiometric dating 
suggests that ALH 84001 is 4.1 billion years 
old. The piece of ► rock has been ejected from 
Mars by an impact event 15 million years ago. 
Thirteen thousand years ago, the meteorite 
landed on Earth. 




66 


Alignment of Dust Grains 


See Also 

► Achondrite 

► Bacteria 

► Fossil 

► Mars 

► Meteorites 

► Rock 

► SNC Meteorites 


Alignment of Dust Grains 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 


Definition 

► Interstellar dust produces not only extinction of 
transmitted starlight but also introduces polariza¬ 
tion of that light, with a positive correlation 
between the amount of reddening and the linear 
polarization. This effect is normally ascribed to 
the alignment of asymmetric grains in the galactic 
magnetic field. When the direction of alignment 
changes along the line of sight, a circularly polar¬ 
ized component is produced. Consequently, obser¬ 
vations of this polarization provide (model- 
dependent) information on both dust grain proper¬ 
ties and on the galactic magnetic field. Various 
mechanisms have been proposed to produce the 
grain alignment. Since circularly polarized light 
could conceivably affect the chiral symmetry of 
irradiated molecules such as amino acids, it could 
possibly play a role in producing the observed 

► enantiomeric excess in some meteoritic organics, 
although this is far from being demonstrated. 


See Also 

► Chirality 

► Enantiomeric Excess 

► Interstellar Dust 

► Reddening, Interstellar 


Aliphatic Carboxylic Acids 

► Fatty Acids, Geological Record of 


Aliphatic Hydrocarbon 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 


Definition 

An aliphatic hydrocarbon is an organic com¬ 
pound composed of carbon and hydrogen which 
does not contain aromatic rings. It may be linear 
or cyclic and may contain unsaturated double or 
triple bonds; thus, alkanes, alkenes, and alkynes 
are all aliphatic compounds. Some illustrative 
examples are ► methane, ethylene, ► acetylene, 
and cyclopentane. 


See Also 

► Acetylene 

► Aromatic Hydrocarbon 

► Methane 


Alkaline Lakes 

► Soda Lakes 







Alkaliphile 


67 


Alkaliphile 

Antonio Ventosa and Rafael R. de la Haba 
Department of Microbiology and Parasitology, 
Faculty of Pharmacy, University of Sevilla, 
Sevilla, Spain 


Keywords 

Alkaline; Extreme habitat; Extremophile; pH; 
Soda lake 


Definition 

Alkaliphiles are microorganisms that grow opti¬ 
mally or very well at pH values above 9, often 
between 10 and 12, but cannot grow or grow 
slowly at the near-neutral pH value of 6.5 
(Horikoshi 1999). 


Overview 

There is no precise definition of what character¬ 
izes an alkaliphilic organism. Several microor¬ 
ganisms exhibit more than one optimum pH for 
growth depending on growth conditions, particu¬ 
larly nutrients, metal ions, and temperature. 
However, the definition given above is the most 
extended one. 

Many different taxa are represented among the 
alkaliphiles, including ► prokaryotes (aerobic 

► bacteria belonging to the genera Bacillus , 
Micrococcus , Pseudomonas , and Streptomyces ; 

► anaerobic bacteria from the genera 
Amphibacillus , Anaerobranca, and Clostridium ; 
halophilic ► archaea belonging to the genera 
Halorubrum , Natrialba , Natronomonas , and 
Natronorubrum ; methanogenic archaea from the 
genus Methanohalophilus ; anaerobic archaea 
from the genus Thermococcus ; cyanobacteria; 
spirochetes; actinomycetes; sulfur-oxidizing and 
sulfate-reducing bacteria), eukaryotes (► yeasts 
and filamentous ► fungi), and even phages 
(Horikoshi 1998, 1999). 


Alkaliphiles require alkaline environments 
and, in most cases, sodium ions for their growth, 
germination, and sporulation (Kudo and 
Horikoshi 1983). Isolation of alkaliphilic micro¬ 
organisms in laboratory conditions must be car¬ 
ried out in alkaline media containing sodium 
carbonate, sodium bicarbonate, or sodium 
hydroxide, following conventional means. 
Alkaliphiles are widely distributed in different 
habitats and isolated from soils, feces, and 
alkaline and/or saline lakes. The frequency of 
alkaliphilic microorganisms in neutral “ordinary” 
soil samples is 10 2 -10 5 /g of soil, which 
corresponds to 1/10 to 1/100 of the population 
of the neutrophilic microorganisms (Horikoshi 
1991). Some studies show that alkaliphilic 
bacteria have also been found in deep-sea 
sediments collected from depths of up to 
10,898 m in the Mariana Trench 
(Takami et al. 1997). 

Most alkaliphiles have an optimal growth at 
around pH 10, which is the most significant dif¬ 
ference from well-investigated neutrophilic 
microorganisms. These alkaliphilic microorgan¬ 
isms can grow in such extreme environments 
because their internal pH is maintained at 
7.5-8.5, despite a high external pH of 8-13 
(Aono et al. 1997). Therefore, one of the key 
features in alkaliphily is associated with the cell 
surface, which discriminates and maintains the 
intracellular neutral environment separate from 
the extracellular alkaline environment. 
Alkaliphiles have two mechanisms of cytoplas¬ 
mic pH regulation. The first one involves the cell 
wall structure, which contains acidic polymers 
that function as a negatively charged matrix and 
may reduce the pH value at the cell surface (Aono 
and Horikoshi 1983). The surface of the cytoplas¬ 
mic membrane must presumably be kept below 
pH 9, because the cytoplasmic membrane is very 
unstable at alkaline pH values (pH 8.5-9.0) 
much below the pH optimum for growth (Aono 
et al. 1992). The second strategy to maintain 
pH ► homeostasis consists of the use of the 
Na + /H + membrane antiporter system (A\J/ 
dependent and ApH dependent), the K + /H + 
antiporter, and ATPase-driven H + expulsion 
(Krulwich et al. 1998). 




68 


Alkanoic Acids 


The flagella motility of alkaliphiles is consid¬ 
ered to be driven by a sodium-motive force 
instead of a proton-motive force, as shown by 
neutrophiles. These alkaliphiles are most motile 
at pH 9.0-10.5, whereas no motility is observed 
at pH 8; in addition, they require Na + for motility 
(Horikoshi 1998). 

Studies of alkaliphiles have led to the discov¬ 
ery of many types of enzymes that exhibit inter¬ 
esting properties. Alkaliphilic microorganisms 
produce some enzymes such as proteases, amy¬ 
lases, cyclomaltodextrin glucanotransferases, 
pullulanases, cellulases, lipases, xylanases, 
pectinases, chitinases, and alginate lyases that 
are of great interest (Horikoshi 1999; Kobayashi 
et al. 2009). 

See Also 

► Anaerobe 

► Archaea 

► Bacteria 

► Cyanobacteria 

► Eukaryote 

► Fungi 

► Homeostasis 

► Methanogens 

► Prokaryote 

► Soda Lakes 

► Yeast 

References and Further Reading 

Aono R, Horikoshi K (1983) Chemical composition of cell 
walls of alkalophilic strains of Bacillus. J Gen 
Microbiol 129:1083-1087 

Aono R, Ito M, Horikoshi K (1992) Instability of 
the protoplast membrane of facultative 
alkaliphilic Bacillus sp. C-125 at alkaline pH values 
below the pH optimum for growth. Biochem 
J 285:99-103 

Aono R, Ito M, Horikoshi K (1997) Measurement of 
cytoplasmic pH of the alkaliphile Bacillus lentus 
C-125 with a fluorescent pH probe. Microbiology 
143:2531-2536 

Horikoshi K (1991) Microorganisms in alkaline environ¬ 
ments. Kodansha-VCH, Tokyo 
Horikoshi K (1998) Alkaliphiles. In: Horikoshi K, Grant 
WD (eds) Extremophiles: microbial life in extreme 
environments. Wiley-Liss, New York, pp 155-179 


Horikoshi K (1999) Alkaliphiles: some applications of 
their products for biotechnology. Microbiol Mol Biol 
Rev 63:735-750 

Kobayashi T, Uchimura K, Miyazaki M, Nogi Y, 
Horikoshi K (2009) A new high-alkaline alginate 
lyase from a deep-sea bacterium Agarivorans 
sp. Extremophiles 13:121-129 

Krulwich TA, Ito M, Hicks DB, Gilmour R, Guffanti AA 
(1998) pH Homeostasis and ATP synthesis: studies of 
two processes that necessitate inward proton translo¬ 
cation in extremely alkaliphilic Bacillus species. 
Extremophiles 2:217-222 

Kudo T, Horikoshi K (1983) Effect of pH and sodium ion 
on germination of alkalophilic Bacillus species. Agric 
Biol Chem 47:665-669 

Takami H, Inoue A, Fuji F, Horikoshi K (1997) Microbial 
flora in the deepest sea mud of the Mariana Trench. 
FEMS Microbiol Lett 152:279-285 


Alkanoic Acids 

► Fatty Acids, Geological Record of 


Allan Hills 84001 

► ALH 84001 


ALMA 

Thijs de Grauuw 

ALMA, Vitacura, Santiago, Chile 


Synonyms 

Atacama large millimeter array; Atacama large 
millimeter/submillimeter array 

Definition 

The Atacama Large Millimeter/submillimeter 
Array (ALMA) is an international radio telescope 
on a dry site at 5,000 m elevation in the Atacama 
Desert of northern Chile. The US$1.4 billion 






Alpha Helix 


69 


ALMA project is a partnership of Europe, Japan, 
and North America in cooperation with the Repub¬ 
lic of Chile. ALMA is funded in Europe by the 
European Organization for Astronomical 
Research in the Southern Hemisphere (ESO), in 
Japan by the National Institutes of Natural Sci¬ 
ences (NINS) in cooperation with the Academia 
Sinica in Taiwan, and in North America by the 
National Science Foundation in cooperation with 
the National Research Council of Canada and the 
National Science Council of Taiwan. Construction 
and operation of the facility are led on behalf of 
Europe by ESO, on behalf of Japan by the National 
Astronomical Observatory of Japan (NAOJ), and 
on behalf of North America by the US National 
Radio Astronomy Observatory (NRAO), which is 
managed by the Associated Universities, Inc. 
(AUI). The telescope consists of 66 high-precision 
antennas operating over the instrument wave¬ 
length range of 0.3-10 mm, with 25 provided by 
the North American partners, 25 by European col¬ 
laborators, and 16 by the Asian collaborators. All 
of the antennas can work together as a single 
telescope. ALMA is fully operational since the 
end of 2013. 


of 0.518. The component A of this system is a 
G2V star (see Spectral Type) with a mass of 1.1 
solar-masses, a luminosity of 1.519 times solar, 
and an effective temperature of 5,790 K. Its com¬ 
ponent B has a spectral type of K1V and its mass, 
luminosity, and effective temperature are equal to 
0.934 solar-mass, 0.5 solar luminosity, and 
5,214 K, respectively. 

In 2012, a team of scientists lead by Xavier 
Dumusque announced the detection of a 1.13 
Earth-mass planet around a Cen B. One year 
later, the existence of this planet, known as a 
Cen Bb, was questioned in an article by Artie 
Hatzes (2013). 

The probable existence of a Cen Bb would 
indicate that, unlike the region around a Cen 
A where terrestrial planet formation encounters 
complications, as predicted by several researchers, 
planet formation around a Cen B may be efficient. 

References and Further Reading 

Dumusque X, Pepe F, Lovis C et al (2012) Nature 491:207 
Guedes JM, Rivera EJ, Davis E et al (2008) Astrophys 
J 679:1582 

Hatzes AP (2013) Astrophys J 770:133 

Th’ebault P, Marzari F, Scholl H (2009) MNRAS 393:L21 




Alpha Centauri Bb 

Nader Haghighipour 

Institute for Astronomy, University of Hawaii - 
Manoa, Honolulu, Hawaii, HI, USA 

Definition 


Alpha Helix 

John H. Chalmers 

Scripps Institute of Oceanography Geosciences 
Research Division, University of California, 
San Diego, La Jolla, CA, USA 


Alpha Centauri Bb is a putative planet orbiting 
the star Alpha Centauri B. Alpha Centauri is a 
triple stellar system consisting of a moderately 
close binary a Cen AB, and a distant M dwarf 
companion known as Proxima Centauri at 
approximately 15,000 AU away from the binary. 
At a distance of 4.37 light years from the Sun, a 
Centauri is the closest stellar system to the solar 
system and is located in the southern constella¬ 
tion of Centaurus. The binary system has a 
semimajor axis of 23.5 AU and an eccentricity 


Definition 

The alpha (or a-) helix is one of the two most 
common ► polypeptide secondary structural 
motifs and consists of a right-handed helix with 
3.6 amino acid residues per turn. The helix has a 
pitch of 0.54 nm and a width of 1.2 nm and is 
stabilized by ► hydrogen bonds between the pep¬ 
tide -C=0- and -NH- moieties of every fourth 
bond. The amino acids proline and glycine tend to 





70 


Alpha Particles 


kink or break alpha helices, whereas alanine, 
leucine, methionine, lysine, and glutamate stabi¬ 
lize them. Protein alpha-helical regions often fold 
into coil-coiled configurations that can span 
membranes, bind DNA, or serve structural roles. 

History 

The term alpha helix was coined by William 
Astbury in the 1930s. Linus Pauling worked out 
the structure accurately in 1948. 

See Also 

► Amino Acid 

► Oligopeptide 

► Peptide 

► Polypeptide 

► Protein 

► Proteins, Secondary Structure 


Alpha Particles 

► Alpha Rays 


Alpha Rays 

Jun-Ichi Takahashi 

NTT Microsystem Integration Laboratories, 
Atsugi, Japan 

Synonyms 

Alpha particles; Helium nuclei 

Definition 

An alpha ray is a stream of alpha particles. An 
alpha particle consists of two protons and two 


neutrons bound together into a particle identical 
to a helium nucleus; it is produced in the radioac¬ 
tive process called alpha decay. Alpha particles, 
like helium nuclei, have a net spin of zero. 
The energy of alpha particles varies, depending 
upon the specific decay reaction, with higher- 
energy alpha particles being emitted from larger 
nuclei, but most alpha particles have energies of 
between 3 and 7 MeV, corresponding to 
extremely long to extremely short half-lives of 
alpha-emitting ► nuclides. They are a highly ion¬ 
izing form of particle radiation that when 
resulting from radioactive alpha decay have low 
penetration depth. Helium nuclei, which form 
10-12 % of cosmic rays, are usually of much 
higher energy than those produced by radioactive 
decay. 


See Also 

► Beta Rays 

► Gamma Rays 

► Radiochemistry 


Alteration 

Nicholas Amdt 

ISTerre, Universite Grenoble Alpes, France 


Definition 

Alteration in geochemistry refers to processes by 
which the mineralogy, composition, and texture 
of a rock are changed as a result of 
re-equilibration under conditions of lower tem¬ 
perature and pressure or through interaction with 
aqueous or C0 2 -rich fluids. The minerals of the 
original rock, which may be magmatic, sedimen¬ 
tary, or metamorphic, are transformed into an 
assemblage of low-temperature, usually finer- 
grained minerals. A typical example is the 






al-TusT, Nasir al-DTn 


71 


replacement of magmatic minerals such as oliv¬ 
ine, pyroxene, and feldspar by chlorite, clay min¬ 
erals, or carbonates. ► Weathering is a type of 
alteration that takes place close to the surface 
through interaction of rock with the atmosphere 
and with ground- or surface waters. Alteration is 
also used in chemistry and biology (e.g., DNA 
alterations). 


See Also 

► DNA Damage 

► Weathering 


al-TusT, Nasir al-Din 

Ahmed Ragab 1 and Aliyssa Metzger 2 
harvard Divinity School, Cambridge, MA, USA 
2 Harvard University, Cambridge, MA, USA 

Keywords 

Islam; Islamic astronomy; Maragha; Medieval; 
Mongol; Zij; Observatory; Tusi couple; 
Avicenna 


Overview 

Nasir al-DIn Tusi (d. 1274) was a Persian scholar 
of mathematics, astronomy, philosophy, and the¬ 
ology; he was considered by many “the Third 
Teacher” after Aristotle and al-Farabi (d. 950). 
Tusl’s most renowned activities took place in the 
Maragha Observatory in what is now Iran, where 
he led a group of scholars including Chinese 
astronomers in different investigations and activ¬ 
ities. It has been suggested that Tusl’s criticisms 
of Ptolemaic astronomy influenced Copernicus’ 
rejection of equants in his De Revolutionibus 
(1543). 


Tusi studied mathematics, medicine, and 
Avicennan philosophy at Nishapur, then jurispru¬ 
dence, mathematics, and astronomy in Iraq. In 
1233, he entered the service of the Shiite Ismaili 
emir, Ibn Abl Mansur, for whom he dedicated his 
work on ethics (Akhlaqi Nasiri). He spent time in 
the Nizari strongholds of Alamut and 
Maymundiz, where he had access to their 
libraries and produced a number of his known 
works. In 1255, he was sent by the lord of Alamut 
to negotiate with Hblegb Khan (r. 1256-1265), 
who led the Mongol westward advances. 
He remained in Hblegb’s service, which may 
have been put him in charge of Muslim 
endowments ( waqfs ) or other important 
financial institutions. Hnlegb patronized Tusl’s 
works and allowed him to start the construction 
of the Maragha Observatory in 1259. Maragha 
became a destination for many scholars who 
benefitted from Mongol patronage and from the 
impressive library that was culled from con¬ 
quered libraries in Mesopotamia, Baghdad, and 
Syria. Tusi and his colleagues at Maragha com¬ 
pleted a zij (table of parameters for calculating 
the positions of the Sun, Moon, and planets; the 
Ilkhanid Zij) around 1270 under Hhlegh’s suc¬ 
cessor, Abaqa Khan (r. 1265-1282). The zij 
might have been one of the more practical tasks 
of the observatory. 

Tusi is best known for the Tusi couple - a 
mathematical device that transforms circular to 
linear motion. By rolling a circle of radius r along 
the inner edge of a circle of radius 2r, such 
that the circles remain tangent and the smaller 
circle completes two rotations for every 
rotation of the larger, a given point on the smaller 
circle appears to oscillate along the diameter of 
the larger. The couple was produced as part of 
Tusl’s attempts to address some of the philosoph¬ 
ical difficulties of the Ptolemaic model of 
planetary movements. Applied to the orbs, the 
couple could potentially allow for the observed 
variable length of the orbital radius without 
compromising the principle of uniform circular 
movement around the earth. Tusi preferred this 
solution to Ptolemy’s equant , which generated 
much opposition. Tusi presented his couple not 






72 


Aluminilite 


as a definitive solution but rather as “an 
indication of a solution,” signaling perhaps 
that this model was only the beginning of a 
longer investigation to be carried out by his 
students and commentators. While an ostensible 
follower of Avicennan philosophy, Tusi 
appeared to have taken a less radical approach 
to dealing with the Ptolemaic model than 
Avicenna (d. 1037) and his student al-Juzjanl 
(d. 1070), preferring to maintain the model for 
its practical values and attempting to 
present important modifications that would 
reconcile its contradictions, as opposed to 
rejecting the model for one that would conform 
better with laws of classical natural 
philosophy - a task that was never accomplished 
satisfactorily. 

In his Ethics, Tusi presented ideas about the 
evolution or “perfection” of species, although his 
arguments had important ethical, theological, and 
mystical underpinnings. 

References and Further Reading 

Dabashi H (1996) The philosopher/vizier: Khwaja Nasir 
Al-Din Al-Tusi and the Isma’ilis. Mediaeval Isma’ili 
history and thought. Cambridge University Press, 
Cambridge, pp 231-245 

Langermann YT (1997) Arabic cosmology. Early Sci Med 
2:185-213 

Ragep FJ (1987) The two versions of the Tusi couple. In: 
King D, Saliba G (eds) From deferent to equant: a vol¬ 
ume of studies in the history of science in ancient and 
medieval near east in honor of E. S. Kennedy, 
vol 500, Annals of the New York Academy of Sciences. 
New York Academy of Sciences, New York 
Ragep FJ (2007) Copernicus and his Islamic predecessors: 

some historical remarks. Hist Sci 45:65-81 
Saliba G (1986) The determination of new planetary 
parameters at the Maragha observatory. Centaurus 
29(4):249-271 

Saliba G (1995a) A history of Arabic astronomy: plane¬ 
tary theories during the golden age of Islam. New York 
University Press, New York 

Saliba G (1995b) The original source of Qutb Al-Din 
Al-Shirazi’s planetary model. In: A history of Arabic 
astronomy: planetary theories during the golden age of 
Islam, vol 19. New York University Press, New York, 
p 119 

Tusi Muhammad Ibn Muhammad Nasir Al-Din, Ragep FJ 
(1993) Nasir Al-Din Al-Tusi’s Memoir on Astronomy: 
Al-Tadhkira Fhlm Al-Hay’a. Springer, New York/ 
Berlin/Paris 


Aluminilite 

► Alunite 


Alunite 

Daniele L. Pinti 

GEOTOP Research Center for Geochemistry and 
Geodynamics, Universite du Quebec a Montreal, 
Montreal, QC, Canada 


Synonyms 

Aluminilite 


Definition 

Alunite is a secondary mineral of chemical 
formula KA1 3 (S0 4 ) 2 (0H) 6 (trigonal crystal 
system). It forms solid solutions with ► jarosite 
KFe 3+ (S0 4 ) 2 (0H) 6 , and it is the product of 
medium-temperature (80-150 °C) hydrothermal 
alteration of feldspar-rich volcanic rocks. 
Acid fluids formed during the oxidation 
and leaching of metal sulfides commonly 
control the alteration. Detection of alunite at 
Terra Sirenum , ► Mars, could be an indicator of 
basalt alteration in contact with H 2 S0 4 -rich 
water. Alunite- ► kaolinite-layered deposits 
detected at Columbus Crater are another indica¬ 
tion of weathering processes at the surface of 
► Mars. 


See Also 

► Hydrothermal Environments 

► Jarosite 

► Mars 

► Weathering 





Amide 


73 


Amazonian 

Ernst Hauber 

Deutsches Zentrum fiir Luft- und Raumfahrt 
(DLR) e.V., Institut fur Planetenforschung, 
Berlin, Germany 

Definition 

It is the youngest of the three systems (of time- 
stratigraphic units) or periods (the chronologic 
equivalents to systems) in the Martian strati¬ 
graphic scheme, named after the region of 
Amazonis Planitia ( Amazonis : from the classical 
land of the Amazons on the island Hesperia; see 
US Geological Survey Gazetteer of Planetary 
Nomenclature). Depending on the different 
models to determine absolute ages on planetary 
surfaces by crater statistics, the Amazonian 
began at some point in time between 3.55 and 
1.8 billion years ago and lasts until the present. 

See Also 

► Chronostratigraphy 

► Hesperian 

► Mars 

► Mars Stratigraphy 

► Noachian 


Ambipolar Diffusion 

Steven W. Stahler 

Department of Astronomy, University of 
California, Berkeley, CA, USA 

Definition 

Ambipolar diffusion is the slippage of neutral 
matter in a plasma with respect to an internal 
magnetic field. This slippage occurs when the 
ionization fraction is so low that collisions 
between neutral species and ions become 


relatively rare. At this point, the neutral atoms 
can move relative to the ions, which are effec¬ 
tively tied to the magnetic field. Ambipolar dif¬ 
fusion is thought to occur in ► molecular clouds, 
which are dense enough to shield much of the 
external, ionizing radiation. The cloud’s self¬ 
gravity can then cause the gas to condense, in 
spite of its internal magnetic field. This conden¬ 
sation ultimately leads to star formation. 

See Also 

► Fragmentation of Interstellar Clouds 

► Gravitational Collapse, Stellar 

► Molecular Cloud 

► Star Formation, Theory 


Amide 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Definition 

In chemistry an amide is an organic compound 
which contains the functional group or the name 
given to a type of bond formed from the conden¬ 
sation of a carboxylic acid and an ► amine. 
Monosubstituted amides may exhibits the reso¬ 
nance shown in Fig. 1. Some important amides 



Amide, Fig. 1 Two states of amide 








74 


Amidocyanogen 


include peptides, urea, and formamide. Amides 
are also important intermediates in the Strecker 
amino acid synthesis. Hydrogen bonding between 
amide functional groups in polypeptides allows 
the formation of secondary structural motifs such 
as a-helices and P-sheets. Amides can be hydro¬ 
lyzed back to the constituent amine and carboxylic 
acid. Cyclic amides are known as lactams. 

See Also 


an amino group has a lone electron pair, amines 
are Lewis bases. Amines are classified as primary 
amines, secondary amines, or tertiary amines 
depending on the number of alkyl substituents 
(primary amines having a single alkyl substitu¬ 
ent) (Fig. 1). The simplest amine is methylamine 
(CH 3 NH 2 ). Methylamine was found as an inter¬ 
stellar molecule in 1974. Amines have also been 
detected among organic compounds extracted 
from carbonaceous ► chondrites. 

See Also 


► Amine 

► Carboxylic Acid 

► Polypeptide 

► Strecker Synthesis 


► Amino Acid 

► Chondrite 

► Molecular Cloud 


Amidocyanogen 

► Cyanamide 

Amidogen 

► Amino Radical 

Amine 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Definition 

An amine is an organic compound containing an 
amino group (-NR 3 ). Since the nitrogen atom in 


Amino Acid 

Jeffrey Bada 

Scripps Institution of Oceanography, La Jolla, 
CA, USA 

Keywords 

Amino group; Carboxyl group 

Synonyms 

Amino alkanoic acid 

Definition 

Amino acids are organic molecules that contain 
at least one primary amino group (NH 2 ) and one 


Amine, Fig. 1 Amine 

R \ 

\ H 

R3 

R \ 


H 

R 2 

R 2 


Primary amine 


Secondary amine 


Tertiary amine 







Amino Acid 


75 



Amino Acid, 

Fig. 1 Generalized 
structural formulas for a-, 

P-, and y-amino acids 

a-Amino-n-butyric 

acid 


Amino Acid, Table 1 The numbers of possible structural 
isomers for amino alkanoic acids (with the formula 
C, ? H 2 „NH 2 COOH) (Henze and Blair 1934) 


Number of carbon atoms 

Number of possible isomers 

2 

1 

3 

2 

4 

5 

5 

12 

6 

31 

10 

1,479 


carboxyl group (COOH). The general formula for 
amino acids with alkyl side chains that have one 
amino and one carboxyl group, known as amino 
alkanoic acids, is C„H 2w NH 2 COOH. 

History 

Most of the biologically important amino acids 
were isolated and characterized in Europe in the 
early nineteenth century (Vickery and Schmidt 
1931). For example, asparagine, the first amino 
acid discovered, was isolated from asparagus by 
Vauquelin and Robiquet in 1806. Glycine was 
isolated by Braconnot in 1820. Laboratory syn¬ 
theses were developed shortly thereafter. 

Overview 

The structural isomers with the amino group on 
the sequential carbon atoms adjacent to the car¬ 
boxyl group are called a, (3, y, etc. -amino acids. 
Thus, a-amino acids are 2-amino alkanoic acids, 
(3-amino acids are 3-amino alkanoic acids, 
etc. General structural formulae for a, (3, and y 
amino acids are shown in Fig. 1 and Table 1. 

The common names of the amino acid isomers 
with up to five carbon atoms are given in Table 2. 


p-Amino-n-butyric y-Amino-n-butyric 

acid acid 


Amino Acid, Table 2 The names of the structural iso¬ 
mers for 2, 3, 4, and 5 carbon amino alkanoic acids 


Number of 
carbon atoms 

Common names 

2 

Glycine 

3 

Alanine, P-alanine 

4 

a-Amino-/?-butyric acid, P-amino- 
n -butyric acid, a-aminoisobutyric 
acid, P-aminoisobutyric acid, 
y-amino-ft-butyric acid 

5 

Valine, isovaline, 

P-aminopentanoic acid, 
y-aminopentanoic acid, 
5-aminopentanoic acid, 
a-methyl-P-aminobutyric acid, 
allo-a-methyl-P-aminobutyric 
acid, a-methyl-y-aminobutyric 
acid, P-methyl-P-aminobutyric 
acid, P-methyl-y-aminobutyric 
acid, a-ethyl-P-aminoproponic 
acid, a-dimethyl-P-aminoproponic 
acid 


Some amino acids have aromatic side chains: 
examples are phenylglycine (a-aminophenylacetic 
acid), phenylalanine (a-amino-P-phenylpropanoic 
acid), and tyrosine (a-amino-(3-(4-hydroxyphenyl) 
propanoic acid). Amino acids can also have side 
chains consisting of an indole (a benzene ring 
linked to a five-membered nitrogen-containing 
pyrrole ring) or an imidazole (five-membered 
diunsaturated ring composed of three carbon 
atoms and two nitrogen atoms at non-adjacent 
positions): two examples of this type of amino 
acid found in biochemistry are tryptophan and 
histidine, respectively. 

There are also amino acids with hydroxyl- and 
sulfur-containing side chains. The common 
names of some examples of these amino acids 
are serine (a-amino-(3-hydroxypropanic acid), 
threonine (a-amino-(3-hydroxybutanoic acid), 
cysteine (a-amino-P-mercaptopropionic acid), 
and methionine (a-amino-y-(methylthio)butyric 





















76 


Amino Acid 



Proline Pipecolic acid 


Amino Acid, Fig. 2 Some cyclic amino acids, proline, 
and pipecolic acid 


acid). Selenium can also substitute for sulfur in 
the sulfur-containing amino acids in some 
organisms. 

Some amino acids have more than one amino 
group (e.g., lysine or a, s-diaminohexanoic acid) 
and/or more than one carboxyl group: for exam¬ 
ple, a-aminomalonic acid, aspartic acid 
(a-aminobutanedioic acid), and glutamic acid 
(a-aminopentanedioic acid). Asparagine 
(a-amino-(3-carbamoylpropanoic acid) and gluta¬ 
mine (a-amino-5-carbamoylbutyric acid) are the 
side group carboxamides of aspartic and glutamic 
acids, respectively. Interestingly, asparagine was 
the first amino acid discovered in 1806 when it 
was crystallized from the “juice” squeezed from 
asparagus shoots. The amino acid arginine 
(a-amino-s-guanidinopentanoic acid) has a 
guanidinium group attached to the end of its 
alkyl side chain. 

Some amino acids have a cyclic secondary 
amine rather than a primary amino group. Exam¬ 
ples include proline (pyrrolidine-2-carboxylic 
acid, C5H9NO2) where the primary amino group 
is replaced with a five-membered pyrrolidine ring 
or tetrahydropyrrole and pipecolic acid 
(piperidine-2-carboxylic acid, C 6 HnN 0 2 ) 
where the amino group is replaced by 
six-membered piperidine ring (Fig. 2). 

The ionization constants (p K a ) at 25 °C of the 
amino and carboxyl groups of amino alkanoic 
acids are in the range 8-10 and 2-4, respectively. 
Thus, at neutral pH, the amino group is proton- 
ated, while the carboxyl group is deprotonated, 
producing a doubly charged ► zwitterion with no 
net charge. Amino acids with other amino or 
carboxyl groups have additional ionization con¬ 
stants characteristic of the particular group. The 
pA" a of the (3-carboxyl group of aspartic acid is 




L-Alloisoleucine D-Alloisoleucine 


Amino Acid, Fig. 3 Enantiomers and diastereomers of 
iso- and alloisoleucine 

3.9 at 25 °C; thus at neutral pH aspartic acid has a 
net negative charge. The pA^ a of the guanidinium 
group of arginine is 12.5, and arginine is thus 
positively charged at neutral pH. 

When a carbon atom in an amino acid has four 
different groups attached to it, referred to as an 
asymmetric or ► chiral carbon, it is optically 
active. For those amino acids with one chiral 
carbon, there are two possible optically active 
isomers designated, the l- and D-enantiomers. 
Some amino acids have more than one chiral 
carbon so several stereoisomers are possible. An 
amino acid with two chiral carbons is said to be 
diastereomeric, and there are thus two diastereo¬ 
mers, each of which has two enantiomers, for a 
total of four possible optical isomers. For the 
diastereomeric pair L-isoleucine/D-alloisoleucine 
(a-amino-(3-methylpentanoic acid), the two sets 
of enantiomers are l- and D-isoleucine and l- and 
D-alloisoleucine, respectively (Fig. 3). 

Amino acids can be linked together by the 
formation of a ► peptide bond that involves the 
amino group of one amino acid and the carboxyl 
group of another. Two amino acids connected in 
















Amino Acid 


77 


O R 



Amino Acid, Fig. 4 A generic dipeptide 

this fashion are called a dipeptide which has the 
structure given below (in this case, one amino 
acid is glycine and the other has a generic 
R-group side chain) (Fig. 4). 

Polypeptides and proteins consist of a large 
number of amino acids connected in peptide link¬ 
ages. A total of 20 different amino acids (for this 
discussion, the amino acids selenocysteine and 
pyrrolysine are not included because they are rel¬ 
atively rare coded amino acids) are decoded from 
DNA sequences and encoded into RNA for incor¬ 
poration into proteins. A list of the “canonical” 
20 protein amino acids and their abbreviations are 
given in Table 3. There are peptides that contain 
additional amino acids other than the standard 
protein amino acids, but these are incorporated 
by posttranslational modifications or the peptides 
themselves are synthesized by nonribosomal pep¬ 
tide synthetases (NRPSs). For example, 
a-aminoisobutyric acid and isovaline are found 
in some fungal peptides synthesized by NRPSs. 

With the exception of achiral glycine, only the 
L-enantiomers of the proteinogenic amino acids are 
incorporated into proteins. The discrimination 
against the incorporation of D-amino acids during 
the protein synthesis process is estimated to be 
greater than 10 4 . However, there are D-amino acids 
present in some peptides, but these are introduced 
either by the conversion of L-amino acids by post¬ 
translational isomerization enzymes or are intro¬ 
duced by NRPSs. Some D-amino acid-containing 
peptides have potent antimicrobial activity. 

The total number of amino acids theoretically 
possible is huge, and several hundred different 
amino acids have been isolated from organisms, 
and an even larger number have been made in the 
laboratory by a variety of synthetic methods. 
Moreover, the synthesis of amino acids is not 
confined to terrestrial biology or laboratory syn¬ 
thesis: amino acids have been detected in 


Amino Acid, Table 3 The 20 amino acids commonly 
found in proteins and their commonly used abbreviations 


Amino acid 

Three-letter 

One-letter 

common name 

abbreviation 

abbreviation 

Aspartic acid 

Asp 

D 

Glutamic acid 

Glu 

E 

Asparagine 

Asn 

N 

Glutamine 

Gin 

Q 

Glycine 

Gly 

G 

Alanine 

Ala 

A 

Valine 

Val 

V 

Isoleucine 

Iso 

I 

Leucine 

Leu 

L 

Phenylalanine 

Phe 

F 

Tyrosine 

Tyr 

Y 

Serine 

Ser 

S 

Threonine 

Thr 

T 

Cysteine 

Cys 

C 

Methionine 

Met 

M 

Lysine 

Lys 

K 

Histidine 

His 

H 

Arginine 

Arg 

R 

Tryptophan 

Trp 

W 

Proline 

Pro 

P 


meteorites, and there are hints that at least the 
simplest amino acid glycine is present in interstel¬ 
lar clouds and comets (see ► Molecules in Space). 
One of the meteorites most extensively studied is 
the ► Murchison carbonaceous chondrite that fell 
in southeastern Australia in 1969. Over 75 differ¬ 
ent amino acids have been detected in Murchison 
(Sephton 2002), with only 8 of these also being 
found in biological proteins. These amino acids 
are clearly of extraterrestrial origin: many are 
unique to the meteorite and do not occur naturally 
on Earth and those with a chiral carbon are race¬ 
mic (or close to racemic). The Murchison amino 
acids are thought to have been synthesized by 
natural reactions, such as the ► Strecker synthesis, 
directly on the juvenile meteorite parent body or in 
the early solar nebula before incorporation into 
planetesimals. Amino acids have been detected 
in even larger quantities in other carbonaceous 
chondrites (Pizzarello and Shock 2010). 

Amino acids may also have been synthesized by 
natural processes on the early Earth as demon¬ 
strated by the classic Miller spark discharge 






























78 


Amino Acid A/-Carboxy Anhydride 


experiment carried out in 1953 (Miller 1953; John¬ 
son et al. 2008). These amino acids could have 
accumulated on the Earth and been available for 
incorporation into the first living entities. To date, 
12 of the amino acids found in the proteins of 
terrestrial organisms have been synthesized in 
spark discharge experiments with various reduced 
gas mixtures. 

The striking overlap between amino acids 
generated in experiments simulating prebiotic 
chemistry and found in meteorites represents evi¬ 
dence for the abiotic plausibility of approxi¬ 
mately half of the canonical amino acid set. 
This is also supported by the thermodynamics of 
their formation (Higgs and Pudritz 2009). Debate 
continues, however, as to whether these amino 
acids would have been sufficient to comprise the 
first functional proteins. It is also unclear how 
these amino acids came to be used by life when 
many others might have been also available 
(Weber and Miller 1981; Cleaves 2010). 

The amino acids absent from abiotic simula¬ 
tions and meteorites are not only difficult to make 
but are also either thermally unstable (Gin, Asn) or 
are unstable under UV conditions (Cys, Met, Trp, 
His, Tyr, Phe). This strongly suggests that these 
amino acids are biological “inventions” and their 
multi enzymatic synthesis pathways appeared only 
after the onset of Darwinian evolution. The order 
of biologically invented amino acid entering the 
code has been hypothesized based on thermody¬ 
namics (Higgs and Pudritz 2009); however, the 
entry and retention of amino acids is likely to be 
complex, with such factors as accessibility, com¬ 
patibility, complementarity with existing code 
members, and stability on transfer RNA all 
playing a role (Weber and Miller 1981; Cleaves 
2010). The culmination of this selection is a set of 
amino acids unchanged since the last universal 
common ancestor (LUCA), which is exceptional 
in breadth and evenness in terms of size, hydro- 
phobicity, and charge (Philip and Freeland 2011). 

See Also 

► Diastereomers 

► Enantiomers 


► l- Amino Acids 

► Molecules in Space 

► Peptide 

► Protein 

► Strecker Synthesis 

References and Further Reading 

Cleaves HJ (2010) The origin of the biologically coded 
amino acids. J Theor Biol 263:490-498 
Henze HR, Blair CM (1934) The number of structural 
isomers of the more important types of aliphatic com¬ 
pounds. J Am Chem Soc 56:157 
Higgs PG, Pudritz RE (2009) A thermodynamic basis for 
prebiotic amino acid synthesis and the nature of the 
first genetic code. Astrobiology 9:483^-90 
Johnson AP, Cleaves HJ, Dworkin JP, Glavin DP, 
Lazcano A, Bada JL (2008) The Miller volcanic 
spark discharge experiment. Science 322:404 
Miller SL (1953) Production of amino acids 
under possible primitive Earth conditions. Science 
117:528 

Philip GK, Freeland SJ (2011) Did evolution select a 
nonrandom “alphabet” of amino acids? Astrobiology 
ll(3):235-240 

Pizzarello S, Shock E (2010) The organic composition of 
carbonaceous meteorites: the evolutionary story ahead 
of biochemistry. In: Deamer D, Szostak J (eds) The 
origins of life. Cold Spring Harbor Press, Washington, 
DC, pp 89-107 

Sephton MA (2002) Organic compounds in carbonaceous 
meteorites. Nat Prod Rep 19:292-311 
Vickery HB, Schmidt CLA (1931) The history of the 
discovery of the amino acids. Chem Rev 9(2): 169-318 
Weber AL, Miller SL (1981) Reasons for the occurrence 
of the twenty coded protein amino acids. J Mol 
Evol 17:273-284 


Amino Acid Af-Carboxy Anhydride 

Laurent Boiteau 

Institut des Biomolecules Max Mousseron, 
UMR5247 CNRS, University Montpellier-2, 
Montepellier, Cedex, France 


Synonyms 

l,3-Oxazolidine-2,5-dione; Leuchs’ Anhydride; 
NCA 




Amino Acid A/-Carboxy Anhydride 


79 


Definition 

An amino acid 7V-carboxy anhydride (or NCA) is a 
cyclic organic compound structurally related to an 

► amino acid, which is an intramolecular mixed 
anhydride of a carboxylic and carbamic acid 
(structure -CO-O-CO-NH-), making it both an 
TV-protected and a CO -activated amino acid. NCAs 
are structurally related to hydantoins but have very 
different chemical reactivity. They are rather unsta¬ 
ble in water and physiological media. The term 
NCA is usually used to refer to the NCAs of 
oc-amino acids (although NCAs of (3-amino acids 
etc. are also possible). NCAs can condense to give 
oligo- or polypeptides, with the release of C0 2 . 
NCAs are postulated or observed intermediates in 
many prebiotically relevant reactions leading to 

► peptides from amino acid derivatives, especially 
in aqueous media in the presence of carbonate. 
NCAs are also considered to be potentially prebiotic 
reagents, as they are versatile free energy carriers 
which can potentially activate other biologically 
relevant chemical species, such as nucleotides. 

History 

Although speculations that NCAs might have 
played a role in prebiotic chemical evolution 
arose in the mid-1970s, notwithstanding their use 
since the late 1970s in “model” prebiotic reactions, 
studies in the early 2000s improved the status of 
NCAs as prebiotically relevant compounds. 

Overview 

Discovered by Hermann Leuchs in 1906, NCAs 
are well-known reactants in both organic and 
polymer synthesis (Kricheldorf 2006). Since 
their most popular preparative method involving 
the reaction of free amino acids with phosgene is 
not prebiotically relevant, NCAs themselves were 
long considered as prebiotically irrelevant (Pascal 
et al. 2005). Nevertheless, NCAs have been con¬ 
tinuously used from the 1970s in model reactions 
of prebiotic peptide formation, especially to assess 
stereoselection hypotheses in relation with the 


emergence of homochirality of the natural amino 
acid pool, e.g., enantiomeric excess amplification 
processes (Kricheldorf 2006; Pascal et al. 2005; 
Illos et al. 2008). NCAs have long been postulated 
as likely intermediates in the reaction of activated 
amino acid esters (e.g., adenylates, thioesters) 
based on the observation that the formation of 
peptides is accelerated by the presence of C0 2 or 
bicarbonate. Since the late 1990s, several 
prebiotically relevant pathways for NCA forma¬ 
tion have been identified, thus confirming the pre¬ 
biotic status of NCAs (Kricheldorf 2006; Pascal 
et al. 2005): 

• The nitrosation of TV-carbamoyl amino acids 
(CAA) promoted by nitrogen oxides 
(Kricheldorf 2006; Pascal et al. 2005) 

• The decomposition of diacyldisulfides 

• The reaction of amino acids with carbonyl 
sulfide in the presence of oxidizing or 
alkylating agents (Leman et al. 2004) 

• The spontaneous decomposition of CAA in 
water (Danger et al. 2006) 

NCAs represent both (1) the structurally sim¬ 
plest activated amino acids (formally resulting 
from condensation with C0 2 ), (2) an unavoidable 
intermediate from any form of CO-activated amino 
acid in a bicarbonate/C0 2 -rich environment, and 
(3) the most activated amino acid species achiev¬ 
able in water in a prebiotic environment. Thermo¬ 
dynamic calculations show NCAs to be quite stable 
(because of the cyclic stmcture) compared to other 
anhydrides, although kinetically they are as reac¬ 
tive as the latter. Furthermore, NCAs may be kinet¬ 
ically competent intermediates from almost any 
inactivated amino acid derivatives, provided their 
spontaneous hydrolysis is slower than NCA forma¬ 
tion (Pascal et al. 2005). 

Such thermodynamic and kinetic features make 
NCAs potential energy carriers in an amino acid- 
based protometabolism, as exemplified by their 
ability to activate inorganic phosphate (Pascal 
et al. 2005) or nucleotides (Biron et al. 2005; 
Leman et al. 2006), which could be coupled to a 
peptide/nucleic acid coevolution scenario 
supporting speculations on the emergence of the 
translation apparatus (Pascal et al. 2005). 



80 


Amino Acid Precursors 


See Also 

► Amino Acid 

► Chirality 

► Metabolism, Prebiotic 

► A-Carbamoyl Amino Acid 

► Peptide 

► Prebiotic Chemistry 

References and Further Reading 

Biron JP, Parkes AL, Pascal R, Sutherland JD 
(2005) Expeditious prebiotic aminoacylation of nucle¬ 
otides. Angew Chem Int Ed 44:6731-6734 

Danger G, Cottet H, Boiteau L, Pascal R (2006) The 
peptide formation mediated by cyanate revisited. 
A-Carboxyanhydrides as accessible intermediates in 
the decomposition of A-carbamoylamino acids. J Am 
Chem Soc 128:7412-7413 

Illos RA, Bisogno FR, Clodic G, Bolbach G, Weissbuch I, 
Lahav M (2008) Oligopeptides and copeptides of 
homochiral sequence, via P-sheets, from mixtures of 
racemic a-amino acids, in a one-pot reaction in water; 
relevance to biochirogenesis. J Am Chem Soc 
130(27): 8651-8659 

Kricheldorf HR (2006) Polypeptides and 100 years of 
chemistry of a-amino acid A-carboxyanhydrides. 
Angew Chem Int Ed 45:5752-5784 (and references 
cited therein) 

Leman L, Orgel LE, Ghadiri MR (2004) Carbonyl sulfide- 
mediated prebiotic formation of peptides. Science 
306:283-286 

Leman LJ, Orgel LE, Ghadiri MR (2006) Amino acid 
dependent formation of phosphate anhydrides in 
water mediated by carbonyl sulfide. J Am Chem Soc 
128(1):20—21 

Pascal R, Boiteau L, Commeyras A (2005) From the prebi¬ 
otic synthesis of a-amino acids towards a primitive 
translation apparatus for the synthesis of peptides. Top 
Curr Chem 259:69-122 (and references cited therein) 


Amino Acid Precursors 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Definition 

► Amino acid precursors are compounds that 
give amino acids after some reactions (usually 


hydrolysis). One of the typical amino acid precur¬ 
sors is ► aminoacetonitrile, which is converted to 
glycine by hydrolysis via glycine ► amide: 

NH 2 CH 2 CN + 2H 2 0 -+ nh 2 ch 2 conh 2 + h 2 o 
-> NH 2 CH 2 COOH + NH 3 . Hydantoins 
(substituted glycolylurea) are also typical amino 
acid precursors and have been found in carbona¬ 
ceous chondrites. Complex organic polymers with 
large molecular weights are also possible precur¬ 
sors. ► Tholins, which are formed by reactions of 
mixtures of nitrogen and methane, are large com¬ 
plex molecules which give amino acids after 
hydrolysis. Amino acids are frequently detected 
in carbonaceous ► chondrites (meteorites), but the 
amount of amino acids recovered usually 
increases after hydrolysis, suggesting that some 
amino acids are present in the form of amino 
acid precursors. 

See Also 

► Amide 

► Amino Acid 

► Aminoacetonitrile 

► Chondrite 

► Complex Organic Molecules 

► Hydantoin 

► Hydrolysis 

► Tholins 


Amino Alkanoic Acid 

► Amino Acid 


Amino Radical 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 

Synonyms 

Amidogen; Aminyl radical; NH 2 






Aminoacetonitrile 


81 


Definition 

This triatomic radical is an important 
intermediary in the interstellar chemistry of 

► ammonia, NH 3 . Like many light hydrides, its 
pure rotational transitions occur at far infrared/ 
submillimeter wavelengths, making its observa¬ 
tion from ground-based observatories difficult 
because of the opacity of the terrestrial 
atmosphere. 

History 

The NH2 radical was first detected in the ► inter¬ 
stellar medium in 1993 (van Dishoeck et al.), at 
submillimeter wavelengths, and has been 
extensively observed toward different 
molecular clouds using the HIFI instrument on 
board the Herschel satellite (Persson et al. 2010, 
2012 ). 

See Also 

► Ammonia 

► Interstellar Medium 

► Molecules in Space 


References and Further Reading 

Persson CM, Black JH, Cemicharo J et al (2010) Nitrogen 
hydrides in interstellar gas. Herschel/HIFI observa¬ 
tions towards G10.6-0.4 (W31C). Astron Astrophys 
521:L45 

Persson CM, De Luca M, Mookerjea B et al (2012) Nitro¬ 
gen hydrides in interstellar gas. II. Analysis of Her- 
schel/HIFI observations towards W49N and G10.6-0.4 
(W31C). Astron Astrophys 543:145 
van Dishoeck EF, Jansen DJ, Schilke P, Phillips TG 
(1993) Detection of the Interstellar NH2 Radical. 
Astrophys J Lett 416:L83-L86 


Aminoacetic Acid 

► Glycine 


Aminoacetonitrile 

Didier Despois 

Laboratoire d’Astrophysique de Bordeaux, 
CNRS-Universite de Bordeaux, France 

Synonyms 

AAN; Cyanomethylamine; Glycinonitrile; 

nh 2 ch 2 cn 

Definition 

Aminoacetonitrile (IUPAC name 2- 
Aminoacetonitrile) is a (toxic) liquid at room tem¬ 
perature and standard pressure. It is a precursor of 
the simplest amino acid, ► glycine, which it forms 
by reaction with liquid water. It is also an interme¬ 
diary in the ► Strecker synthesis of glycine. It was 
identified in the interstellar medium in 2008. 

History 

Although its rotational spectrum has been studied 
since the 1970s, and modeled explicitly for a 
search in the interstellar medium in 1990, 
aminoacetonitrile has only been detected recently 
in space, in a large molecular cloud Sagittarius 
B2 (Sgr B2) at the center of the Galaxy (Belloche 
et al. 2008). 

See Also 

► Glycine 

► Molecular Cloud 

► Molecules in Space 

► Strecker Synthesis 

References and Further Reading 

Belloche A, Menten KM, Comito C, Miiller HSP, 
Schilke P, Ott J, Thorwirth S, Hieret C (2008) Detec¬ 
tion of amino acetonitrile in Sgr B2(N). Astron 
Astrophys 482:179-196 





82 


Aminobutyric Acid 


Aminobutyric Acid 

Mark Dorr 

University of Southern Denmark, Odense M, 
Denmark 


Synonyms 

Butyrine; Ethyl-glycine 


See Also 

► Amino Acid 


Aminoethanoic Acid 

► Glycine 


Definition 


Aminoisobutyric Acid 


Aminobutyric acid is the term for a variety of 
structural isomers of amino acids derived from n- 
or isobutyric acid with the chemical formula 
C 4 H 9 N0 2 . They belong to the substance class of 
amino acids, since they contain an amino func¬ 
tional group and a carboxylic acid functional 
group. In nature, several different isomers of 
aminobutyric acid are found: (1) a-aminobutyric 
acid (aABA), a key intermediate in the biosynthe¬ 
sis of ophthalmic acid, (2) (3-aminobutyric acid 
(PABA), (3) y-aminobutyric acid (GABA), 
which modulates the excitability of neurons of 
vertebrates and muscle tone, and 
(4) a-aminoisobutyric acid (aAIB), which is 
found in some fungal membrane peptides. Several 
aminobutyric acid isomers have been found in 
carbonaceous chondrite meteorites. 

a, P, and y denote the position of the amino 
group relative to the carboxyl group in the 
► amino acid molecule: a refers to the first, P 
the second, and y the third position. 



Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, 

Tokyo, Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Synonyms 

AIB 


Definition 

Amino isobutyric acid (AIB) is an amino acid 
derived from isobutyric acid. There are two struc¬ 
tural isomers of amino isobutyric acid (Fig. 1), 
a-aminoisobutyric acid (aAIB), which is achiral, 
and P-aminoisobutyric acid (PAIB), which has 
two ► stereoisomers, a D and L form. Both 


H 2 N COOH 

x 


aAIB 

Aminoisobutyric Acid, Fig. 

mers of aminoisobutyric acid 


COOH 



PAIB 


1 The two structural iso- 


y-amino butyric acid 














Amitsoq Gneisses 


83 


isomers have been found in carbonaceous chon¬ 
drites, with aAIB often being one of the most 
abundant amino acids. This is thought to be sig¬ 
nificant as aAIB is not found in proteins, 
suggesting an extraterrestrial origin of this com¬ 
pound. However, several fungi are now known to 
synthesize this compound for incorporation in 
non-ribosomally encoded peptide antibiotics. 

See Also 

► Carbonaceous Chondrites, Organic 
Chemistry of 

► Stereoisomers 


Aminonitrile 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, 

Tokyo, Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Definition 

An aminonitrile is a compound containing both 
an amino and a nitrile functional group. The 
simplest aminonitrile is ► cyanamide. 
a-Aminonitriles, such as a-aminoacetonitrile, 
are important intermediates in the ► Strecker 
synthesis of amino acids, as they are hydrolyzed 
consecutively to a-amino amides and finally to 
a-amino acids (Fig. 1). a-Aminoacetonitrile was 
detected in interstellar space in 2008. 


See Also 

► Amino Acid 

► Amino Acid Precursors 

► Cyanamide 

► Strecker Synthesis 


Aminyl Radical 

► Amino Radical 


Amitsoq Gneisses 

Herve Martin 

Laboratoire Magmas et Volcans, Universite 
Blaise Pascal, OPGC, CNRS, IRD, Clermont- 
Ferrand, France 

Keywords 

Greenland; Isua Supracrustal Belt; Archean; 
TTG; Gneiss; Metamorphic rocks 

Synonyms 

Itsaq Gneiss Complex 

Definition 

The Amitsoq gneisses are among the older meta¬ 
morphic rock complexes yet discovered on Earth. 
These rocks outcrop on the southwestern coast of 
Greenland, where they extend over more than 
50 km northeast of Nuk (Godthab). The oldest 


Aminonitrile, 

Fig. 1 Strecker amino acid 
synthesis via aminonitrile 


A, 


nh 4 cn 


HoN CN 


HoO 


HpN CONHp 


HpO 


R 2 R 1 
a-amino nitrile 


R 2 Rt 
a-amino amide 


H 2 N COOH 

- X 

r 2 Ri 

a-amino acid 









84 


Amitsoq Gneisses 


age obtained on a zircon crystal extracted from a 
tonalitic gneiss sample is of 3.872 =b 0.010 Ga. 

Overview 

The Amitsoq gneisses outcrop on the southwest¬ 
ern coast of Greenland, where they extend over 
more than 50 km northeast of Nuk (Godthab), 
along the southern coast of the Godthabsfjord. 
After long and detailed field work, Me Gregor 
(1968, 1973) was the first who recognized these 
Archaean terrains as among the oldest in the 
world. He distinguished two groups of gneisses: 

(1) very old ones cut by mafic dykes (Ameralik 
dykes) that he called the Amitsoq gneisses, 

(2) younger ones emplaced after the Ameralik 
dykes and that are known as the Nuk gneisses. 
Both groups are crosscut by the late Qorqut gran¬ 
ite. The first dating of the Amitsoq gneisses was 
conducted by Black et al. (1971), who obtained a 
Rb-Sr isochron age of 3.98 d= 0.17 Ga, and 
Moorbath et al. (1972), who measured a slightly 
younger age (3.74 ±0.1 Ga) using the same 
method. More recent researches showed that the 
so-called Amitsoq gneisses were heterogeneous 
and made up of several intrusive bodies. In order 
to account for this diversity, Nutman et al. (1996) 
proposed to refer to these formations as the Itsaq 
Gneiss Complex. In fact, both terms are used in 
geological literature. 

Amitsoq Gneisses, 

Fig. 1 General view of the 
~3.8 Ga Amitsoq gneisses. 

They consist in grey gneiss, 

TTG in composition. On 
this photo, they are crosscut 
by a black Ameralik dyke 
(Photo G. Gruau) 


This view has been subsequently corroborated 
by intensive zircon dating (Nutman et al. 1996; 
Nutman and Hiess 2009) that determined that the 
emplacement of Amitsoq gneiss protolith 
(protolith is the original, unmetamorphosed rock 
from which a metamorphic rock is formed) 
occurred between 3.88 and 3.60 Ga, during at 
least three main petrogenetic episodes at 
-3.80 Ga; -3.7 Ga, and -3.65 Ga. It must be 
noted that some ages older than 3.85 Ga were 
also measured (Horie et al. 2010; Nutman 
et al. 2013). Indeed, a zircon crystal extracted 
from a tonalitic gneiss sample gave an age of 
3.872 ± 0.010 Ga, which is the oldest reliable 
age so far measured in Amitsoq gneisses. The 
same authors reported an age of 
3.883 ± 0.009 Ga measured in a zircon core, 
while the rim provided a slightly younger age of 
3.861 ± 0.022 Ga; these dates are assumed to be 
those of parental magma crystallization. 

The Amitsoq gneisses outcrop over vast areas, 
over about 3,000 km 2 . Their protolith was a felsic 
plutonic rock, having a tonalitic, trondhjemitic, 
and granodioritic (TTG) composition (O’Nions 
and Pankhurst 1978; Nutman and Bridgwater 
1986; Nutman et al. 2000, 2007, 2013; Steenfelt 
et al. 2005; Hiess et al. 2009). In Archean ter¬ 
rains, TTGs are very abundant; these are by far 
the most abundant rocks of the Archean continen¬ 
tal crust (Moyen and Martin 2012). They are 
generated by partial melting of a hydrous basalt, 




Amitsoq Gneisses 


85 


possibly in a subduction-like environment 
(Martin 1986; Martin et al. 2005). Subsequently, 
they underwent granulite facies metamorphism at 
about 3.6 Ga (Friend and Nutman 2005). 

Before the Cretaceous, and the development 
of the Labrador ridge and the Baffin Bay basin, 
west Greenland and Labrador were closer to each 
other. At that time, Archean terrains on both sides 
should have been connected. Indeed, along the 
northern coast of Labrador outcrop the Uivak 
gneisses, which are metamorphic rocks, mostly 
TTG in composition and very similar to the 
Amitsoq gneisses. The Uivak gneisses contain 
zircon crystals that have been dated at 
3.733 dz 0.009 Ga; however, they also contain 
rounded cores dated at 3.863 ± 0.012 Ga 
(Bridgwater and Collerson 1976; Bridgwater 
and Schiotte 1991). Contrarily to Greenland, in 
Labrador these rocks suffered a Neoarchean 
granulite facies metamorphism (Collerson and 
Bridgwater 1979) (Fig. 1). 

See Also 

► Archean Eon 

► Earth’s Atmosphere, History of the Origins 

► Greenland 

► Isua Supracrustal Belt 

► Metamorphic Rock 

► Tonalite-Trondhjemite-Granodiorite 


References and Further Reading 

Black LP, Gale NH, Moorbath S, Pankhurst RJ, McGregor 
VR (1971) Isotopic dating of very early Precambrian 
amphibolite facies gneisses from the Godthaab district, 
West Greenland. Earth Planet Sci Lett 12:245-259 

Bridgwater D, Collerson KD (1976) The major petrolog¬ 
ical and geochemical characters of the 3600 
m.y. Uivak gneisses from Labrador. Contrib Mineral 
Petrol 54:43-60 

Bridgwater D, Schiotte L (1991) The Archaean gneiss 
complex of northern Labrador. A review of current 
results, ideas and problems. Bull Geol Soc Den 
39:153-166 

Lriend CRL, Nutman AP (2005) Complex 3670-3500 Ma 
orogenic episodes superimposed on juvenile crust 
accreted between 3850-3690 Ma, Itsaq Gneiss Com¬ 
plex, southern West Greenland. J Geol 113:375-398 


Hiess J, Bennett VC, Nutman AP, Williams IS (2009) In 
situ U-Pb, O and Hf isotopic compositions of zircon 
and olivine from Eoarchaean rocks, West Greenland: 
new insights to making old crust. Geochim 
Cosmochim Acta 73:4489-4516 

Horie K, Nutman AP, Lriende CRL, Hidaka H (2010) 
The complex age of orthogneiss protoliths 
exemplified by the Eoarchaean Itsaq Gneiss Complex 
(Greenland): SHRIMP and old rocks. Precambrian Res 
183:25^3 

Martin H (1986) Effect of steeper Archean geothermal 
gradient on geochemistry of subduction-zone magmas. 
Geology 14:753-756 

Martin H, Smithies RH, Rapp R, Moyen J-F, Champion 
D (2005) An overview of adakite, tonalite- 
trondhjemite-granodiorite (TTG), and sanukitoid: 
relationships and some implications for crustal evolu¬ 
tion. Lithos 79:1-24 

McGregor VR (1968) Field evidence of very old Precam¬ 
brian rocks in Godthaab area, West Greenland. 
Rapp Gronlands Geol Unders 19:31 

McGregor VR (1973) The early Precambrian geology of 
the Godthab district, West Greenland. Phil Trans 
R Soc Lond A 273:243-258 

Moorbath S, O’Nions RK, Pankhurst RJ, Gale NH, 
McGregor VR (1972) Further rubidium-strontium 
age determinations on the very eary Precambrian 
rocks of Godthaab region, West Greenland. Nature 
240:78-82 

Moyen J-F, Martin H (2012) Forty years of TTG research. 
Lithos 148:312-336 

Nutman AP, Bennett VC, Friend CLR, Horie K, Hidaka 
H (2007) -3,850 Ma tonalites in the Nuuk region, 
Greenland: geochemistry and their reworking within 
an Eoarchaean gneiss complex. Contrib Mineral Petrol 
154:385-408 

Nutman AP, Bennet VC, Friend CLR, McGregor VR 
(2000) The early Archaean Itsaq Gneiss 
Complex of southern Greenland: the importance 
of field observations in interpreting age 
and isotopic constrains for early 
terrestrial evolution. Geochim Cosmochim Acta 
64:3035-3060 

Nutman AP, Bridgwater D (1986) Early 
Archaean Amitsoq tonalites and granites of the 
Isukasia area, southern West Greenland: development 
of the oldest known sial. Contrib Mineral Petrol 
94:137-148 

Nutman AP, McGregor VR, Friend CLR, Bennet VC, 
Kinny PD (1996) The Itsaq gneiss complex of southern 
Greenland; the world’s most extensive record of early 
crustal evolution (3900-3600 Ma). Precambrian Res 
78:1-39 

Nutman AP, Bennett VC, Friend CLR, Hidaka H, Yi K, 
Ryeol Lee S, Kamiichi T (2013) The Itsaq 
Gneiss Complex of Greenland: episodic 3900 to 
3660 Ma juvenile crust formation and recycling in 
the 3660 to 3600 Ma Isukasian orogeny. Am J Sci 
313:877-911 



86 


Ammonia 


Nutman AP, Hiess J (2009) A granitic inclusion suite 
within igneous zircons from a 3.81 Ga tonalite 
(W. Greenland): restrictions for Hadean crustal evolu¬ 
tion studies using detrital zircons. Chem Geol 
261:76-81 

O’Nions RK, Pankhurst RJ (1978) Early Archaean rocks 
and geochemical evolution of the Earth’s crust. Earth 
Planet Sci Lett 38:211-236 

Steenfelt A, Garde AA, Moyen J-F (2005) Mantle wedge 
involvement in the petrogenesis of Archaean grey 
gneisses in West Greenland. Lithos 79:207-228 


Ammonia 

Alexander Smirnov 

Department of Earth and Marine Science, 
Dowling College, Oakdale, NY, USA 

Keywords 

Prebiotic synthesis; Nitrogen; Abiotic reduction 


Synonyms 

Azane; Nitro-sil; Trihydrogen nitride 


Definition 

Ammonia (NH 3 ) is a chemical compound com¬ 
posed of ► nitrogen and hydrogen which exists as 
a gas at standard conditions of temperature 
and pressure. In the trigonal pyramidal ammonia 
molecule, the lone electron pair of the nitrogen 
atom is responsible for its dipole moment 
(polarity) and its behavior as a base (proton 
acceptor). It dissolves readily in water and its 
protonation results in the formation of the conju¬ 
gate acid ammonium ion (NH 4 + ) with both spe¬ 
cies coexisting in a pH-dependent equilibrium 
(p K a NH 4 + = 9.25 at 25 °C). Liquid ammonia 
(boiling point —33.35 °C at atmospheric 
pressure) is an ionizing solvent with physical 
properties and behavior similar to water 
(Lagowski 2007). 


History 

Ammonia has been known since ancient times, 
although it was first isolated by Priestly in 1774. 
In 1785, Berthollet determined its composition. 
The Haber-Bosch process to synthesize ammonia 
from nitrogen and hydrogen was developed by 
Fritz Haber and Carl Bosch in 1909. It was found 
in space by Cheung et al. (1968) and in comets by 
Altenhoff et al. (1983) using radioastronomical 
techniques. 

Overview 

Ammonia has been detected throughout our solar 
system as well as in interstellar space (see ► Mol¬ 
ecules in Space). The deuterated ammonium ion 
NH 3 D + has recently been detected in the inter¬ 
stellar medium (Cemicharo et al. 2013; note that 
the symmetry of the principle isotopic form, 
NH 4 + , leads to a zero electric dipole moment 
and hence no pure rotational transitions that 
might be observed astronomically). Ammonia is 
found as a gas in planetary atmospheres and in the 
solid form (ice) in cometary nuclei and planetary 
surfaces. Ammonia is hypothesized to be present 
in liquid form in a subsurface ocean on some 
outer planet satellites (e.g., ► Titan) where it 
would effectively lower the freezing point of 
water (Raulin 2008). 

On the early Earth, ammonia was likely a 
necessary precursor for prebiotic organic synthe¬ 
sis, such as the ► Strecker synthesis of amino 
acids. It was used as the nitrogen source in the 
Miller-Urey experiment, which produced a suite 
of organic compounds such as amino acids from a 
mixture of reduced gases simulating the primor¬ 
dial atmosphere (Miller 1953). However, most 
current models suggest the early atmosphere 
was only mildly reducing, with the redox state 
linked to the evolution and oxidation state of the 
Hadean and early Archaean mantle, with 
► dinitrogen (N 2 ) as the dominant nitrogen spe¬ 
cies (Kasting and Catling 2003). 

It has been experimentally shown that 
ammonia-containing environments are more effi¬ 
cient in organic synthesis than those dominated 




Ammonium, Deuterated 


87 


by dinitrogen in both aqueous and gaseous envi¬ 
ronments. This notion is not unexpected, consid¬ 
ering that the strong triple bond (948 kJ.mol -1 ) of 
the N 2 molecule results in large reaction activa¬ 
tion energy barriers even if the overall reaction is 
thermodynamically favored. The process of con¬ 
version (e.g., reduction) of unreactive dinitrogen 
to reactive and prebiologically useful ammonia is 
referred to as ► nitrogen fixation. 

Mechanisms suggested for abiotic ammonia 
production on the early Earth include reduction 
of atmospherically derived nitrite (N0 2 _ ) by fer¬ 
rous iron or iron-bearing minerals (Summers and 
Chang 1993); hydrolysis of atmospherically pro¬ 
duced HCN (Zahnle 1986); reduction of 
dinitrogen on mineral surfaces (sulfides, metals, 
alloys) in hydrothermal systems (Brandes 
et al. 2008; Smirnov et al. 2008; Singireddy 
et al. 2012); or delivery of reduced nitrogen 
(nitride, N 3- ) in iron meteorites followed by dis¬ 
solution and reaction with H + (Smirnov 
et al. 2008). The concentrations of ammonia 
and/or ammonium ion in the prebiotic atmosphere 
and hydrosphere were likely controlled by mech¬ 
anisms such as photolytic destruction, sequestra¬ 
tion in clay minerals by substitution for K + and 
formation of N-bearing organic molecules. 


See Also 

► Amino Acid 

► Dinitrogen 

► Hydrogen Cyanide 

► Mildly Reducing Atmosphere 

► Nitrogen 

► Nitrogen Fixation 

► Prebiotic Chemistry 

► Strecker Synthesis 

► Titan 

References and Further Reading 

Altenhoff WJ, Batrla W, Huchtmeirs WK (1983) Radio 
observations of Comet 1983 D. A & A 187:502 
Brandes JA, Hazen RM, Yoder HS (2008) Inorganic nitro¬ 
gen reduction and stability under simulated hydrother¬ 
mal conditions. Astrobiology 8:1113-1126 


Cemicharo J, Tercero B, Fuente A, Domenech JL, 
Cueto M, Carrasco E, Herrero VJ, Tanarro I, 
Marcelino N, Roueff E (2013) Detection of the ammo¬ 
nium ion in space. Astrophys J 771:L10-L13 

Cheung AC, Rank DM, Townes CH, Thornton DD, Welch 
WJ (1968) Detection of NH 3 molecules in the inter¬ 
stellar medium by their microwave emission. Phys Rev 
Lett 21:1701 

Kasting JF, Catling D (2003) Evolution of a habitable 
planet. Annu Rev Astron Astrophys 41:429^63 

Lagowski JJ (2007) Liquid ammonia. Synth React Inorg 
Met 37:115-153 

Miller SL (1953) A production of amino acids under 
possible primitive Earth conditions. Science 
117:528-529 

Raulin F (2008) Astrobiology and habitability of Titan. 
Space Sci Rev 135:37-48 

Singireddy S, Gordon AD, Smirnov A, Vance MA, 
Schoonen MA, Szilagyi RK, Strongin DR 
(2012) Reduction of nitrite and nitrate to ammonium 
on pyrite. Orig Life Evol Biosph 42:275-294 

Smirnov A, Hausner D, Laffers R, Strongin D, Schoonen 
MA (2008) Abiotic ammonium formation in the pres¬ 
ence of Ni-Fe metals and alloys and its implications for 
the Hadean nitrogen cycle. Geochem Trans 9:5 

Summers DP, Chang S (1993) Prebiotic ammonia from 
reduction of nitrite by iron(II) on the early Earth. 
Nature 365:630-632 

Zahnle K (1986) Photochemistry of methane and the for¬ 
mation of Hydrocyanic acid (HCN) in Earth’s early 
atmosphere. J Geophys Res 91:2819-2834 


Ammonium, Deuterated 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 


Synonyms 

Deuterated ammonium ion 


Definition 

The deuterated ammonium ion, NH 3 D + , has been 
detected by radio astronomers toward a cold, 
dense ► molecular cloud core in the ► Milky 
Way galaxy (Cernicharo et al. 2013; 
cf. ► Ammonia). Note that the symmetry of the 
corresponding principal ► isotopolog, NH 4 + , 




88 


Amoebae 


leads to a zero electric dipole moment and hence 
no pure rotational transitions, making its inter¬ 
stellar detection very difficult. Large isotopic 
fractionation for deuterium/hydrogen isotopologs 
is expected, and indeed observed for many mol¬ 
ecules, in cold molecular clouds. 

See Also 

► Ammonia 

► Isotopic Fractionation (Interstellar Medium) 

► Molecules in Space 

► Radio Astronomy 

References and Further Reading 

Cernicharo J, Tercero B, Fuente A, Domenech JL, 
Cueto M, Carrasco E, Herrero VJ, Tanarro I, 
Marcelino N, Roueff E (2013) Detection of the ammo¬ 
nium ion in space. Astrophys J 771:L10-L13 


Amoebae 

Emmanuelle J. Javaux 
Palaeobiogeology-Palaeobotany- 
Palaeopalynology, Geology Department, 
Universite de Liege, Liege, Belgium 

Definition 

Amoebae are microscopic unicellular eukaryotes 
(► Protists) able to deform their cytoplasm to 
move (amoeboid or crawling-like movement). 
They represent a large diversity of unrelated 
groups of eukaryotes. Some are surrounded by a 
cell coat (glycocalyx); others are naked. Some are 
pathogens. Others produce a mineral test made of 
siliceous plates, an organic test, or an agglutinated 
test made of external organic or mineral particles 
(thecamoebae or testate amoebae). Some amoebae 
demonstrate a social behavior when several indi¬ 
viduals join to form complex multicellular struc¬ 
tures such as slugs or fruiting bodies. The oldest 
fossil amoeba reported so far is 750 Ma old. 


See Also 

► Eukaryote 

► Protists 


Amorphous Carbon 

Akira Kouchi 

Institute of Low Temperature Science, Hokkaido 
University, Kita-ku, Sapporo, Hokkaido, Japan 

Keywords 

Amorphous carbon; Carbon star; Carbonaceous 
chondrites; Cometary particles; Hydrogenated 
amorphous carbon; Interplanetary dust particles 


Synonyms 

Glassy carbon; Vitreous carbon 


Definition 

Amorphous carbon is a noncrystalline solid allo- 
tropic form of carbon. There is no long-range 
order in the positions of the carbon atoms, but 
some short-range order is observed. Chemical 
bonds among atoms are a mixture of sp 2 - and 
sp 3 -hybridized bonds with a high concentration 
of dangling bonds. Because amorphous carbon is 
thermodynamically in a metastable state and the 
ratio of sp 2 - and sp 3 -hybridized bonds is variable, 
the properties of amorphous carbon vary greatly 
depending on the formation methods and condi¬ 
tions (Silva and Ravi 2003). Amorphous carbon 
is often abbreviated as “< 2 -C.” 


Overview 

In the laboratory, amorphous carbon can be pro¬ 
duced by physical vapor deposition, chemical 





Amorphous Carbon 


89 


vapor deposition, sputtering, and ion irradiation 
of diamond or graphite. The structure of amor¬ 
phous carbon has been analyzed by X-ray and 
electron diffraction methods. The ratio of sp 2 - 
and sp 3 -hybridized bonds can be determined by 
electron energy loss spectroscopy, X-ray 
photoelectron spectroscopy, and Raman spec¬ 
troscopy. Amorphous carbon whose dangling 
bonds are terminated with hydrogen is called 
hydrogenated amorphous carbon (< 2 -C:H). 
Depending on the sp 2 and sp 3 ratios, the proper¬ 
ties of amorphous carbon differ greatly. When a 
significant fraction of sp 3 bonds is present in 
amorphous carbon, this is called tetrahedral 
amorphous carbon (ta- C) or diamond-like car¬ 
bon. Tetrahedral amorphous carbon is hard, 
transparent, and electrically insulating and has 
higher density than a-C and a- C:H. 

In space, the occurrence of amorphous carbon 
is observed in circumstellar envelopes around 
carbon stars. When carbon stars lose mass to 
stellar winds, carbonaceous materials, such as 
polycyclic aromatic hydrocarbons (PAH), SiC, 
and amorphous carbon (< 2 -C/< 2 -C:H), that con¬ 
dense in their extended atmospheres are released 
to the interstellar medium. The conditions for the 
formation of amorphous carbon {a-C) grain have 
been investigated theoretically (Gail and 
Sedlmayr 1984), and the occurrence of amor¬ 
phous carbon {a-C) and SiC has been deduced 
by observing the spectra of carbon stars (Blanco 
et al. 1990). 

Very recently, amorphous carbon has been 
found in various extraterrestrial materials. 
Cometary particles from comet 81P/Wild 2, cap¬ 
tured by NASA’s Stardust mission, were ana¬ 
lyzed by transmission electron microscopy, and 
a small amount of amorphous carbon grains less 
than 200 nm in size was found (Matrajt 
et al. 2008). In interplanetary dust 
particles (IDPs), investigated with Raman and 
infrared spectroscopy, the dominant type of 
carbon is found to be either a form of amorphous 
carbon {a-C) or of hydrogenated amorphous 
carbon (< 2 -C:H), depending on the type of 
IDP (Munoz Caro et al. 2006). It has been pro¬ 
posed that amorphous carbon in cometary parti¬ 
cles and IDPs was formed by energetic 


processing (UV photons and cosmic rays) of icy 
grains in interstellar molecular clouds 
(Greenberg 1998; Kouchi et al. 2005). Amor¬ 
phous carbon grains have also been found in the 
matrix of carbonaceous chondrites (Brearley 
2008). These grains are essentially made of pure 
carbon embedded in an amorphous silicate 
matrix. It has been proposed that these grains 
were originally primitive macromolecular 
organic material that has undergone mild thermal 
metamorphism in the parent bodies of carbona¬ 
ceous chondrites. 


See Also 

► Insoluble Organic Matter 

► Kerogen 

► Molecular Cloud 

► Organic Refractory Matter 

► Polycyclic Aromatic Hydrocarbon 


References and Further Reading 

Blanco A et al (1990) Amorphous carbon and carbona¬ 
ceous materials in space II.-Astrophysical implica¬ 
tions. Nuovo Cimento C 13:241-247 

Brearley AJ (2008) Amorphous carbon-rich grains in the 
matrices of the primitive carbonaceous chondrites, 
ALH77307 and Acfer 094. Lunar Planet Sci 
XXXIX: 1494 

Gail H-P, Sedlmayr E (1984) Formation of crystalline and 
amorphous carbon grains. Astron Astrophys 
132:163-167 

Greenberg JM (1998) Making a comet nucleus. Astron 
Astrophys 330:375-380 

Kouchi A et al (2005) Novel routes for diamond formation 
in interstellar ices and meteoritic parent bodies. 
Astrophys J 626:L129-L132 

Matrajt G et al (2008) Carbon investigation of two Star¬ 
dust particles: a TEM, NanoSIMS, and XANES study. 
Meteor Planet Sci 43:315-334 

Munoz Caro GM et al (2006) Nature and evolution of the 
dominant carbonaceous matter in interplanetary dust 
particles: effects of irradiation and identification with a 
type of amorphous carbon. Astron Astrophys 
459:147-159 

Silva S, Ravi P (eds) (2003) Properties of amorphous 
carbon, institution of engineering and technology. 
INSPEC, London 



90 


Amorphous Solid 


Amorphous Solid 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 

Definition 

An amorphous solid lacks long-range order in the 
positioning of its constituent atoms; glass is an 
example. This contrasts with a crystalline solid, 
where such order is present, e.g., quartz. Both the 
ices and the silicates in ► interstellar dust grains 
are typically amorphous, although crystalline sili¬ 
cates are present in some circumstellar and come¬ 
tary dust. The conversion of amorphous to 
crystalline water ice has often been invoked as an 
energy source in cometary outbursts at large helio¬ 
centric distances. The presence of crystalline sili¬ 
cates (presumably formed in the hot and dense 
inner solar system, possibly under the action of 
energetic particles from the young Sun) in 
► comets, which are formed in the cold outer 
part of the solar system, suggests that mixing of 
material was important in the ► solar nebula. 


See Also 

► Comet 

► Interstellar Dust 

► Interstellar Ices 

► Solar Nebula 


Amphibolite Facies 

Nicholas Arndt 

ISTerre, Universite Grenoble Alpes, France 

Definition 

Amphibolite facies refers to rocks formed under 
metamorphic conditions of moderate to high 


temperatures (400-600 °C) and pressures 

(200-900 MPa). Rocks in most Archean gneiss 
belts are metamorphosed at the amphibolite 
facies. The name-giving rock is amphibolite, a 
dense and dark green to black rock generated by 
metamorphism under moderate temperature 
(ca. 500 °C) and pressure (1 GPa) from a mafic 
(basaltic) protolith or, more rarely, from impure 
dolostone (carbonate rock). It consists mainly of 
hornblende, a type of amphibole, with lesser pro¬ 
portions of plagioclase, and in some cases biotite, 
epidote, titanite, and iron oxides. Amphibolite is 
a common constituent of metamorphosed oceanic 
crust or of mafic intrusions in orogenic belts. 


See Also 

► Metamorphic Rock 

► Oceanic Crust 


Amphiphile 

David Deamer 

Department of Chemistry, University of 
California, Santa Cruz, Santa Cruz, CA, USA 

Synonyms 

Detergent; Lipid; Surfactant 

Definition 

An amphiphile is a molecule having both a 
hydrophobic nonpolar group and a hydrophilic 
polar group. The nonpolar hydrophobic portion 
of the molecule is typically a hydrocarbon chain 
ranging from 10 to 20 or more carbon atoms in 
length, and the polar moiety can be a carboxylic 
acid, phosphate, sulfate, amine, or alcohol group, 
among other possibilities. Examples of 
amphiphiles are fatty acids, detergents, and 
all lipids including phospholipids and sterols. 






Amphoteric Compounds 


91 


All amphiphiles are surface active and form 
monolayers at air-water interfaces. Some amphi¬ 
philes, particularly those with a single hydrocar¬ 
bon chain, assemble into ► micelles in aqueous 
solutions. Other amphiphiles with two hydrocar¬ 
bon chains, for instance, phospholipids, typically 
self-assemble into bilayer membranes that are the 
permeability barriers defining most forms of cel¬ 
lular life. Amphiphilic molecules resembling 
fatty acids are present in carbonaceous meteorites 
and are plausible membrane-forming compo¬ 
nents of the first living cells. 


See Also 

► Lipid Bilayer 

► Self-Assembly 


Amphiphilicity 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Definition 

Amphiphilicity refers to the property of some 
molecules to have an affinity to two phases and 
most notably in biochemical systems the affinity 
to both a polar solvent phase (in this case water) 
and hydrophobic phase (such as the interior of 
cell membranes or proteins). Amphiphilic mole¬ 
cules usually contain both hydrophobic (e.g., 
benzyl or alkyl) and hydrophilic groups (e.g., 
-OH, -NH 2 and -COOH). Amphiphilic molecules 
are often useful as surfactants. Sodium 
dodecylbenzene sulfonate is a typical amphi¬ 
philic molecule used as a laundry detergent or 
shampoo and complexes hydrophobic substances 
such as dirt and oil with its hydrophobic 
dodecylbenzene moiety (Ci 2 H 2 5 -C 6 H 4 -) and is 
dispersed by affinity of the sulfonate moiety 
(-SO 3 H - ) to water. 


Amphiphilic molecules can assemble in vari¬ 
ous solvents. Phospholipids are typical amphi¬ 
philic biomolecules, having hydrophilic heads 
including phosphate ions or charged tertiary or 
quaternary amines and hydrophobic tails includ¬ 
ing fatty acids. Many phospholipids form lipid 
bilayer membranes in water, where the polar 
heads face toward the solvent and hydrophobic 
tails which aggregate to form the inner part of the 
vesicle. 


See Also 

► Hydrophobicity 

► Membrane 

► Self-Assembly 

► Self-Assembly, Biological 


Ampholytes 

► Amphoteric Compounds 


Amphoteric Compounds 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 


Synonyms 

Ampholytes 


Definition 

An amphoteric compound is a compound that can 
act both as an acid and as a base. Some metal 
oxides or metal hydroxides, such as aluminum 
oxide (A1 2 0 3 ), show amphotericity: 






92 


Amplification (Genetics) 


With a base : A1 2 0 3 + 2 NaOH + 3H 2 0 
^ 2Na[Al(OH) 4 ]“ 

With an acid : A1 2 0 3 + 6 HC1 = 2 A1C1 3 + 3 H 2 0 

Some organic compounds also show 
amphotericity. These include amino acids, com¬ 
pounds having both carboxylic group(s) and 
amino group(s). For instance, glycine is predom¬ 
inantly present as a zwitterion ( + NH 3 -CH 2 - 
COO) in circumneutral aqueous solution, and 
it can neutralize either an acid or a base as 
follows: 

With a base: + H 3 NCH 2 COCT + NaOH 

^ H 2 NCH 2 COO _ Na + + H 2 0 

With an acid: + H 3 NCH 2 COO“ Htr HC1 
^ Cl + H 3 NCH 2 COOH 

Amino acids and their polymers (proteins) 
dissolved in aqueous solution possess both 
positively and negatively charged groups. 

In acidic solution, there are typically more 
positively charged groups, while there are 

typically more negatively charged groups in 
basic solution, though this depends somewhat 
on the sequence of the protein. At a defined 
pH called the isoelectric point (p/), amino 
acids or proteins have balanced positive and 
negative charges. At the isoelectric point of a 
protein, its hydrophobicity becomes 

maximum, and its solubility to water becomes 

minimum. 


See Also 

► Amino acid 

► Zwitterion 


Amplification (Genetics) 

Carlos Briones 

Centro de Astrobiologia (CSIC/INTA), 

Consejo Superior de Investigaciones Cientificas, 
Madrid, Spain 

Definition 

In molecular biology, amplification is a process 
by which a ► nucleic acid molecule is enzymat¬ 
ically copied to generate a progeny population 
with the same sequence as the parental one. The 
most widely used amplification method is the 

► polymerase chain reaction (PCR). The result 
of a PCR amplification of a segment of ► DNA 
is called an “amplicon.” Nucleic acids can also 
be amplified in an isothermal reaction involving 
a reverse transcriptase, which copies 

► RNA^DNA, and a DNA-dependent RNA 
polymerase, which transcribes DNA^RNA. Iso¬ 
thermal amplification does not generate double- 
stranded DNA, and it is mainly used for copying 
RNA. Ligase-based methods, including the 
so-called ligase chain reaction (LCR), can be 
also used for specific DNA or RNA amplification. 
A fourth general method for nucleic acid ampli¬ 
fication involves ► cloning the selected DNA 
molecule into bacterial or eukaryotic cells, 
allowing them to reproduce, and collecting the 
amplified DNA. 


See Also 

► Cloning 

► DNA 

► Nucleic Acids 

► Plasmid 

► Polymerase Chain Reaction 

► Replication (Genetics) 

► RNA 




Anaerobe 


93 


Anabolism 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 


Synonyms 

Biosynthesis 


Definition 

Anabolism is the subset of metabolic networks by 
which cell components are derived from 
organic or inorganic precursors. Anabolism 
requires a source of energy - usually in the form 
of ATP - and reducing power, usually as 
NADPH. 


See Also 

► Assimilative Metabolism 

► Catabolism 

► Metabolism 


Anaerobe 

Jose Luis Sanz 

Departamento de Biologia Molecular, 
Universidad Autonoma de Madrid, 
Madrid, Spain 


Synonyms 

Non-aerobic 


Definition 

Anaerobes are organisms that do not require oxy¬ 
gen to obtain energy or to grow. Anaerobic 
metabolism is restricted to microorganisms, 
both prokaryotic (► Bacteria and ► Archaea) 
and eukaryotic (yeast, microsporidia), although 
an anaerobic multicellular organism (phylum 
Loricifera) has been recently discovered in 
marine sediments. 

Overview 

There are two main categories of anaerobic 
microorganisms: (1) facultative anaerobes that 
can use oxygen for ► respiration if it is 
present but in its absence obtain energy from 

► fermentation (such as enterobacteria or 
yeasts), ► anaerobic respiration (some Pseudo¬ 
monas, Thiobacillus , Bacillus , and many others), 
and anoxygenic photosynthesis (some 
Proteobacteria) and (2) obligate anaerobes, 
which never use oxygen. These can, in turn, be 
divided into two subcategories: (a) strict or 
obligate anaerobes, for whom oxygen is poison¬ 
ous (i.e., oxygen is extremely toxic to 

► methanogens), and (b) aeroduric or 
aerotolerant anaerobes that can grow in the pres¬ 
ence of oxygen, although they never use it (i.e., 
bacteria involved in lactic acid fermentations). 
Cultivating strict anaerobes in the laboratory is 
an arduous task due to their extreme sensitivity to 
oxygen. Anaerobic jars or chambers are neces¬ 
sary for the isolation and growth of methanogenic 
archaea, sulfur-reducing bacteria, or bacteroides. 

Some anaerobes are etiological agents of 
important diseases, such as tetanus ( Clostridium 
tetani ), botulism ( Clostridium botulinum), chol¬ 
era ( Vibrio cholera ), salmonellosis and typhoid 
fever ( Salmonella enterica ), or peptic ulcers 
( Helicobacter pylori). Others, such as the lactic 
acid fermenters Lactobacillus and Lactococcus , 
are involved in the production of food from dairy 
(yogurt, cheese, kefir, sour cream), vegetables 





94 


Anaerobic Photosynthesis 


(sauerkraut, olives, pickles), or meat (sausages). 
Some yeast (, Saccharomyces ) are responsible for 
bread, beer, and wine production. Finally, the 
methanogenic archaea carry out the last step of 
anaerobic degradation of organic matter in the 
absence of oxygen and, therefore, play a key 
role in anaerobic wastewater treatment and 
biomethanization of municipal solid waste pro¬ 
cesses. It is important to underline that Earth’s 
atmospheric 0 2 is of biological origin, and for an 
extended period of biological evolution, includ¬ 
ing the period in which the ► origin of life is 
suggested, the Earth remained strictly 
anaerobic. Anaerobes are of astrobiological inter¬ 
est because anaerobic conditions prevail on many 
planets, for instance, ► Mars. 


See Also 

► Anaerobic Respiration 

► Anoxygenic Photosynthesis 

► Archaea 

► Bacteria 

► Fermentation 

► Mars 

► Methanogens 

► Origin of life 

► Respiration 

References and Further Reading 

Madigan M, Martinko J, Dunlap P, Clark D (2009) Brock 
biology of microorganisms, 12th edn. Person Education, 
Benjamin Cummings, San Francisco, Chapters 18, 21 

Sowers KR, Noll KM (1995) Techniques for anaerobic 
growth. In: Robb FT, Place AR, Sowers KR, Schreier 
HJ, Dassarma S, Flischmann EM (eds) A laboratory 
manual: methanogens. Cold Spring Harbor Faboratory 
Press, New York, pp 15—47 

Willey JM, Sherwood FM, Woolverton CJ (2008) Pres¬ 
cott, Harley, and Kleins. Microbiology, 7th edn. 
McGraw-Hill, Boston, Chap. 9 


Anaerobic Photosynthesis 

► Anoxygenic Photosynthesis 


Anaerobic Respiration 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, 

Valencia, Spain 

Definition 

Anaerobic ► respiration is a metabolic process in 
which oxidized organic compounds, such as 
fumarate, or inorganic molecules, such as nitrate, 
sulfate, or ferric ion, serve as the terminal ► elec¬ 
tron acceptor of an electron transport chain. 

See Also 

► Aerobic Respiration 

► Electron Acceptor 

► Respiration 


Analog Sites 

► Terrestrial Analog 


Angular Diameter 

Daniel Rouan 

LESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 


Definition 

The angular diameter of a celestial object, seen 
from Earth, is the apparent diameter measured in 
angular units. Planets in the solar system have 
typical angular diameters between a few arcsec 
up to 50 arcsec (0.25 m-radians). 







Angular Momentum 


95 


References and Further Reading 

Arrhenius S (1903) Die Verbreitung des Lebens im 
Weltenraum. Umschau 7:481-485 
Arrhenius S (1908) Worlds in the making: the evolution of 
the universe. Harper & Row, New York 


Angular Momentum 

Jerome Perez 

Applied Mathematics Laboratory, ENSTA 
ParisTech, Paris Cedex 15, France 


Keywords 

Rotating body 


Definition 

In mechanics, angular momentum is the vector 
cross product between the position vector and the 
momentum vector of a point mass system. This 
definition can be extended to a solid by 
summation. 


Overview 

The movement of a point mass m is defined by its 
position r and its velocity v. These quantities are 
vectors relative to some reference system. This 
movement splits into two parts: a movement of 
translation and a movement of rotation. The 
amount of movement is measured by the linear 
momentum (impulsion) p = mv (for simple 
cases), which is a conserved quantity for a trans¬ 
lation invariant system. The amount of rotation is 
measured by the angular momentum L = r x /?, 
which is a conserved quantity for a rotation 
invariant system. Note that the vector cross prod¬ 
uct a x b = ab sin On , where 9 is the smaller 
angle between a and b (0° < 6 < 180°), a and 
b are the magnitudes of vectors a and b , and n is a 
unit vector perpendicular to the plane containing 


a and b in the direction given by the right- 
hand rule. 

Variations of velocity are produced by forces, 
in accordance with Newton’s second law of 
dynamics. If forces that apply on the point are 
aligned with the position vector r, they are called 
central, the system is invariant under rotation, 
and its angular momentum is conserved. As 

► gravitation is a central force, this conservation 
occurs frequently in astronomy. 

When the system is extended, such as a solid 
planet described by a distribution of points whose 
relative distances are fixed, the total angular 
momentum is the sum of the contributions of all 
these points. In this case, it is distributed between 
the spin of the planet itself and the angular 
momentum of its orbit. 

The conservation of angular momentum of 
celestial bodies is a fundamental tool for analyz¬ 
ing their properties. For example: 

• In a two-body problem (see ► Gravitation), 
if one of the two bodies is much heavier than 
the other, the conservation of angular momen¬ 
tum implies Kepler’s third law (see ► Orbital 
Resonance) and allows us to obtain the value 
of the large mass from observations of the 
period and of the semimajor axis of the 
small mass. 

• If a planet is found to rotate slower than 
expected, one can suspect that this planet 
is accompanied by a satellite, because the 
total angular momentum is shared between 
the planet and its satellite in order to be 
conserved. 

• The tidal torque the Moon exerts on the Earth 
implies a slowing down of the rotation rate of 
the Earth (at about 42 ns/day). As a conse¬ 
quence and because the total angular momen¬ 
tum of the whole system is conserved, the 
distance between the Earth and Moon gradu¬ 
ally increases by 4.5 cm/year. 

See Also 

► Gravitation 

► Orbital Resonance 




96 


Animalcules 


Animalcules 

Stephane Tirard 

Centre Francis Viete d’Histoire des 
Sciences et des Techniques EA 1161, Faculte 
des Sciences et des Techniques de Nantes, 
Nantes, France 

Definition 

From the seventeenth century to the early nine¬ 
teenth century, animalcule meant the very small 
living beings that were observed through a micro¬ 
scope. The famous microscopist, Antony van 
Leeuwenhoek (1632-1723), one of the major 
improvers of this instrument during the second 
part of the seventeenth century, used the expres¬ 
sion spermatic animalcules. 

See Also 

► Bacteria 

► Protists 


Anion 

Steven B. Chamley 

Solar System Exploration Division, Code 
691, Astrochemistry Laboratory, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 


Definition 

An anion is an atom or molecule that has gained 
an electron (e.g., CN“, OH - , C 4 H“). Neutral 
molecules with large electron affinities (EAs) 
can attach an electron in a variety of chemical 
reactions, such as electron photo attachment. 
Long carbon-chain molecules have large EA 
values, and C 6 H“ was the first anion discovered 
in the interstellar medium in 2006. 


See Also 

► Circumstellar Chemistry 

► Molecules in Space 

► Photochemistry 


Annefrank 

Stefano Mottola 

German Aerospace Center (DLR), Institute of 
Planetary Research, Berlin, Germany 

Definition 

(5535) Annefrank is a small S-class, main-belt 
asteroid named after the Jewish victim of Nazi 
persecution famous for her diary. The Discovery 
spacecraft Stardust encountered the asteroid on 
November 2, 2002 on its route to comet Wild 
2. During the fast flyby, the space probe recorded 
an image sequence lasting about 15 min and 
consisting of over 70 images. Although the imagery 
had a comparatively low resolution in the range of 
300-185 km/pixel and covered only about 40 % of 
the surface, the sequence revealed a body with 
approximate dimensions of 6.6 x 5.0 x 3.4 km 
and an angular appearance, reminiscent of a contact 
binary or of a re-accumulated pile of fragments. 


Anorthosite 

Nicholas Amdt 

ISTerre, Universite Grenoble Alpes, France 

Definition 

Anorthosite is a magmatic intrusive rock. It is 
light colored (leucocratic) and has a medium to 
coarse grain size (phaneritic). It is mainly com¬ 
posed of plagioclase (andesine, labradorite, 
bytownite) and minor pyroxene, olivine, and 







Antarctic Continent 


97 


iron-titanium oxides (ilmenite, magnetite). Prote¬ 
rozoic anorthosite forms large massifs associated 
with granitoids (North America, Scandinavia). 
Archean coarse-grained (megacrystic) anortho¬ 
site occurs in intrusions (dikes and sills) and 
flows of basaltic composition. 

Anorthosite is a common constituent of the 
lighter surfaces of the Moon called lunar high¬ 
lands or terrae. Formation of anorthosite requires 
the concentration of plagioclase from mafic 
magma by flotation in a magma ocean (as is pro¬ 
posed to have occurred on the Moon), ascent of 
plagioclase-rich mushes, or low-pressure crystal¬ 
lization in magma chambers. 

See Also 

► KREEP 

► Mafic and Felsic 

► Moon, The 


Anoxic 

Ricardo Amils 

Departamento de Biologia Molecular, 
Universidad Autonoma de Madrid, 

Madrid, Spain 

Definition 

Anoxic is a term used to describe a condition, 
environment, or habitat depleted of oxygen. 

See Also 

► Anaerobe 


Anoxic Ocean 

► Sulfidic Oceans 


Anoxygenic Photosynthesis 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 


Synonyms 

Anaerobic photosynthesis 


Definition 

Anoxygenic ► photosynthesis is a bacterial 
photosynthesis that occurs under anaerobic 
conditions, using the photo synthetic electron 
transport chain in a noncyclic mode and 
reduced inorganic electron donors, such as 
hydrogen sulfide, hydrogen, or ferrous ion, as 
► electron donors. There are also cases of 
anaerobic photosynthetic electron transport 
chains acting cyclically; in this case, the 
generation of reducing power is not needed or 
it is decoupled from the photo synthetic 
reaction. The prototypical noncyclic 
anoxygenic photosynthesis is present in green 
bacteria. 


See Also 

► Electron Donor 

► Photosynthesis 

► Photosynthesis, Oxygenic 


Antarctic Continent 

► Antarctica 







98 


Antarctica 


Antarctica 

Daniele L. Pinti 

GEOTOP Research Center for Geochemistry and 
Geodynamics, Universite du Quebec a Montreal, 
Montreal, QC, Canada 

Keywords 

Glaciation; Ice sheets; Mars natural analog; 
Weathering 

Synonyms 

Antarctic continent 

Definition 

Antarctica is the ice-covered continent located in 
the Southern Hemisphere of the Earth. It is situ¬ 
ated almost entirely south of the Antarctic Circle 
and is surrounded by the Southern Ocean. 

Overview 

Antarctica, the coldest and driest continent on 
Earth, is technically considered a desert, with 
only 200 mm per year of average precipitation. 
Antarctica also recorded the coldest temperature 
on Earth measured so far, of —89.2 °C at Vostok 
station. Ninety-eight percent of Antarctica’s 
14 million km 2 surface area is covered by a 
1.6 km thick ice sheet, corresponding to 90 % of 
the world’s ice. It has been covered by ice for the 
past 15 Ma. About 400 subglacial lakes lie at the 
base of the continental ice sheet, the best known 
being Lake Vostok. Lake Vostok has remained 
isolated for 14 million years, making it a valuable 
analog for exploring deep biosphere niches. 

Antarctica ice surface shares similarities with 
those of ► Jupiter’s moon ► Europa and ► Mars. 
Antarctica has been for long time a privileged 
natural analog terrain for studying morphological 
processes shaping the Mars surface or for testing 
instrumentation and field exploration procedures 
for future manned Mars missions. Particularly, 


ice-free Antarctica McMurdo Dry Valleys reflect 
surface conditions similar to those of the Mars 
surface. Dry Valleys are located mainly in the 
Victoria Land west of McMurdo Sound. Dry val¬ 
leys are so named because of their extremely low 
humidity and their lack of snow and ice cover. 
Their surfaces are covered by loose gravel and 
show ice-wedge polygonal-patterned ground. 
Polygonal-patterned ground is a geometric land- 
form with characteristic honeycomb patterns 
surrounded by ice crests that develop in periglacial 
regions which experience intense freezing and 
thawing cycles. High Resolution Imaging Science 
Experiment (HiRISE) camera on NASA’s ► Mars 
Reconnaissance Orbiter have clearly shown the 
same patterns on high latitudes of Mars and at 
the bottom of some Mars crater. Antarctica Dry 
Valleys and Mars mid-latitudes soil formation his¬ 
tories shares similarities, particularly involving 
slow processes of sublimation and poleward 
migration of water (Wentworth et al., 2005). 

Antartica permafrost hard surfaces are 
privileged site of several Mars analog missions, 
because the soils share physical similarities with 
that of Mars. One of the most recent 
missions took place in the Marambio Island, 
Western Antarctic Peninsula, where field explo¬ 
ration, sample collection, instrument deploy¬ 
ment, and spacesuit testing were carried out on 
a Mars-like rocky, permafrost-rich landscape 
(Rask et al., 2012). 

See Also 

► Europa 

► Mars Analogue sites 

► Vostok, Subglacial Lake 

References and Further Reading 

Rask JC, De Leon P, Marinova MM, McKay CP 
(2012) The exploration of Marambio Antarctica as a 
Mars analog. 43rd Lunar and Planetary Science Con¬ 
ference Abstract, 2455 

Wentworth SJ, Gibson EK, Velbel MA, McKay DS 
(2005) Antarctic Dry Valleys and indigenous 
weathering in Mars meteorites: implications for 
water and life on Mars. Icarus 174:383-395 




Anticodon 


99 


Antibiotic 

Ricardo Amils 

Departamento de Biologia Molecular, 
Universidad Autonoma de Madrid, 
Madrid, Spain 


Synonyms 

Antimicrobial agent; Functional inhibitor 


Definition 

Antibiotics are chemical substances produced 
by a wide range of microorganisms, among 
them fungi and bacteria, that kill or 
inhibit the growth of other organisms. A large 
number of antibiotics have been identified in 
nature, most of them as products of secondary 
metabolism. Antibiotic producers must be 
resistant to the active form of the 
antibiotic. Important targets of antibiotics are 
the synthesis of ► cell membrane and 

► cell wall, replication, ► transcription, and 

► translation. Antibiotics are considered 
regulators of microbial populations rather 
than part of microbial warfare. The susceptibility 
of organisms to individual antibiotics or 
other chemotherapeutic agents varies signifi¬ 
cantly and is the base of their 
pharmacological use. 


See Also 

► Cell Membrane 

► Cell Wall 

► Replication (Genetics) 

► Ribosome 

► Sporulation 

► Transcription 

► Translation 


Antibody 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 

Definition 

Antibody is a complex ► protein 
(immunoglobulin) produced as a response to a 
chemical agent (antigen) as a part of a defensive 
system (immune system) in multicellular ani¬ 
mals. The combination of antibody and antigen 
is specific (albeit not necessarily absolute), 
non-covalent, and reversible. There are many 
methodological applications of antibodies, 
either as a heterogeneous population of immuno¬ 
globulins (polyclonal antibodies) or as a homo¬ 
geneous preparation (monoclonal antibodies). 
Antibodies show a broad applicability in biotech¬ 
nology, including the development of affinity 
biosensors. 


See Also 

► Biosensor 

► Protein 


Anticodon 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, 

Valencia, Spain 


Definition 

Anticodon is a triplet of nucleotides in a tRNA, 
complementary to a codon in the mRNA. 






100 


Antimicrobial Agent 


See Also 

► Codon 

► Genetic Code 

► RNA 

► Translation 

► Wobble Hypothesis (Genetics) 


Antimicrobial Agent 

► Antibiotic 


AOGCM 

John Lee Grenfell 

German Aerospace Center (DLR), Berlin, 
Germany 


Synonyms 

Atmosphere-ocean general circulation model 


Definition 

An AOGCM refers to a 3D numerical model 
which solves the central conservation equations, 
e.g., mass, momentum, and energy, to derive the 
characteristic global-scale fluid dynamical flow 
(the “general circulation”) as well as temperature 
of a planetary atmosphere and ocean. The atmo¬ 
sphere and ocean modules are coupled via surface 
exchange fluxes of energy (e.g., via evaporation 
and condensation) and momentum (e.g., via wind 
stresses at the ocean surface). 


See Also 

► GCM 


Apex Basalt, Australia 

Nicholas Amdt 

ISTerre, Universite Grenoble Alpes, France 

Definition 

The Apex Basalt is a ca. 3.46-Ga-old formation 
comprising tholeiitic pillow basalts, komatiitic 
basalts, and komatiites intercalated with thin 
chert layers. It is located near Marble Bar in the 

► Pilbara Craton of Western Australia. ► Micro¬ 
fossils, morphological biomarkers, and filamen¬ 
tous carbon structures in the lower chert beds 
have been interpreted as fossil prokaryotes 
(mainly cyanobacteria but also thermophiles) 
and are claimed to represent the oldest fossil 
record of life on Earth. For this reason, outcrops 
of this formation are considered one of the most 
important astrobiological sites on Earth. 

See Also 

► Apex Chert 

► Apex Chert, Microfossils 

► Mars Analogue Sites 

► Microfossils 

► Pilbara Craton 


Apex Chert 

Tanja Elsa Zegers 

Paleomagnetic Laboratory, Institute of Earth 
Sciences, Utrecht University, Utrecht, CD, 
The Netherlands 


Definition 

The 3.465 Ga Apex Chert is a chert unit within 
the Apex Basalt in the Warrawoona Group, 
which is part of the oldest greenstone sequence 
in the Pilbara granite-greenstone terrain. The 
Apex Basalt is stratigraphically below the 







Apex Chert, Microfossils 


101 


Strelley Pool Chert, a unit known for hosting the 
oldest ► stromatolite on Earth. In the Apex Chert, 
small carbonaceous filaments with 5 13 C as low as 
—22.5 to — 25%o were reported to represent evi¬ 
dence for ► cyanobacteria able to recycle inor¬ 
ganic carbon through ► RubisCO. The Apex 
Chert microfossils occur in rounded grains of micro¬ 
crystalline silica, which have been interpreted as 
clasts in a conglomerate deposited in a wave-washed 
beach or a stream mouth, an ideal environment for 
cyanobacteria. Subsequent work suggested that the 
chert was deposited from hydrothermal fluids with a 
temperature higher than 250 °C and that the 
microtextures may result from abiotic processes 
under those temperatures. If biogenic, microfossils 
could represent remains of thermophile 
chemothrophs living close to hydrothermal vents. 

See Also 

► Apex Basalt, Australia 

► Apex Chert, Microfossils 

► Archean Traces of Life 

► Biomarker, Isotopic 

► Biomarkers, Morphological 

► Carbon Isotopes as a Geochemical Tracer 

► Cyanobacteria 

► Pilbara Craton 

► Rubisco 

► Stromatolites 


Apex Chert, Microfossils 

Daniele L. Pinti 1 and Wladyslaw Altermann 2 
1 GEOTOP Research Center for Geochemistry 
and Geodynamics, Universite du Quebec a 
Montreal, Montreal, QC, Canada 
department of Geology, University of Pretoria, 
Pretoria, South Africa 

Keywords 

Apex Chert; Apex Basalt; Biomarkers; 
Cyanobacteria; Microfossils 


Definition 

The Apex Chert is a bedded, microcrystalline 
silica (Si0 2 ) deposit interlayered with ► pillow 
lavas and massive flows of the Apex Basalt For¬ 
mation, ► Pilbara Craton, Western Australia. The 
► basalts were dated at 3,465-3,458 Ma. The 
origin of the chert is disputed, and interpretations 
of primary silica deposition on the ocean floor or 
alternatively secondary, hydrothermal silicifica- 
tion (chertification) of clastic or carbonate sedi¬ 
mentary and volcano-sedimentary rocks rival one 
another. The putative ► microfossils of Apex 
Chert are carbonaceous filaments found in 
ca. 3,465 Ma old chert lenses at the so-called 
Schopf locality, Chinaman Creek near Marble Bar. 

Overview 

The name of the famous “Schopf locality” where 
the microfossils were found, derives from the 
American paleontologist and paleobiologist, 
J. William (Bill) Schopf, who, at this site, 
reported 11 morphological taxa of prokaryotic, 
filamentous, and coccoidal microfossils embed¬ 
ded in chert clasts. At that time, the host rock was 
thought to constitute a sedimentary layer and 
later reinterpreted as sedimentary fill of a hydro- 
thermal vein. The kerogenous (carbonaceous) fil¬ 
aments, up to several tens of micrometers long 
and 1-20 pm wide, show in most cases a typical 
cyanobacteria-like septation and terminal cells of 
varying morphology (Fig. 1). They form single 
cell chains and single coccoids that were 
interpreted as the Earth’s oldest microfossils 
(Schopf 1993). The morphology of the filaments 
and their organic carbon isotopic composition 
(5 13 C) ranging from —22 %o to —26 %o (whole 
rock measurements), and the sedimentary envi¬ 
ronment interpreted as shallow marine, strongly 
suggested that some of these filaments were 
cyanobacteria. The hypothesis of cyanobacterial 
life 3.5 billion years ago implied, for uniformi- 
tarianism, that oxygenic photosynthesis might 
have acted very early in the Earth’s history and 
that life was already well advanced one billion 
years after the Earth formation. Though the 




102 


Apex Chert, Microfossils 



Apex Chert, Microfossils, Fig. 1 Microfossils from the 
early Archean Apex Chert of Australia (From Schopf 
1993). Microfossils (A-J, holotypes) with interpretative 

evidence of microfossils in Apex Chert, as well as 
the paleoenvironmental and depositional condi¬ 
tions, have been later highly debated, the Apex 
Chert and its putative microfossils have greatly 
contributed to a general interest in the origin 
and evolution of life and in many ways toward 
astrobiology, encouraging the search for extrater¬ 
restrial life, the improvement of our understand¬ 
ing of abiotic and biotic, evolutionary and 
taphonomic (processes by which organisms 
become fossilized) processes, and to the develop¬ 
ment of careful investigation methods and defi¬ 
nition of unambiguous biosignatures. 


drawings. All at a magnification as shown in (A), (a-e) 
Primaevifilum amoenum; (f-j) Primaevifilum 
conicoterminatum (with conical terminal cells) 

Geology of the Schopf Locality 

The Apex Chert is a unit within the 4 km thick 
Apex Basalt Formation of the Salgash Subgroup 
of the Warrawoona Group of ► Pilbara Craton, 
Western Australia. The Apex Basalt consists of 
► greenschist facies metamorphosed ► basalts, 
komatiitic basalts, and serpentinized ► perido- 
tites and minor felsic volcaniclastic rocks with 
locally intruded dolerite sills which form part of 
the Marble Bar ► greenstone belt. 

The “Schopf locality” (Schopf and Packer 
1987; Schopf 1993), north of Marble Bar, is 
well known for its chert formations. The Apex 












Apex Chert, Microfossils 


103 


Chert, with an assigned age of 3,465 =b 5 Ma, is a 
bedded unit consisting of up to 10 m thickness of 
white, gray, and black-layered chert, interbedded 
with felsic tuff, which contains sills of massive 
black silica. The bedded deposits overlie a swarm 
of weakly radiating black silica veins that extend 
up to 750 m stratigraphically down into 
metabasalts, but which do not penetrate above 
the bedded chert horizon, cut by an unconformity. 
The veins themselves are composed of several 
phases of intrusive silica that vary in color 
from very dark blue-black, through shades of 
blue-gray, to white. They migrate sidewards 
into the sedimentary layers replacing them 
with silica. The veins comprise dominantly 
massive dark blue-black silica, but can include 
multiple generations of dark gray to black 
silica to white quartz, core zones of felsic 
tuff ► breccia, and phreatomagmatic 
breccias with a jigsaw puzzle fit with exploded 
fragments at their tops (Van Kranendonk and 
Pirajno 2004). The bedded chert of the Schopf 
microfossil locality is the stratigraphically lowest 
of five bedded chert units within the pillowed 
Apex Basalt. 

Microfossils at the Schopf Locality 

The “Schopf locality,” where the microfossils 
were discovered, is controversially within a 
black chert vein radiating from the bedded chert 
unit and is not from the bedded Apex Chert Unit 
itself. However, the fossiliferous specimen 
deposited by Schopf at the Natural History 
Museum, London, shows bedded structure and 
brownish color, implying that they come from 
the bedded part of the section. Microfossils 
were discovered in rounded grains of microcrys¬ 
talline silica, apparently within one of the blue- 
black veins beneath the lowermost of the bedded 
chert units of the Apex Basalt Formation. Schopf 
(1993, 1999) interpreted the grains as clasts of a 
conglomerate deposited in a wave-washed beach 
or a stream mouth, an ideal environment for 
cyanobacteria. Fragments of stromatolites pro¬ 
vide evidence that at least part of the clasts is of 
sedimentary origin. Schopf (1993) observed hun¬ 
dreds of filaments, tens of micrometers long and 
1-20 pm wide, some of them showing a septate 


division that morphologically resembled 
cyanobacteria (Fig. 1). Next to the filaments, 
hundreds of solitary unicell-like spheroidal struc¬ 
tures resembling coccoidal microfossils were 
identified. Based on morphology, Schopf and 
Packer (1987) and Schopf (1992, 1993, 2006) 
recognized 11 morphotypes of putative microfos¬ 
sils in the Apex Chert, as listed below: 

1. Narrow unbranched septate prokaryotic fila¬ 
ments incertae sedis cf. bacteria? 
(Archaeotrichion septatum) 

2. Narrow unbranched septate prokaryotic fila¬ 
ments incertae sedis cf. bacteria? 
(Eoleptonema apex) 

3. Narrow unbranched septate prokaryotic fila¬ 
ments incertae sedis cf. bacteria? or 
cyanobacteria? ( Primaevijilum minutum) 

4. Narrow unbranched septate prokaryotic fila¬ 
ments incertae sedis cf. bacteria? or 
cyanobacteria? ( Primaevijilum delicatulum) 

5. Intermediate-diameter unbranched septate 
prokaryotic filaments incertae sedis 
cf. cyanobacteria? ( Primaevijilum amoenum) 

6. Intermediate-diameter unbranched septate 
prokaryotic filaments having disk-shaped 
medial cells incertae sedis 
cf. cyanobacteria? (, Archaeoscillatoriopsis 
disciformis) 

7. Broad unbranched septate prokaryotic fila¬ 
ments having conical end cells incertae 
sedis cf. cyanobacteria? ( Primaevijilum 
conic oterminatum) 

8. Broad unbranched septate prokaryotic fila¬ 
ments having equant medial cells incertae 
sedis cf. cyanobacteria? ( Primaevijilum 
laticellulosum) 

9. Broad unbranched septate prokaryotic fila¬ 
ments incertae sedis cf. cyanobacteria? 
(Archaeoscillatoriopsis grandis) 

10. Broad unbranched markedly tapering septate 
prokaryotic filaments incertae sedis 
cf. cyanobacteria? (Primaevijilum 
attenuatum) 

11. Broad unbranched septate prokaryotic fila¬ 
ments having hemispheroidal end cells 
incertae sedis cf. cyanobacteria? 
(Archaeoscillatoriopsis maxima) 



104 


Apex Chert, Microfossils 


The Debate 

Remapping of the Marble Bar area including the 
Schopf locality and detailed petrology and min¬ 
eralogy of the Apex Basalt Formation and Apex 
Chert Unit (Brasier et al. 2002, 2005; Van 
Kranendonk and Pirajno 2004) revealed that the 
Apex Chert is largely a breccia infilling one of 
multiple generations of metalliferous hydrother¬ 
mal veins. These veins crosscut pillow basalts 
and feed into, and are continuous with the over- 
lying stratiform-bedded chert unit of the Apex 
Basalt Formation. 

The discussion on the reality of Schopf’s 
(1993) findings was triggered by claims that the 
filaments are branching, unlike prokaryotic fila¬ 
ments, and do not contain carbon. Simulta¬ 
neously, it was claimed that life did not exist on 
Earth prior to ca. 2,500 Ma (Brasier et al. 2002, 
2004). At reexamination, the Apex Chert, how¬ 
ever, was found to contain cellular-preserved 
kerogenous microfossil remains, revealing 
advanced biostratonomic to metamorphic, tapho- 
nomic changes. It was suggested that thermal 
alteration is the cause of taphonomic changes in 
cyanobacterial microfossils, resulting in the pre¬ 
sent form of microfossil preservation in the Apex 
Chert (Kazmierczak and Kremer 2002). The pre¬ 
served morphological variation indicates biolog¬ 
ical behavior and fulfills the requirements for 
microfossil recognition (Buick 1990). Claims of 
branching of the filaments or of incomplete, 
selective photomontages of the microstructures, 
mimicking a biological appearance (Brasier 
et al. 2002, 2004), result from misinterpretation 
of auto-montages of photographs taken at differ¬ 
ent depth of focus and superimposed on each 
other (Fig. 2). However, the lack of assessment 
of the geological context of the Apex microfossil 
assemblage together with the generally poor pres¬ 
ervation due to possible biological, diagenetic, 
and metamorphic degradation cast some doubts 
on the applied taxonomy in some cases 
(Altermann 2005). 

Scanning electron microscopy (SEM) showed 
the presence of metals (Ni, Cu, Zn, Sn), sulfides, 
barite, jarosite, alunite, phyllosilicates, and Fe 
oxides, suggesting a high-temperature hydrother¬ 
mal environment where microbial life could 


hardly have survived (Brasier et al. 2002), except 
for chemoautolithotroph thermophiles (Brasier 
et al. 2006). Alternatively, an acid-sulfate 
epithermal environment of alteration, syn- or 
post-genetic with the precipitation of the chert, 
has also been suggested (van Kranendonk and 
Pirajno 2004). The abundance of sulfate and 
lack of argilitic alteration indicated depositional 
temperatures up to 350 °C. Recently, Pinti 
et al. (2009) showed that medium-low tempera¬ 
ture weathering processes could explain the min¬ 
eralogy of the Apex Chert so that high- 
temperature hydrothermal fluid-rock interactions 
are not required. Alternatively, the metal rich 
fluids might have passed at a much later time 
through these rocks. 

These observations invigorated the debate on 
the ► biogenicity of the carbonaceous filaments 
and their putative inclusion in the phylum 
cyanobacteria. Laser-Raman imagery of carbona¬ 
ceous filaments (Schopf et al. 2002,2007; Brasier 
et al. 2002) and disseminated carbonaceous 
(kerogenous) matter in the Apex Chert 
(De Gregorio and Sharp 2006) gave controversial 
results. Schopf et al. (2002) interpreted the car¬ 
bon as of biological origin. Brasier et al. (2002) 
proposed that it rather could be amorphous car¬ 
bon reorganized in the form of filamentous 
strains after devitrification processes of the chert 
veins. De Gregorio and Sharp (2006) suggested 
that the carbonaceous material is similar in struc¬ 
ture to microfossil kerogen, but may also be pro¬ 
duced abiotically via Fischer-Tropsch-type 
(FTT) synthesis reactions, in an ancient hydro- 
thermal vent. However, it has never been con¬ 
firmed that the FTT process can produce 
particulate carbon. Three-dimensional confocal 
laser microscopy and Raman imagery demon¬ 
strated that the structures are indeed cellular- 
made filaments and coccoids (Schopf and 
Kudryavtsev 2005). 

The carbon isotopic composition is also contro¬ 
versial. The in situ, on single microfossils, mea¬ 
sured 5 13 C values from —27 %o to —34 %o could 
be related to photosynthesis (5 13 C = —25 %o ± 
10 %o; Schopf 2006), methanogenesis (Brasier 
et al. 2002), or abiotic FTT reactions (e.g., 
McCollom and Seewald 2006). 



Apex Chert, Microfossils 


105 


§ 


0 



* 




* 


l^jm 



* 


\ 



Apex Chert, Microfossils, Fig. 2 The same specimen of 
Archaeoscillatoriopsis disciformis filament photographed 
from the original material deposited by Schopf at the 
Natural History Museum, London. Upper left , as depicted 
by Schopf (1993), and upper right, as shown by Brasier 
et al. (2002): the difference created the impression that 
Schopf (1993) has manipulated the microphotographs in 
reality showing a branching and therefore impossibly 
cyanobacterial filament. The following lower micro¬ 
graphs show the same filament at different depth of 

Buick (1984) suggested that carbonaceous fil¬ 
aments in the silica swarm dykes of the North 
Pole and Marble Bar, including Apex Chert, were 
contaminants introduced in the microfracturing 
of the silica veins during the tectonic uplift of the 
region, 2.75 Ga ago. Pinti et al. (2009) observed 
branched microstructures suggesting post- 
depositional colonization of microcracks and fis¬ 
sures by microbes. However, Schopf’s 
kerogenous microfossils are embedded in pri¬ 
mary chert, in clasts deposited within the Apex 


focus within the several tens of pm thick petrographic 
thin section (from left to right and downwards). It 
becomes clear that Schopf (1993) has shown only one 
filament located closer to the surface of the section, 
while Brasier et al. (2002) have shown a sandwich photo¬ 
graph, including all depth of focus and exhibiting two 
filaments coincidentally superimposed one above the 
other within the thickness of the section (Photograph by 
W. Altermann in M. in Brasier’s lab 2003) 

Chert dyke or beds. Some clasts contain stromat- 
olitic laminae and relict carbonate minerals and 
therefore must have been silicified during early 
diagenesis at their source of origin (Fig. 3). The 
hydrothermal chert distinctly differs from these 
clasts. However, in some places, hydrothermal 
recrystallization strongly affects the clasts and 
they become almost non-discemible from the 
hydrothermal chert matrix. The clasts are thus 
clearly older than the hydrothermal dike 
(Altermann and Kazmierczak 2003; Altermann 



106 


Apex Chert, Microfossils 



Apex Chert, Microfossils, Fig. 3 Stromatolitic clast 
within the microfossiliferus samples deposited by Schopf 
at the Natural History Museum, London, exhibiting 
microbial lamination, pyrite grains, and dark organic 


matter. The clast is cut by two parallel silica veinlets 
with pyrite enrichment (Photograph by W. Altermann in 
M. Brasier’s lab, 2003) 


2007). The Apex Chert seems to have been 
affected by several hydrothermal and supergene 
episodes of weathering, suggesting that it is 
unlikely to have preserved any early forms of life. 
Nevertheless, it contains stromatolitic clasts, and 
stromatolites are known within this stratigraphic 
succession. Moreover, even older microfossils 
and stromatolites were described from equally 
metamorphosed and altered shallow marine and 
hydrothermal environments of the underlying 
Dresser Formation (3,490 Ma) (Awramik 
et al. 1983; Ueno et al. 2001; Allwood et al. 2006). 

Whether the carbonaceous filaments of 
J. William Schopf are genuine ancient fossilized 
prokaryotes (Schopf 1993; Altermann 2005), 
later biological contamination (Pinti et al. 
2009), or abiotic products (Brasier et al. 2005), 
this rock is still the most fascinating challenge in 
Archean paleobiology and astrobiology. The critical 
point in views opposing the microfossil interpreta¬ 
tion is that most of these investigations were not 
made on the original specimen described by Schopf 
1993 and deposited in the Natural History Museum, 
London, but on rocks collected years later, in the 
same outcrops but not exactly the same location. In 
recent discussions, Schopf has reinforced his argu¬ 
ments for microfossils, introducing new data and 
new investigation techniques (Schopf and 
Kudryavtsev 2012; 2013, Pinti et al. 2013). 


Applications 

Most of all the techniques developed for deter¬ 
mining the biogenicity and syngenicity of 
Archean traces of life have been tested on Apex 
Chert (e.g., De Gregorio and Sharp 2006), and 
several among them were specifically 
developed to resolve the dilemma of the Schopf 
microfossils (e.g., Schopf et al. 2002, 2005). 
This rock represents thus the best challenge 
for determining the reality of very ancient 
traces of life and developing successful method¬ 
ologies and strategies of search for 
extraterrestrial life. 


Future Directions 

The uniqueness of these microfossils constrains 
the use of destructive methods for determining 
the environmental context of deposition of this 
chert unit and the reality of these microfossils. 
New nondestructive techniques such as 
NanoSIMS imagery of microfossils (Oehler 
et al. 2009) or a combination of analytical tech¬ 
niques could be useful for determining whether 
the chemical structure of such putative microfos¬ 
sils is consistent with a biological origin 
(Derenne et al. 2008). 







Apex Chert, Microfossils 


107 


See Also 

► Apex Basalt, Australia 

► Apex Chert 

► Archean Traces of Life 

► Biogenicity 

► Biomarkers 

► Biomarker, Isotopic 

► Biomarkers, Morphological 

► Cyanobacteria, Diversity and Evolution of 

► Dubiofossil 

► Earth, Formation and Early Evolution 

► Microfossils 

► Microfossils, Analytical Techniques 

► Pilbara Craton 

► Pseudofossil 

► Syngenicity 


References and Further Reading 

Allwood AC, Walter MR, Kamber BS, Marshall CP, 
Burch IW (2006) Stromatolite reef from the 
Early Archaean era of Australia. Nature 
44 1:714-718. doi: 10.103 8/nature04764 
Altermann W (2005) The 3.5 Ga Apex fossil 
assemblage - consequences of an enduring discussion. 
In: 14th international conference on the origin of life, 
ISSOL’05, Beijing, pp 136-137 
Altermann W (2007) The early Earth’s record of enig¬ 
matic cyanobacteria and supposed extremophilic bac¬ 
teria at 3.8 to 2.5 Ga. In: Seckbach J (ed) Algae and 
cyanobacteria in extreme environments. Cellular ori¬ 
gin, life in extreme habitats and astrobiology (COLE) 
11. Springer, Berlin, pp 759-778 
Altermann W, Kazmierczak J (2003) Archean microfos¬ 
sils: a reappraisal of early life on Earth. Res Microbiol 
154:611-617 

Awramik SM, Schopf JW, Walter MR (1983) Filamentous 
fossil bacteria from the Archean of Western Australia. 
Precambrian Res 20:357-374 
Brasier MD, Green OR, Jephcoat AP, Kleppe AK, Van 
Kranendonk MJ, Lindsay JF, Steele A, Grassineau NV 
(2002) Questioning the evidence for Earth’s oldest 
fossils. Nature 416:76-81 

Brasier M, Green O, Lindsay J, Steele A (2004) Earth’s 
oldest (similar to 3.5 Ga) fossils and the “Early Eden 
hypothesis” questioning the evidence. Orig Life 
Evol Biosph 34:257-269 

Brasier M, Green O, Lindsay J, Mcloughlin N, Steele A, 
Stoakes C (2005) Critical testing of Earth’s oldest 
putative fossil assemblage from the ~3.5 Ga Apex 
chert, Chinaman Creek, Western Australia. Precam¬ 
brian Res 140:55-102 


Brasier M, Mcloughlin N, Green O, Wacey D (2006) 
A fresh look at the fossil evidence for early Archaean 
cellular life. Philos Trans R Soc B 361:887-902 
Buick R (1984) Carbonaceous filaments from North Pole 
Western Australia: are they fossil bacteria in Archaean 
stromatolites? Precambrian Res 24:157-172 
Buick R (1990) Microfossil recognition in archean rocks: 
an appraisal of spheroids and filaments from a 3500 
M.Y. Old Chert-Barite Unit at North Pole, Western 
Australia. Palaios 5:441^159 
De Gregorio BT, Sharp TG (2006) The structure and 
distribution of carbon in 3.5 Ga Apex chert: implica¬ 
tions for the biogenicity of earth’s oldest putative 
microfossils. Am Mineral 91:784-789 
Derenne S, Robert F, Skrzypczak-Bonduelle A, 
Gourier D, Binet L, Rouzaud J-N (2008) Molecular 
evidence for life in the 3.5 billion year old 
Warrawoona chert. Earth Planet Sci Lett 272:476-480 
Kazmierczak J, Kremer B (2002) Thermal alteration of the 
Earth’s oldest fossils. Nature 420:447-478 
McCollom T, Seewald J (2006) Carbon isotope composi¬ 
tion of organic compounds produced by abiotic syn¬ 
thesis under hydrothermal conditions. Earth Planet Sci 
Lett 243:74-84 

Oehler DZ, Robert F, Walter MR, Sugitani K, All wood A, 
Meibom A, Mostefaoui S, Selo M, Thomen A, Gibson 
EK (2009) NanoSIMS: insights to biogenicity and 
syngeneity of Archaean carbonaceous structures. Pre¬ 
cambrian Res 173:70-78 

Pinti DL, Mineau R, Clement V (2009) Hydrothermal alter¬ 
ation and microfossil artefacts of the 3, 465-million- 
year-old Apex chert. Nat Geosci 2:640-643 
Pinti DL, Mineau R, Clement V (2013) Comment on 
“Biogenicity of Earth’s earliest fossils: a resolution of 
the controversy”. Gondwana Research 23:1652-1653 
Schopf JW (1992) Paleobiology of the Archean. In: 
Schopf JW, Klein C (eds) The Proterozoic biosphere. 
Cambridge University Press, New York, pp 25-39 
Schopf JW (1993) Microfossils of the early Archean apex 
chert: new evidence of the antiquity of life. Science 
260:640-646 

Schopf JW (1999) The cradle of life. Princeton University 
Press, New York 

Schopf WJ (2006) Fossil evidence of Archaean life. Phil 
Trans R Soc B 361:869-885 

Schopf JW, Kudryavtsev AB (2005) Three-dimensional 
Raman imagery of Precambrian microscopic organ¬ 
isms. Geobiology 3:1-12 

Schopf JW, Kudryavtsev AB (2012) Biogenicity of 
Earth’s earliest fossils: a resolution of the controversy. 
Gondwana Res 22:761-771 

Schopf JW, Kudryavtsev AB (2005) Reply to the com¬ 
ments of D.L. Pinti, R. Mineau and V. Clement, and 
A.O. Marshall and C.P. Marshall on “Biogenicity of 
Earth’s earliest fossils: a resolution of the controversy” 
Gondwana Research 23:1656-1658 
Schopf JW, Kudryavtsev AB (2013) Reply to the com¬ 
ments of D.L. Pinti, R. Mineau and V. Clement, and 
A.O. Marshall and C.P. Marshall on “Biogenicity of 



108 


Aphelion 


Earth’s earliest fossils: a resolution of the contro¬ 
versy”. Gondwana Res 23:1656-1658 
Schopf JW, Packer BM (1987) Early Archean (3.3- billion 
to 3.5-billion-year-old) microfossils from 

Warrawoona Group, Australia. Science 237:70-73 
Schopf JW, Kudryavtsev AB, Agresti DG, Wdowiak TJ, 
Czaja AD (2002) Laser-Raman imagery of Earth’s 
earliest fossils. Nature 416:73-76 
Schopf JW, Kudryavtsev AB, Agresti DG, Czaja AD, 
Wdowiak TJ (2005) Raman imagery: a new approach 
to assess the geochemical maturity and biogenicity of 
permineralized Precambrian fossils. Astrobiology 
5:333-371 

Schopf JW, Kudryavtsev AB, Czaja AD, Tripathi AB 
(2007) Evidence of Archean life: stromatolites and 
microfossils. Precambrian Res 158:141-155 
Ueno Y, Maruyama S, Isozaki Y, Yurimoto H (2001) 
Early Archean (ca. 3.5 Ga) microfossils and 13 C- 
-depleted carbonaceous matter in the North Pole area, 
Western Australia. In: Nakashima S, Maruyama S, 
Brack A, Windley BF (eds) Field occurrence 
and geochemistry, in geochemistry and the 
origin of life. Universal Academic Press, Tokyo, 
pp 203-236 

Van Kranendonk MJ, Pirajno F (2004) Geochemistry of 
metabasalts and hydrothermal alteration zones associ¬ 
ated with c. 3.45 Ga chert and barite deposits. Impli¬ 
cations for the geological setting of the Warrawoona 
Group, Pilbara Craton, Australia. Geochem Explor 
Environ Anal 4:253-278 


Aphelion 

Daniel Rouan 

LESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 


Definition 

The aphelion is the point on a body’s orbit around 
the Sun (planets, comets, asteroids) where the 
body is farthest from the Sun. 


See Also 

► Keplerian Orbits 

► Orbit 

► Periastron 


Apolar Molecule 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 


Synonyms 

Nonpolar molecule 

Definition 

In interstellar chemistry, apolar molecules are 
molecules lacking a permanent electric dipole 
moment. The lack of a dipole moment results 
from the symmetry of the charge density distri¬ 
bution in the molecule. Such molecules have no 
pure rotational transitions; hence, in the gas 
phase, they must be observed via their vibrational 
or electronic transitions. 


See Also 

► Polar Molecule 


Apollo Asteroid 

Alan W. Harris 

DLR, Institute of Planetary Research, Berlin, 
Germany 


Definition 

An Apollo ► asteroid is a near-Earth asteroid 
with a semimajor axis of more than 1 astronomi¬ 
cal unit (AU) and a perihelion distance of less 
than 1.017 AU (the Earth’s aphelion distance). 
The ► orbit of such an ► asteroid may intersect 
that of the Earth, giving rise to an impact hazard. 
Apollo asteroids are named after the asteroid 






Apollo Mission 


109 


1862 Apollo, which is the first to be discovered 
having these dynamical characteristics. 

See Also 

► Asteroid 

► Near-Earth Objects 

► Orbit 


Apollo Mission 

Gerda Horneck 

DLR German Aerospace Center, Institute of 
Aerospace Medicine, Radiation Biology, 

Koln, Germany 

Keywords 

Biological effects of space; Exposure experi¬ 
ments; Human space flight; Lunar missions 

Synonyms 

NASA lunar landing mission 

Definition 

The Apollo missions were the heart of NASA’s 
manned Lunar Landing Program that took place 
between 1969 and 1972 with 6 successful land¬ 
ings of 12 astronauts on the Moon. 


History 

On July 20,1969, the astronauts N. A. Armstrong 
and E. E. Aldrin were the first humans to set foot 
on the Moon. Herewith, NASA had reached the 
ambitious goal of its manned Lunar Landing Pro¬ 
gram. It was made possible by the strong com¬ 
mitment of the United States to manned lunar 


exploration with President J. L. Kennedy’s 
announcement in 1961 of sending an American 
safely to the Moon before the end of the decade 
and at same time the progress in the technical 
capabilities of space transportation. The Apollo 
program ultimately placed 12 men on the lunar 
surface. In 1972, with Apollo 16 and 17, the era of 
human exploration beyond Earth’s orbit was ter¬ 
minated and so far it has not been resumed. 


Overview 

The Apollo missions to the Moon were 
performed between 1968 and 1972 (Table 1). 

The Apollo missions were the first and so far 
only human space missions beyond Earth’s orbit. 
They provided in-depth knowledge of the geol¬ 
ogy of the Moon (Schaber 2005) and biomedical 
data on human health issues during space flight 
(Johnston et al. 1975). Biological responses to the 
parameters of outer space were studied in the 
following experiments: 

• ► Biostack experiments on board of the 
Apollo 16 and 17 Command Module on the 
responses of a variety of biological systems in 
resting state to the heavy ion component of 
cosmic rays (Biicker and Homeck 1975) 

• ALFMED experiment during the Apollo 

16 and 17 mission that demonstrated that the 
light flash phenomenon observed by the crew 
members after dark adaptation was attributed 
to the passage of cosmic ray ions through the 
retina of the eye (Johnston et al. 1975; Benton 
et al. 1977) 

• BIOCORE experiment during the Apollo 

17 mission that studied brain effects in pocket 
mice caused by the passage of single heavy 
ions (► HZE particles) of cosmic radiation 
(Klein 1981) 

• MEED during the Apollo 16 mission that stud¬ 
ied the effects of space vacuum and solar UV 
radiation on different functions of microor¬ 
ganisms (Taylor 1974) 

The radiobiological experiments performed 
during the Apollo missions are the only ones 




110 


Apollo Mission 


Apollo Mission, Table 1 Summary of human flights in the Apollo program to the Moon 


Apollo 

mission 

Mission description 

Launch date 
day/month/year 

Stay lunar 
surface (h) 

Astronauts 

7 

Earth orbit test 

11/9/68 


Schirra, 

Cunningham, 

Eisele 

8 

Circumlunar flight 

21/12/68 

- 

Borman, 

Lovell, Anders 

9 

Earth orbit test of LM 

3/3/69 

- 

McDivitt, Scott, 
Schweickert 

10 

Circumlunar flight, LM separation 

18/5/69 

- 

Stafford, 

Cernan, Young 

11 

Lunar landing, sample return 

16/7/69 

22.2 

Armstrong, 
Collins, Aldrin 

12 

Lunar landing, surface experiment package 

14/11/69 

31.5 

Conrad, 

Gordon, Bean 

13 

Lunar landing aborted 

11/4/70 

- 

Lovell, Swigert, 
Haise 

14 

Lunar landing, highland exploration 

31/1/71 

33.5 

Shepard, 

Roosa, Mitchell 

15 

Lunar landing and rover, geological sampling 

26/7/71 

67 

Scott, Worden, 
Irwin 

16 

Lunar landing and rover, geological sampling, 
Biostack and MEED experiments 

16/4/72 

71 

Young, 

Mattingly, 

Duke 

17 

Lunar landing and exploration of the Moon’s 
geology and history, Biostack experiments 

7/12/72 

75 

Cernan, Evans, 
Schmitt 


LM lunar module 


that studied the biological effects of the complete 
interplanetary radiation field, not attenuated by 
the Earth’s magnetic field. 

See Also 

► Biostack 

► Cosmic Rays in the Heliosphere 

► HZE Particle 

► MEED 

► Microorganism 

► Moon, The 

► Radiation Biology 

► Solar UV Radiation, Biological Effects 

► Space Vacuum Effects 

References and Further Reading 

Benton EV, Henke RP, Peterson DD (1977) Plastic 
nuclear track detector measurements of high-LET 


particle radiation on Apollo, Skylab, and ASTP space 
missions. Nucl Track Detect 1:27-32 

Biicker H, Horneck G (1975) The biological 
effectiveness of HZE-particles of cosmic 
radiation studied in the Apollo 
16 and 17 Biostack experiments. Acta Astronaut 
2:247-264 

Golombeka MP, McSween HY Jr (2007) Mars: landing 
site geology, mineralogy and geochemistry. In: 
McFadden L-A, Weissman PR, Johnson TV (eds) 
Encyclopedia of the solar system, 2nd edn. Elsevier, 
Amsterdam, pp 331-348 

Johnston RS, Dietlein F, Berry CA (eds) (1975) Biomedi¬ 
cal results of Apollo. NASA SP-368. NASA, Wash¬ 
ington, DC 

Klein HP (1981) U.S. biological experiments in space. 
Acta Astronaut 8:927-938 

Schaber GG (2005) The U.S. geological survey, 
branch of astrogeology - a chronology of 
activities from conception through the end of project 
Apollo (1960-1973). U.S. Department of the Interior 
U.S. Geological Survey, Open-File Report 

2005-1190. http://www.legislative.nasa.gov/alsj/ 
Schaber.html 

Taylor G (1974) Space microbiology. Annu Rev 
Microbiol 28:121-137 




















Apsidal Angle 


111 


(99942) Apophis 

► Apophis Asteroid 


Apophis Asteroid 

Gerhard Hahn 

Asteroids and Comets, DLR, Institute of 
Planetary Research, Berlin, Germany 

Synonyms 

(99942) Apophis 

Definition 

(99942) Apophis is an Aten-type asteroid, which 
will make a very close approach to our planet on 
April 13, 2029, passing within less than 
40,000 km, close to the ring of geostationary 
satellites. Its size is about 375 m and its rotation 
period 30.6 h. This close approach will change 
the orbit substantially, from Aten type to Apollo. 

History 

Apophis was discovered on June 19, 2004 by 
R. A. Tucker, D. J. Tholen, and F. Bernardi at 
Kitt Peak. It was temporarily lost and 
rediscovered in December 2004. Shortly thereaf¬ 
ter, the close approach in 2029 was realized; even 
a collision at that time was possible. This has 
been ruled out based on extensive observations, 
including radar; the orbital evolution after 2029 is 
still uncertain allowing an impact probability of 
5.7 x 10 -6 (see impact monitoring sites at JPL 
and the University of Pisa). 

See Also 

► Near-Earth Objects 


References and Further Readings 

Famochia D, Chesley SR, Chodas PW, Micheli M, Tholen 
DJ, Milani A, Elliott GT, Bemardi F (2014) 
Yarkovsky-driven impact risk analysis for asteroid 
(99942) Apophis. Icarus 224:192-200 
JPL NEO Program Site Risk Page, http://neo.jpl.nasa.gov/ 
risk/. Last accessed 5 May 2014 
NEODyS Risk Page, http://newton.dm.unipi.it/neodys/ 
index.php?pc=4.0. Last accessed 5 May 2014 
Sansaturio ME, Arratia O (2008) Apophis, the 
story behind the scenes. Earth Moon Planet 
102:425-434 


Apparent Motion 

► Proper Motion 


Apsidal Angle 

Rory Bames 

Astronomy Department, University of 
Washington, Seattle, WA, USA 


Definition 

In planetary dynamics, the apsidal angle is the 
angle between the directions of closest approach 
(the apse) of two planets, as measured from 
the origin of the coordinate system (usually the 
center of the star). This angle may change 
with time and is coupled to the eccentricities 
of the orbits. The apsidal angle may oscillate 
about a fixed value (called apsidal libration) or 
circulate. 


See Also 

► Secular Dynamics 

► Secular Resonance 







112 


Aptamer 


Aptamer 

Carlos Briones 

Centro de Astrobiologia (CSIC/INTA), 

Consejo Superior de Investigaciones Cientificas, 
Madrid, Spain 

Keywords 

Molecular evolution; In vitro evolution; RNA 
world; Combinatorial nucleic acid library; Ribo- 
zyme; Peptide 

Definition 

An aptamer (from the Latin aptus, fit, and Greek 
meros , unit or part) is an in vitro selected 
oligonucleotide or peptide molecule that binds 
to a specific target molecule. Nucleic acid 
aptamers are target-binding DNA or RNA 
molecules obtained by in vitro evolution. 
A peptide aptamer is an individual member of a 
library of random peptide sequences that can be 
selected for its ability to interact with a target 
molecule. 

History 

By the end of the 1980s, the possibility to chem¬ 
ically synthesize nucleic acid pools of random 
sequence, as well as the availability of all the 
required enzymes for nucleic acid amplification, 
allowed the selection of target-binding RNA mol¬ 
ecules from combinatorial nucleic acid libraries. 
The term “aptamer” was coined to denote the 
in vitro evolved, target-binding RNA (Ellington 
and Szostak 1990), while the amplification- 
selection process was termed “systematic evolu¬ 
tion of ligands by exponential enrichment” or 
SELEX (Tuerk and Gold 1990). The RNA 
aptamers selected in those two pioneering exper¬ 
iments were able to specifically bind different 
organic dyes and a viral enzyme - the bacterio¬ 
phage T4 DNA polymerase - respectively. Three 


years later, the first RNA aptamer targeted to a 
small biomolecule was directed at ATP 
(Sassanfar and Szostak 1993). 

Over the last two decades, a growing number 
of RNA and DNA aptamers have been developed 
against a variety of molecular targets, including 
simple ions; small molecules, such as amino 
acids, nucleotides, antibiotics, or metabolites; 
peptides; proteins; nucleic acids; macromolecu- 
lar assemblies; viruses; organelles; or even whole 
cells (Klussmann 2006; Stoltenburg et al. 2007). 
In 2004, the first aptamer-based drug, called 
Pegaptanib , brand name Macugen , was approved 
by the US Food and Drug Administration in 
treatment for age-related macular degeneration 
(Gragoudas et al. 2004). 

In parallel, peptide aptamers were obtained by 
high-throughput selection methods aimed at 
identifying members of a randomized peptide 
library - usually attached at both ends to a given 
protein scaffold - by means of their interaction 
with a target molecule (Colas et al. 1996). Addi¬ 
tionally, a method termed “mRNA display” 
allowed the in vitro selection of peptides and 
proteins with the desired target-binding proper¬ 
ties (Roberts and Szostak 1997). 

Overview 

The preparation of a nucleic acid aptamer is cur¬ 
rently easy and quick, since only 6-15 rounds of 
in vitro selection or evolution are typically 
required, using a combinatorial nucleic acid 
library as the starting material. Moreover, the 
sensitivity and specificity of the molecular recog¬ 
nition between a nucleic acid aptamer and its 
target rival those of the antibody-antigen pairs. 
Additionally, different ways to increase the resis¬ 
tance of aptamers to degradation by nuclease 
enzymes have been reported. These reasons, 
together with their cost-effectiveness, make 
nucleic acid aptamers not only relevant model 
systems to address the RNA world hypothesis 
(Joyce and Orgel 2006) but very useful tools in 
biotechnology with increasing applications in 
biosensing, diagnostics, and therapy (Klussmann 
2006; Mayer 2009; Germer et al. 2013). 




Aptamer 


113 


The outcome of an in vitro evolution process is 
usually monitored at the level of genotype, nucle¬ 
otide sequence of the evolved aptamer, and phe¬ 
notype, secondary/tertiary structure of the 
oligonucleotide, affinity and specificity of the 
aptamer for its target molecule. Although nucleic 
acid aptamers are artificial molecules, 
riboswitches have been considered “natural 
aptamers” embedded in messenger RNAs since 
they act as regulatory elements for gene expres¬ 
sion by directly sensing small effector molecules 
(Zhang et al. 2010). Allosteric ribozymes that 
fuse one aptamer and one nucleic acid enzyme 
have been developed, the ribozyme activity being 
modulated by the binding of an effector molecule 
to the aptamer domain. The biotechnological 
applications of such “aptazymes” - also known 
as artificial riboswitches - are increasingly rec¬ 
ognized (Wieland and Hartig 2008). Recently, 
the unveiled ability of certain nucleic acid ana¬ 
logues to fold into three-dimensional structures 
allowed the in vitro evolution of aptamers har¬ 
boring different molecular scaffolds, some of 
which bind their targets with an affinity similar 
to that of RNA or DNA aptamers (Pinheiro 
et al. 2012). 

In addition to nucleic acid aptamers, the pep¬ 
tide aptamer approach has utilized small inert 
scaffold proteins to expose the randomizable pep¬ 
tide region. Alternatively, the mRNA display 
technique has been used to develop peptide 
aptamers, and “stand-alone” interfering peptides 
have also been selected. The ability of peptide 
aptamers to specifically interact with different 
proteins and other target molecules offers broad 
applicability in biochemistry and biomedicine 
(Mayer 2009; Li et al. 2011). 

See Also 

► Amplification (Genetics) 

► Aptasensor 

► Combinatorial Nucleic Acid Library 

► DNA 

► Evolution, In Vitro 

► Evolution, Molecular 

► Peptide 


► Ribozyme 

► RNA 

► RNA World 

► Selection 

References and Further Reading 

Colas P, Cohen B, lessen T, Grishina I, McCoy J, Brent 
R (1996) Genetic selection of peptide aptamers that 
recognize and inhibit cyclin-dependent kinase 
2. Nature 380:548-550 

Ellington AD, Szostak JW (1990) In vitro selection of 
RNA molecules that bind specific ligands. Nature 
346:818-822 

Germer K, Leonard M, Zhang X (2013) RNA aptamers 
and their therapeutic and diagnostic applications. Int 
J Biochem Mol Biol 4:27^10 
Gragoudas ES, Adamis AP, Cunningham ET Jr, 
Feinsod M, Guyer DR, VEGF Inhibition Study in 
Ocular Neovascularization Clinical Trial 
Group (2004) Pegaptanib for neovascular 
age-related macular degeneration. N Engl J Med 
351:2805-2816 

Joyce GF, Orgel LE (2006) Progress toward understand¬ 
ing the origin of the RNA world. In: Gesteland RF, 
Cech TR, Atkins JF (eds) The RNA world. Cold 
Spring Harbor Laboratory Press, New York 
Klussmann S (ed) (2006) The aptamer handbook. Wiley- 
VCH, Weinheim 

Li J, Tan S, Chen X, Zhang CY, Zhang Y (2011) Peptide 
aptamers with biological and therapeutic applications. 
Curr Med Chem 18:4215-4222 
Mayer G (ed) (2009) Nucleic acid and peptide aptamers. 

Methods and protocols. Springer, Heidelberg 
Pinheiro VB, Taylor Al, Cozens C, Abramov M, 
Renders M, Zhang S, Chaput JC, Wengel J, Peak- 
Chew SY, McLaughlin SH, Herdewijn P, Holliger 
P (2012) Synthetic genetic polymers capable of hered¬ 
ity and evolution. Science 336:341-344 
Roberts RW, Szostak JW (1997) RNA-peptide fusions for 
the in vitro selection of peptides and proteins. Proc 
Natl Acad Sci U S A 94:12297-12302 
Sassanfar M, Szostak JW (1993) An RNA motif that binds 
ATP. Nature 364:550-553 

Stoltenburg R, Reinemann C, Strehlitz B (2007) 
SELEX - a (r)evolutionary method to generate high- 
affinity nucleic acid ligands. Biomol Eng 24:381-403 
Tuerk C, Gold L (1990) Systematic evolution of 
ligands by exponential enrichment: RNA ligands to 
bacteriophage T4 DNA polymerase. Science 
249:505-510 

Wieland M, Hartig JS (2008) Artificial riboswitches: syn¬ 
thetic mRNA-based regulators of gene expression. 
Chembiochem 9:1873-1878 

Zhang J, Lau MW, Ferre-D’Amare AR (2010) Ribozymes 
and riboswitches: modulation of RNA function by 
small molecules. Biochemistry 49:9123-9131 



114 


Aptamer-Based Biosensor 


Aptamer-Based Biosensor 

► Aptasensor 


Aptasensor 

Miguel Moreno 

Centro de Astrobiologia, CSIC, Madrid, Spain 

Keywords 

Aptamer; Biosensor; DNA; RNA 

Synonyms 

Aptamer-based biosensor 

Definition 

An aptasensor is a particular class of biosensor 
where the biological recognition element is a 
DNA or RNA aptamer. In an aptasensor, the 
aptamer recognizes the molecular target against 
which it was previously in vitro selected. The 
aptamer-target reaction is independent of both 
the type of detection system and the kind of 
transducer employed. Aptasensors can be easily 
multiplexed to detect a variety of aptamer-target 
reactions simultaneously. 

History 

Since the development of the first glucose bio¬ 
sensor in 1962 (Clark and Lions 1962), an exten¬ 
sive choice of biosensors has been developed. 
Among them, nucleic acid-based biosensors are 
of particular interest due to their practical appli¬ 
cations in different fields of genomic research. In 
1990 two independent groups simultaneously 
described aptamers as target-binding nucleic 


acid molecules (Tuerk and Gold 1990; Ellington 
and Szostak 1990). Adapting both technologies, 
aptamers-based biosensors were established in 
1996 when Drolet and coworkers (Drolet 
et al. 1996) described a modification of the 
renowned enzyme-linked immunosorbent assay 
(ELISA) which utilized an aptamer instead an 
antibody as biorecognition element. The assay 
was named “enzyme-linked oligonucleotide 
assay” (ELONA), and this evidence opened the 
door to novel ways of biosensing using nucleic 
acids to detect a wide range of molecules in a 
variety of formats. 

Overview 

Aptamers are attracting interest in the areas of 
therapeutics and diagnostics and offer themselves 
as ideal candidates for use as the recognition 
elements in biosensors since they possess many 
advantages over the state-of-the-art affinity sen¬ 
sors. Aptasensors show very high sensitivity, 
specificity, and reproducibility against a wide 
variety of targets. Thus, they are rapidly emerg¬ 
ing as promising candidates for high-throughput 
analytical methods that have to deal with tiny 
quantities of the queried analytes. Analogous to 
immunoassays (those based on the antigen- 
antibody interaction), aptamer-based bioassays 
can adopt different configurations to transduce 
biorecognition events, including aptamer-based 
microarrays (Collett et al. 2005), aptamer-capped 
gold nanoparticles (Song et al. 2012), quantum- 
dot aptamer conjugates (Levy et al. 2005), and 
electrical (Willner and Zayats 2007) and electro¬ 
chemical (Moreno et al. 2011) aptasensors, 
among many others (Citartan et al. 2012). 

Aptamers offer an extensive range of advan¬ 
tages over other existing biological recognition 
elements in terms of stability, design flexibility, 
and cost-effectiveness. To name a few, aptamers 
can bind to their targets with affinities and spec¬ 
ificities equivalent to those of monoclonal anti¬ 
bodies and can be selected to bind a wide range of 
targets including those that are toxic or not inher¬ 
ently immunogenic. Additionally, the affinities 





Aqueous Interfaces 


115 


and specificities of aptamers can be easily tai¬ 
lored (in contrast to those of antibodies) and can 
be more readily engineered than antibodies for 
their use as biosensing elements. Finally, 
aptamers can be synthesized, chemically modi¬ 
fied, and stored until needed and are resistant to 
denaturation and degradation. The in-depth 
knowledge of aptamer conformational properties 
and ligand-binding mechanisms has triggered 
profound attention among researchers for devel¬ 
oping aptasensor bioassays, as reflected in the 
exponential increase of published articles 
(Citartan et al. 2012). 

Nevertheless, aptasensors compete with other 
well-established biosensors, essentially 
antibodies-based ones, and they have been 
mainly focused on the applications where anti¬ 
bodies cannot achieve the desired goals. The 
most straightforward application of aptasensors 
lies in the fields of food safety testing and envi¬ 
ronmental pollution control. Thus, aptasensors 
developed for the detection of small molecule 
contaminants including antibiotics, toxins, pesti¬ 
cides, and heavy metals (that may be present in a 
wide variety of food products and environmental 
samples) are of particular interest (Cho 
et al. 2009; Fischer et al. 2007). 

In astrobiology, aptasensors are called to be a 
functional tool for the detection of both mole¬ 
cules with limited antigenicity present in differ¬ 
ent extreme environments and biosignatures of 
extinct or extant life in planetary exploration. In 
the field of biomarker detection in space mis¬ 
sions, robust and very stable aptasensors might 
be developed with extended capabilities to over¬ 
come the extreme conditions of long travel time 
and planetary exploration. 

See Also 

► Antibody 

► Aptamer 

► Biomarkers 

► Biosensor 

► Combinatorial Nucleic Acid Library 

► Evolution, In Vitro 


References and Further Reading 

Cho EJ, Lee J-W, Ellington AD (2009) Applications 
of aptamers as sensors. Annu Rev Anal Chem 
2:241-264 

Citartan M, Gopinath SCB, Tominaga J, Tan S-C, Tang 
T-H (2012) Assays for aptamer-based platforms. 
Biosens Bioelectron 34:1-11 

Clark LC, Lions C (1962) Electrode systems for continu¬ 
ous monitoring in cardiovascular surgery. Ann Acad 
Sci 102:29 

Collett JR, Cho EJ, Ellington AD (2005) Production and 
processing of aptamer microarrays. Methods 37:4-15 

Drolet DW, Moon-McDermott L, Romig TS (1996) An 
enzyme-linked oligonucleotide assay. Nat Biotechnol 
14:1021-1025 

Ellington AD, Szostak JW (1990) In vitro selection of 
RNA molecules that bind specific ligands. Nature 
346:818-822 

Fischer NO, Tarasow TM, Tok JBH (2007) Aptasensors 
for biosecurity applications. Curr Opin Chem Biol 
11:316-328 

Levy M, Cater SF, Ellington AD (2005) Quantum-dot 
aptamer beacons for the detection of proteins. 
Chembiochem 6:2163-2166 

Moreno M, Gonzalez VM, Rincon E, Domingo A, 
Dominguez E (2011) Aptasensor based on the selec¬ 
tive electrodeposition of protein-linked gold 
nanoparticles on screen-printed electrodes. Analyst 
136:1810-1815 

Song K-M, Jeong E, Jeon W, Cho M, Ban C (2012) 
Aptasensor for ampicillin using gold nanoparticle 
based dual fluorescence-colorimetric methods. Anal 
Bioanal Chem 402:2153-2161 

Tuerk C, Gold L (1990) Systematic evolution of 
ligands by exponential enrichment: RNA ligands to 
bacteriophage T4 DNA polymerase. Science 
249:505-510 

Willner I, Zayats M (2007) Electronic aptamer-based sen¬ 
sors. Angew Chem Int Ed 46:6408-6418 


Aqueous Interfaces 

Veronica Vaida and Elizabeth C. Griffith 
University of Colorado, Boulder, CO, USA 


Keywords 

Water surface; Unique reaction environment; 
Amphiphilic molecules; Surfactant film 




116 


Aqueous Interfaces 


Definition 

An aqueous interface is the dividing surface 
between two media, one of which is water. 

History 

Atmospheric interfaces including rocks and clays 
have long been considered in the origin of life 
scenarios. Aqueous interfaces (water surfaces) as 
found on oceans, lakes, rivers, and atmospheric 
aerosols were first suggested by Goldacre (1958) 
to be interesting in a prebiotic context due to their 
ability to concentrate organic molecules and sub¬ 
sequently fold and pinch off into enclosures rem¬ 
iniscent of cells. The use of Global atmospheric 
aerosols were pointed out in this context (Shah 
1972) and suggested as effective prebiotic 
microreactors in different contexts later 
(Lerman 2010; Dobson et al. 2000; Tverdislov 
and Yakovenko 2008). In addition, aqueous inter¬ 
faces have recently been suggested as favorable 
environments for biomolecular synthesis that is 
difficult or impossible in the bulk ocean (Dobson 
et al. 2000; Ruiz-Bermejo et al. 2010; Griffith 
et al. 2012). 


Overview 

Aqueous interfaces are found throughout nature: 
at the surface of lakes and oceans, at the surface 
of atmospheric aerosol particles, or even at the 
interface between a membrane and its surround¬ 
ing bulk water environment. Air-aqueous inter¬ 
faces are particularly interesting in an 
astrobiological context due to their provision of 
a unique reaction environment, having the ability 
to concentrate and align surface active molecules 
(Goldacre 1958; Shah 1972). It was pointed 
out that the vast collective surface area of 
atmospheric aerosols provides diverse and fluc¬ 
tuating environments for chemistry and is appli¬ 
cable to any rotating planetary body with a liquid 
ocean (Dobson et al. 2000; Griffith et al. 2012). 
A planet rotating on a tilted axis results in thermal 
and pressure gradients that produce wind. 
This wind acting on a liquid ocean produces 
sea spray from which aqueous atmospheric aero¬ 
sols are bom (as depicted in the Fig. 1). Any 
organic material residing at or near the ocean 
surface will be entrained in these aerosols and 
can partition to their surface (an aqueous inter¬ 
face), forming a surfactant film around an aque¬ 
ous core. 


Aqueous Interfaces, 

Fig. 1 Depiction of birth 
of aerosols from sea spray 
as well as schematic 
representation of peptide 
bond formation at the 
air-aqueous interface from 
amino acid ( AA ) precursors 













Aquifer (Mars) 


117 


These interfaces allow for concentration of 
reactant species over the bulk aqueous solution, 
alteration of the ionization state of surface- 
residing reactants, and orientation of amphiphilic 
molecules, and they can even promote chemistry 
that is inaccessible in bulk water (Griffith and 
Vaida 2013). One example of a key reaction 
made possible by an aqueous interface is the 
formation of peptide bonds in the absence of 
enzymatic catalysis (Griffith and Vaida 2012) 
illustrated schematically in Fig. 1. Peptide 
bonds are a key bond in modern biology as they 
are the link between amino acid building blocks 
in proteins (one of the three principle biopoly¬ 
mers along with RNA and DNA). In addition, 
theoretical and experimental studies have been 
devised to investigate the interaction and folding 
of bimolecular assemblies at the surface of liquid 
water to model systems of biophysical interest 
(Pratt and Pohorille 2002). 


Cross-References 

► Aerosols 

► Amino Acid 

► Amphiphile 

► Membrane 

► Water, Solvent of Life 

References and Further Reading 

Dobson CM, Ellison GB, Tuck AF, Vaida V (2000) Atmo¬ 
spheric aerosols as prebiotic chemical reactors. Proc 
Natl Acad Sci U S A 97(22): 11864-11868 

Goldacre RJ (1958) Surface films, their collapse on com¬ 
pression, the shape and size of cells and the origin of 
life. In: Danielli JF, Parkhurst KGA, Riddiford AC 
(eds) Surface phenomena in chemistry and biology. 
Pergamon Press, New York, pp 12-27 

Griffith EC, Vaida V (2012) In situ observation of peptide 
bond formation at the water-air interface. Proc Natl 
Acad Sci U S A 109(39): 15697-15701 

Griffith EC, Vaida V (2013) Ionization state of 
L-phenylalanine at the air-water interface. J Am 
Chem Soc 135(2):710-716 

Griffith EC, Tuck AF, Vaida V (2012) Ocean-atmosphere 
interactions in the emergence of complexity in simple 
chemical systems. Acc Chem Res 45(12):2106-2113 

Lerman L (2010) The primordial bubble: water, 
symmetry-breaking, and the origin of life. In: 


Lynden-Bell RM, Morris SC, Barrow JD, Finney JL, 
Harper CL Jr (eds) Water and life: the unique proper¬ 
ties of water. CRC Press, Boca Raton, pp 259-290 
Lynden-Bell RM, Morris SC, Barrow JD, Finney JL, 
Harper CL Jr (eds) (2010) Water and life: the unique 
properties of water. CRC Press, Boca Raton 
Pratt LR, Pohorille A (2002) Hydrophobic effects and 
modeling of biophysical aqueous solution interfaces. 
Chem Rev 102(8):2671-2691 
Ruiz-Bermejo M, Menor-Salvan C, Zorzano MP, 
El-Hachemi Z, Osuna-Esteban S, Veintemillas- 
Verdaguer S (2010) Water interfacial processes in 
prebiotic chemistry. In: Hegedus S, Csonka J (eds) 
Astrobiology: physical origin, biological evolution 
and spatial distribution. Nova Science Publishers 
Inc., New York, pp 27-57 

Shah DO (1972) The origin of membranes and related 
surface phenomena. Exobiology. C. Ponnamperuma. 
North-Holland Publishing Co., Amsterdam, 
pp 235-265 

Tuck A (2002) The role of atmospheric aerosols in the 
origin of life. Surv Geophys 23(5):379-409 
Tverdislov VA, Yakovenko LV (2008) Physical aspects of 
the emergence of living cell precursors: the ion and 
chiral asymmetries as two fundamental asymmetry 
types. Mosc Univ Phys Bull 63(3): 151-163 


Aquifer (Mars) 

Alessandro Airo 

Institut fur Geologische Wissenschaften 
Tektonik und Sedimentare Geologie, Freie 
Universitat Berlin, Fachbereich 
Geowissenschaften, Berlin, Germany 

Definition 

It is widely accepted that liquid water was present 
on the surface of Mars during its early history. 
Although parts of this water have vanished into 
space or were consumed in chemical reactions, 
substantial amounts are still present today. The 
current physical conditions on Mars’ surface usu¬ 
ally do not allow liquid water to be stable, and 
therefore, it occurs as water ice within the pore 
space of the permafrost soil or as few km-thick 
polar ice caps. It can be assumed that at a certain 
depth below the surface, usually estimated to be a 
few kilometers, the cryosphere transitions into an 
aquifer (Lasue et al. 2013). The depth at which 




118 


Arachnoid 


the water ice turns into groundwater depends on 
not well known factors, such as the water salinity, 
the soil porosity and permeability, or the geother¬ 
mal gradient and thermal conductivity of the sub¬ 
surface. The presence of groundwater on Mars is 
insofar of interest to astrobiologists as aquifers on 
Earth are populated by microbial life down to a 
depth of a few kilometers (Michalski et al. 2013). 

See Also 

► Crater Lakes (Mars) 

► Gullies 

► Habitability on Mars 

► Heat Transfer, Planetary 

► Outflow Channels 

► Polar Caps (Mars) 

References and Further Reading 

Lasue J, Mangold N, Hauber E, Clifford S, Feldman W, 
Gasnault O, Grima C, Maurice S, Mousis O (2013) 
Quantitative assessment of the Martian hydrosphere. 
Space Sci Rev 174:155-212 

Michalski JR, Cuadros J, Niles PB, Parnell J, Rogers AD, 
Wright SP (2013) Groundwater activity on Mars and 
implications for a deep biosphere. Nat Geosci 
6:133-138 


Arachnoid 

Jorn Helbert 

DLR, Institut fur Planetenforschung, Berlin, 
Germany 

Definition 

An Arachnoid is a type of landform only seen on 
the surface of ► Venus, which is believed to have 
a volcanic origin. Arachnoids get their name from 
their resemblance to spider webs. They appear as 
concentric ovals surrounded by a complex net¬ 
work of fractures, and are spanned up to 200 km. 
Over 30 arachnoids have been identified on 
Venus, so far. 


See Also 

► Venus 


Archaea 

Antonio Ventosa and Rafael R. de la Haba 
Department of Microbiology and Parasitology, 
Faculty of Pharmacy, University of Sevilla, 
Sevilla, Spain 

Keywords 

Domain; Evolution; Extremophiles; Molecular 
adaptation; Phylogeny; 16S rRNA sequencing 

Synonyms 

Archaeobacteria 

Definition 

The Archaea are a phylogenetically coherent 
group of prokaryotes that have a different orga¬ 
nization than the ► Bacteria. 


History 

Woese and Fox (1977) proposed that prokaryotes 
were not a monophyletic group. Based on the 
comparison of their small subunit ribosomal 
RNA sequences, the prokaryotes comprise two 
distinct evolutionary lineages that are represented 
by the ► Bacteria and the Archaea (that formerly 
were designated as Archaebacteria by Woese 
et al. 1978). The concept of a third domain of 
life, which explained several structural, meta¬ 
bolic, and molecular differences with respect to 
other prokaryotes, was initially poorly accepted 
by the scientific community. However, the con¬ 
cept of the Archaea was advanced through 





Archaea 


119 


studies and meetings carried out by O. Kandler, 
W. Zillig, and K.O. Stetter, among others. The 
Archaea have similarities and are considered 
phylogenetically more closely related with the 

► Eukarya (Woese et al. 1990). 

Overview 

Archaea have distinct molecular characteristics 
that clearly distinguish them from the Bacteria 
and the Eukarya , and evolutionary studies have 
highlighted their role on the development of life 
on our planet. Archaea have been associated with 

► extreme environments and many of them are 
extremophilic microorganisms, showing interest¬ 
ing characteristics and applications for industrial 
and other purposes. Many of them are considered 
to be microorganisms that are able to grow on the 
limits of life. Their ability to thrive in extreme 
environments has expanded the horizons for 
Astrobiology as they are considered counterparts 
for extraterrestrial life. 

The Archaea are characterized by a cellular 
morphology similar to those of most Bacteria 
(rods, cocci, irregular cells, etc.). However, 
myceliar or multicellular stages with cellular dif¬ 
ferentiation have not been described. On the con¬ 
trary, unique morphologies have been described 
for some Archaea , such as the square flat cells of 
some haloarchaea ( Haloquadratum walshyi) or 
amoeba-like cells ( Thermoplasma and other 
microorganisms). Other characteristics of the 
Archaea that define their differential status with 
respect to the other living organisms are: (1) the 
presence of phytanyl ether instead of fatty acid 
ester lipids in their membranes; (2) the absence of 
peptidoglycan (murein) in their cell walls and a 
frequent presence of proteinaceous S-layers (only 
a few have a polysaccharide cell wall), as well as 
the absence of a periplasmic space; (3) their com¬ 
plex DNA-dependent RNA polymerases (early 
in vitro studies using several inhibitors showed 
that the transcription machinery in Archaea is 
more closely related to that of Eukarya than to 
Bacteria ); the sequences of the archaeal RNA 
polymerases resemble some eukaryotic RNA 
polymerases and consist of up to 13 different 


units; (4) although the translation machinery of 
Archaea is similar to that of bacteria (70S ribo¬ 
somes with 50S and 30S subunits, similar length 
ribosomal RNAs, transcriptional and transla¬ 
tional coupling, etc.), there are an important num¬ 
ber of specific features not present in Bacteria , 
some of which are specific to Archaea while 
others are similar to Eukarya. For example, 
almost all antibiotics that inhibit bacterial trans¬ 
lation are ineffective in the Archaea ; Bacteria use 
A-formyl-methionyl-tRNA for translational start 
codons, while Archaea use unmodified initiator 
methionine in translation, similar to Eukarya. 
Besides, Archaea and Eukarya share a common 
characteristic, elongation factor 2 (EF-2), which 
is ADP-ribosylated by diphtherial toxin. 

The Archaea are subdivided into five phyla, of 
which two, the Crenarchaeota and the 
Euryarchaeota , are most extensively studied. 
The classification of Archaea has been widely 
discussed and several proposals have been published. 
The most widely accepted include the Archaea 
as a higher taxon with the range of “Domain” 
which includes the following five phyla: 
Crenarchaeota , Euryarchaeota , Korarchaeota , 
Nanoarchaeota , and Thaumarchaeota (Parte 2015). 
The phylum Crenarchaeota includes a single class, 
Thermoprotei , with five orders: Acidilohales , 
Desulfurococcales , Fervidicoccales , Sulfolobales , 
and Thermoproteales. The phylum Euryarchaeota 
includes eight classes: Archaeoglobi , Halobacteria , 
Methanobacteria , Methanococci , Methanomicrobia , 
Methanopyri , Thermococci , and Thermoplasmata. 
The phylum Korarchaeota includes nonculti- 
vated Archaea designated as “Candidatus 
Korarchaeum,” the phylum Nanoarchaeota 
includes the genus “ Nanoarchaeum ,” and finally, 
the phylum Thaumarchaeota includes the genus 
“Cenarchaeum.” 

The phylum Euryarchaeota includes two of 
the most typical groups that were identified in 
the early studies by Woese and coworkers as 
members of the Archaea : the ► methanogens 
and the haloarchaea (also designated as 
halobacteria). The methanogenic Archaea are 
anaerobic organisms that produce methane as 
the major end product of their metabolism. Phy¬ 
logenetically methanogens are very diverse and 





120 


Archaea 


are represented by a large number of species 
belonging to many genera, grouped in 12 families 
within 6 orders. They are found on a variety of 
anoxic environments such as ocean and lake sed¬ 
iments, hydrothermal vents, animal digestive 
tracts, anaerobic sludge digesters, etc. The typical 
growth compounds of methanogens are H 2 and 
C0 2 , or short-chain (Ci-C 5 ) organic compounds 
(formate, acetate, ethanol, trimethylamine, etc.). 
H 2 is used as electron donor for C0 2 reduction, 
and electrons can also be derived from 
formate, CO, or specific alcohols. Among the 
microorganisms that have been used as models 
for studying methanogenesis are species of the 
genera Methanobacterium , Methanother- 

mobacter , Methanobrevibacter , Methanosarcina , 
Methanococcus , among others (Dworkin 
et al. 2002; Madigan et al. 2008). 

Haloarchaea are represented by a group of 
extremely halophilic aerobic Archaea , which tax- 
onomically are placed within a single class, 
Halobacteria , order Halobacteriales , family 
Halobacteriaceae (Grant et al. 2001). Currently 
they are represented by almost 50 genera and a 
large number of species that are characterized by 
their Na + requirements. They are considered to be 
organisms that are able to grow under higher salt 
concentrations, in saturated NaCl habitats. Their 
optimal NaCl requirements are in the range 
3.5-4.5 M NaCl and they are not able to grow in 
media without NaCl, thus, they have a specific 
requirement for NaCl, which has led to detailed 
studies of their mechanisms of haloadaptation. In 
contrast to most other prokaryotes, which accu¬ 
mulate intracellular organic compounds desig¬ 
nated as ► compatible solutes, haloarchaea 
compensate for the high salt concentration in 
the environment by accumulating ions, mainly 
up to 5 M KC1. They are normal inhabitants of 
hyper saline environments, being the predominant 
microbiota of saturated ponds of salterns and salt 
lakes (they may reach high cell densities, 
>10 7 cell ml -1 ); they are also found in salt or 
salted products (salted fish or meats, salted 
fermented foods), salt deposits (mines), salted 
hides, and saline soils. Most haloarchaea grow 
at neutral pH values but some species are 
haloalkaliphilic, being able to grow optimally at 


alkaline pH and inhabiting soda lakes. Other typ¬ 
ical features of haloarchaea are: their production 
of red- to pink-pigmented colonies due to the 
presence of bacterioruberins (C 50 carotenoids), 
although there are a few exceptions; the presence, 
in some of them, of retinal-based pigments 
(bacteriorhodopsin), that act as a proton pump 
driven by light energy; or the presence of typical 
archaeal polar lipids, with ether-linked 
phosphoglycerides that can be easily detected 
by thin-layer chromatography (a feature that is 
widely used for the taxonomic differentiation of 
most genera of haloarchaea) (Grant et al. 2001). 

Haloarchaea are excellent models for the 
study of the molecular biology and other struc¬ 
tural features of Archaea , as well as their mecha¬ 
nisms of adaptation to extreme conditions of 
salinity, alkaline pH, and moderate temperature, 
and several species have been used for such 
purposes due to their ease of manipulation 
under laboratory conditions: they grow in complex 
media (with the appropriate salt content) under aer¬ 
obic conditions using the standard procedures uti¬ 
lized for most nonfastidious prokaryotes. Some 
species used for such studies include Halobacterium 
salinarum , Haloarcula marismortui , Haloferax 
volcanii , and more recently, the square 
haloarchaeon Haloquadratum walsbyi (recently iso¬ 
lated and referred to as “Walsby’s square bacte¬ 
rium”). In addition, several biotechnological 
applications have been suggested, such as the com¬ 
mercial production of bacteriorhodopsin, the pro¬ 
duction of extracellular hydrolytic enzymes or 
exopolysaccharides, the use of polyhydrox- 
yalkanoates (PHAs) as bioplastics, or the production 
of halocins (archaeocins, proteinaceous archaeal 
antimicrobials). 

With a few bacterial exceptions, most 
► hyperthermophiles (defined as organisms 
showing optimal growth at 80 °C or higher) are 
species of Archaea. They are inhabitants of 
hot springs, solfataric and volcanic areas, 
deep-subsurface aquifers, submarine vents 
(“black smokers”), etc. Hyperthermophiles 
include several methanogens, as well as 
members of a variety of genera of the 
Archaeoglobales , Thermococcales , Desulfuro- 
coccales , Thermoproteales , or Sulfolabales. 



Archaea 


121 


They are excellent models for the study of the 
metabolisms of sulfur and inorganic sulfur com¬ 
pounds; many species use inorganic sulfur com¬ 
pounds as electron acceptors or donors. Some of 
the most hyperthermophilic organisms known are 
Pyrolobus fumarii (optimal growth at 106 °C, 
range 90-113 °C), Pyrodictium occultum 

(optimal growth at 105 °C, range 85-110 °C), 
Pyrococcus furiosus and Pyrococcus woesei 
(optimal growth at 100-103 °C, range 

70-105 °C), Pyrobaculum aerophylum (optimal 
growth at 100 °C, range 75-104 °C), and 
Pyrobaculum islandicum (optimal growth at 100 
°C, range 74-102 °C). 

The phylum Nanoarchaeota is known for a 
single species, Nanoarchaeum equitans , to date 
a hyperthermophilic archaeon that lives in a sym¬ 
biotic association with the Crenarchaeote 
Ignicoccus , a sulfur-dependent anaerobic hyper¬ 
therm ophile. The cells are spherical and only 
about 400 nm in diameter; they grow attached to 
the surface of a specific archaeal host (Hubber 
et al. 2002). This archaeon was isolated from a 
submarine hot vent, but recent studies have 
shown that nanoarchaea may be widely dispersed 
in hyperthermophilic and mesophilic halophilic 
environments (Casanueva et al. 2008; Rinke et al. 
2013). 


See Also 

► Bacteria 

► Compatible Solute 

► Crenarchaeota 

► Domain (Taxonomy) 

► Eukarya 

► Euryarchaeota 

► Extreme Environment 

► Halophile 

► Hyperthermophile 

► Korarchaeota 

► Membrane 

► Methanogens 

► Nanoarchaeota 

► Phylogenetic Tree 

► Prokaryote 


References and Further Reading 

Blum P (ed) (2001) Archaea: ancient microbes, extreme 
environments, and the origin of life. Academic, San 
Diego 

Blum P (ed) (2008) Archaea: new models for prokaryotic 
biology. Caister Academic Press, Norfolk 

Boone DR, Castenholz RW, Garrity GM (2001) Bergey’s 
manual of systematic bacteriology, 2nd edn. The 
Archaea and the deeply branching and phototrophic 
Bacteria, vol 1. Springer, New York 

Brochier-Armanet C, Boussau B, Gribaldo S, Forterre 
P (2008) Mesophilic crenarchaeota: proposal for a 
third archaeal phylum, the Thaumarchaeota. Nat Rev 
Microbiol 6:245-252 

Casanueva A, Galada N, Baker GC, Grant WD, Heaphy S, 
Jones B, Yanhe M, Ventosa A, Blarney J, Cowan DA 
(2008) Nanoarchaeal 16S rRNA gene sequences are 
widely dispersed in hyperthermophilic and mesophilic 
halophilic environments. Extremophiles 12:651-656 

Cavicchioli R (ed) (2007) Archaea: molecular and cellular 
biology. ASM Press, Washington, DC 

Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, 
Stackebrandt E (eds) (2002) The prokaryotes: an 
evolving electronic resource for the microbiological 
community, 3rd edn, release 3.19 ed. Springer, New 
York, http://link.springer-ny.com/link/service/books/ 
10125/ 

Garret RA, Klenk H-P (eds) (2007) Archaea: 
evolution, physiology and molecular biology. Black- 
well, Oxford 

Grant WD, Kamekura M, McGenity TJ, Ventosa A (2001) 
Class III. Halobacteria class. In: Boone DR, 
Castenholz RW, Garrity GM (eds) Bergey’s manual 
of systematic bacteriology, 2nd edn. The Archaea and 
the deeply branching and phototrophic Bacteria, 
vol 1. Springer, New York 

Hubber H, Hohn MJ, Rachel R, Fuchs T, Wimmer VC, 
Stetter KO (2002) A new phylum of archaea 
represented by a nanosized hyperthermophilic symbi¬ 
ont. Nature 417:63-67 

Kates M, Kushner DJ, Matheson AT (1993) The biochem¬ 
istry of Archaea (Archaebacteria). Elsevier, 
Amsterdam 

Madigan MT, Martinko JM, Dunlap PV, Clark DP 
(2008) Brock biology of microorganisms, 12th edn. 
Benjamin Cummings, San Francisco 

Parte A (2015) List of prokaryotic names with standing in 
nomenclature, http://www.bacterio.cict.fr/. 

Pfeifer F, Palm P, Schleifer K-H (1994) Molecular biology 
of Archaea. Gustav Fischer Verlag, Stuttgart 

Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Ander¬ 
son IJ, Cheng JF, Darling A, Malfatti S, Swan BK, 
Gies EA, Dodsworth JA, Hedlund BP, Tsiamis G, 
Sievert SM, Liu WT, Eisen JA, Hallam SJ, Kyrpides 
NC, Stepanauskas R, Rubin EM, Hugenholtz P, 
Woyke T (2013) Insights into the phylogeny and cod¬ 
ing potential of microbial dark matter. Nature 
499:431-437 



122 


Archaeobacteria 


Robb FT, Place AR, Sowers KR, Schreier HJ, 
DasSarma S, Fleischmann EM (eds) (1995) Archaea: 
a laboratory manual. Cold Spring Harbor, New York 

Ventosa A (2006) Unusual micro-organisms from unusual 
habitats: hypersaline environments. In: Logan NA, 
Lappin-Scott HM, Oyston PCF (eds) Prokaryotic 
diversity: mechanisms and significance. Cambridge 
University Press, Cambridge 

Woese CR, Fox GE (1977) The phylogenetic structure of 
the prokaryotic domain: the primary kingdoms. Proc 
Natl Acad Sci U S A 74:5088-5090 

Woese CR, Wolfe RS (eds) (1985) The bacteria: a treatise 
on structure and function. Archaeabacteria, vol VII- 
I. Academic, New York 

Woese CR, Magrum LJ, Fox GE (1978) Archaebacteria. 
J Mol Evol 11:245-251 

Woese CR, Handler O, Wheelis ML (1990) Towards a 
natural system of organisms: proposal for the domains 
Archaea, Bacteria and Eukarya. Proc Natl Acad Sci 
USA 87:4576^1579 


Archaeobacteria 

► Archaea 


Archean Biosignatures 

► Archean Traces of Life 


Archean Drilling Projects 

Nicholas Arndt 

ISTerre, Universite Grenoble Alpes, France 

Definition 

There are several scientific drilling projects that 
have been carried out in Archean terrains in the 
past decade and others that are planned in the near 
future. The aim of most of these drilling projects 
is to recover relatively well-preserved rock sam¬ 
ples from below the present weathering profile 
and to obtain continuous rock cores that retain 
soft or friable units that outcrop poorly at the 


surface. Astrobiology-related studies such as 
search of pristine morphological or chemical 
traces of early life form an important part of 
these projects. 

Overview 

To date, both volcanic and sedimentary 
sequences have been targeted, and the recovered 
cores have been analyzed to investigate condi¬ 
tions at the surface of the Archean Earth - the 
composition, temperature, and redox state of the 
Archean ocean and atmosphere and the volcanic 
and sedimentary processes that operated early in 
Earth history - and, above all, to search for evi¬ 
dence of primitive life. The focus has been the 
► Pilbara Craton in Western Australia, where 
four separate programs have been carried out, 
each involving collaboration between geologists 
from Australian universities, the Western Austra¬ 
lian Geological Survey, and foreign agencies. 
The four programs are (1) the Archean Biosphere 
Drilling Project (ABDP) cosponsored by several 
Japanese Universities, (2) the Deep Time Drilling 
Project (DTDP) of the NASA Astrobiology Insti¬ 
tute, (3) the Pilbara Drilling Project (PDP) of IPG 
Paris, and (4) Dixon Island-Cleaverville Drilling 
Project (DXCL-DP) supported by the Japanese 
Ministry of Education, Culture, Sports, Science, 
and Technology (MEXT). 

In South Africa’s ► Barberton Greenstone 
Belt, two drilling projects were completed to date: 

The Barberton Barite Drilling Project (CNRS, 
IPGP) had the objective to obtain a representa¬ 
tive sequence of black cherts, shales, tuffaceous 
sandstones and siltstones, jasper deposits, and 
bedded barite which is a conspicuous assem¬ 
blage of rock types typically observed from 
Early Archean seafloor hydrothermal settings. 
They well penetrated a section in the west limb 
of the Baryte Syncline to a depth of 182 m. 
The Barberton Drilling Project (ICDP; July 
2011-May 2012) included five diamond-core 
holes, each several hundred meters long. 
BARB-1 and BARB-2 targeted komatiitic 
rocks near Tjakastad in the southern part of the 






Archean Environmental Conditions 


123 


belt, whereas BARB-3 drilled 899.5 m through 
the Buck Reef Chert, both of the ► Onverwacht 
Group. BARB-4 targeted turbidites and banded- 
iron formation and BARB-5 ► barite, turbidites, 
and ► spherules, both of the Mapepe Formation 
(lower Fig Tree Group). A total of 3,052 m of 
core was recovered. 

Two programs focused on the Archean- 
Proterozoic transition. A series of short holes 
have been drilled in Russian Fennoscandia to 
sample the 500-million-year interval defining 
the Archean-Paleoproterozoic transition; the 
Agouron Griqualand Paleoproterozoic Drilling 
Project straddled a similar interval in the North¬ 
ern Cape province of South Africa. 


See Also 

► Archean Traces of Life 

► Barberton Greenstone Belt 

► Early Archean 

► Microfossils 

► Pilbara Craton 

► Proterozoic Eon 


Archean Environmental Conditions 

Christoph Heubeck 1 and Nicholas Arndt 2 
^nstitut fur Geowissenschaften, Friedrich- 
Schiller-Universitat Jena, Jena, Germany 
2 ISTerre, Universite Grenoble Alpes, France 

Keywords 

Chert; Komatiite; Oceans; Sediment; Traces of 
life; Carbonates 

Definition 

The term “Archean environmental conditions” 
refers to the geological, physical, and chemical 


conditions of the surface of the Earth during the 
► Archean eon. The surface of the Archean Earth 
was in many ways similar to that of today. Oceans 
likely covered most of the globe, but there were 
also regions of dry land. However, the oceanic 
crust was almost as thick as the ► continental 
crust, mountain ranges were not very high, and 
parts of oceanic ridges and plateaus (thick piles of 
flat-lying lava flows) were emergent. Geological 
processes such as volcanism, erosion, and sedi¬ 
ment deposition operated but were influenced by 
a lack of vegetation, higher ocean temperatures, 
different water composition, and a hotter, more 
aggressive, acidic atmosphere. In addition, 
coastal settings may have been subjected to 
more intense reworking by high and more fre¬ 
quent tides. 

Overview 

The surface of the Archean Earth was in many 
ways similar to that of today. Oceans covered 
most of the globe, but there were also regions of 
dry land. The total area covered by oceans was 
greater than now for three reasons. First, the 
volume of continental crust may have been less, 
if continental crust indeed grew (progressively or 
in spurts) through time (Benn et al. 2006). 
Second, the oceans might have been more 
voluminous because high temperatures in the 
mantle (Nisbet et al. 1993) destabilized 
hydrous minerals and drove water to the 
surface. Third, oceanic crust was thicker. Its 
top lay at a shallower depth than today’s 
sea floor, thus displacing water which 
inundated low-lying margins of continents 
(Eriksson 1999). 

Mountain ranges existed but were not as high 
as those of today because the continental crust 
was heated internally and rendered more ductile 
by more abundant radioactive elements. Conti¬ 
nental crust was relatively thin, while oceanic 
crust, produced by high-degree melting of the 
hotter mantle, was far thicker (Sleep and Windley 
1982). The subdued topography, the limited con¬ 
trast between the thicknesses of oceanic and con¬ 
tinental crust, combined with bigger oceans, 




124 


Archean Environmental Conditions 


meant that much of the continental crust was 
flooded (Arndt 1998). 

Just as during more recent geological 
history, global temperatures waxed and waned. 
The world’s oldest glaciation is reported 
from the 2.9 Ga-old Mozaan Group on South 
Africa’s Kaapvaal Craton (Young et al. 1998) 
but on the whole temperatures appear to have 
been clement or high. The O and Si isotopic 
compositions of Archean ► cherts suggest 
that ocean temperatures were commonly above 
40 °C and possibly as high as 80 °C (Knauth and 
Lowe 2003). The atmosphere contained very 
little or no free oxygen but was richer in C0 2 ; 
rainwater was thus somewhat acid. Due to the 
absence of a protective ozone shield, UV flux at 
the Earth’s surface was high. The atmosphere 
also contained SO and S0 2 , causing sulfuric 
acid haze; haze from nitrous oxides and 
organics likely occurred as well. The normal 
cycle of erosion, transport, and deposition of sed¬ 
iment operated, but the rivers flowed through a 
landscape that was very different from that of 
today. 

The feature that most starkly distinguished the 
Archean and modem land surface was the lack of 
vegetation. Microbes doubtlessly colonized the 
subsurface and constructed ► biofilms and 
thicker biomats which covered moist areas, pos¬ 
sibly including low-lying fluvial floodplains, but 
most of the landscape likely had the appearance 
of bare rocks we see on recent Mars. The rate of 
weathering was enhanced by higher temperatures 
and a more aggressive atmospheric composition, 
possibly also by violent thunderstorms, but was 
slowed down by a lack of humic acid and thick 
soils that today greatly enhance weathering rates. 
These processes and rates are difficult to quan¬ 
tify. Erosion was likely enhanced by the lack of 
vegetation and thus lack of stabilized river banks, 
but restrained by the overall more modest mean 
elevation of continents. Active volcanism cov¬ 
ered much of the surface with lava flows or pyro¬ 
clastic deposits. The Moon, in a closer orbit and 
rotating faster about the Earth, caused higher and 
more frequent tides which may have raked the 


barren shorelines in much wider tidal belts than 
we see today. 

The oceanic crust was composed of basaltic 
lavas like that of modem crust, but was more 
magnesian (picritic) in places (Sleep and 
Windley 1982). Parts of mid-ocean ridges and 
the summits of oceanic plateaus may have been 
emergent, forming what might be called 
“melano- (dark-colored) continents.” The pelagic 
sediment that covered this crust was different 
from that of today. An absence of shell-forming 
organisms precluded the formation of biogenic 
calcareous or siliceous oozes; in their place 
occurred Si- or Fe-rich sediments that precipi¬ 
tated directly from the high-temperature seawater 
that contained high concentrations of these ele¬ 
ments. Depending on the intensity of weathering 
of mafic material on exposed regions, much clay 
may have been produced, washed into the sea and 
deposited on oceanic crust. Hydrothermal 
venting of Si-charged seawater resulted in rapid 
silicification of most near-surface sediments and 
exposed igneous rocks, along with the formation 
of primary ► cherts. Expulsion of fluids at hydro- 
thermal vents led to the deposition of exhalative 
sediments, variably composed of sulfides, sul¬ 
fates, carbonates or silica minerals (Russell 
et al. 2005). 

The earliest Archean coincided with the end of 
the ► Late Heavy Bombardment, a time of more 
frequent meteorite impacts. The largest of these 
would have vaporized parts of the oceans, raised 
oceanic and atmopsheric temperatures signifi¬ 
cantly, and resurfaced parts of the Earth’s sur¬ 
face. Whether their overall impact, in particular 
on the biosphere, was local or global, possibly 
extending to sterilization of Earth’s surface envi¬ 
ronments, is debated (Abramov and Mojzsis 
2009). 

See Also 

► Archean Eon 

► Archean Tectonics 

► Barberton Greenstone Belt 



Archean Eon 


125 


► Chert 

► Continental Crust 

► Craton 

► Earth, Formation and Early Evolution 

► Hydrothermal Environments 

► Isua Supracrustal Belt 

► Komatiite 

► Late Heavy Bombardment 

► Ocean, Chemical Evolution of 

► Oxygen Isotopes 

► Pilbara Craton 

► Silicon Isotopes 

► Snowball Earth 

► Weathering 


References and Further Reading 

Abramov O, Mojzsis SJ (2009) Microbial habitability of 
the Hadean Earth during the late heavy bombardment. 
Nature 459:419^122 

Arndt NT (1998) Why was flood volcanism on submerged 
continental platforms so common in the Precambrian? 
Precambrian Res 97:155-164 
Benn K, Mareschal J-C, Condie KC (eds) (2006) Archean 
geodynamics and environments. Geophysical 
monograph series. American Geophysical Union 
164, p 320 

Eriksson PG (1999) Sea level changes and the continental 
freeboard concept: general principles and application 
to the Precambrian. Precambrian Res 97:143-154 
Hoffman PF, Kaufman AJ, Halverson GP, Schrag DP 
(1998) A Neoproterozoic snowball Earth. Science 
281:1342-1346 

Knauth LP, Lowe DR (2003) High Archean climatic tem¬ 
perature inferred from oxygen isotope geochemistry of 
cherts in the 3.5 Ga Swaziland Supergroup, South 
Africa. Geol Soc Am Bull 115:566-580 
Nisbet EG, Cheadle MJ, Arndt NT, Bickle MJ 
(1993) Constraining the potential temperature of the 
Archaean mantle: a review of the evidence from 
komatiites. Lithos 30:291-307 
Russell MJ, Hall AJ, Boyce AJ, Fallick AE (2005) On 
hydrothermal convection systems and the emergence 
of life. Econ Geol 100:419^38 
Sleep NH, Windley BF (1982) Archaean plate tectonics: 

constraints and inferences. J Geol 90:363-379 
Young G, von Brunn V, Gold D, Minter WEL 
(1998) Earth’s oldest reported glaciation: 
physical and chemical evidence from the Archean 
Mozaan Group (~2.9 Ga) of South Africa. J Geol 
106:523-538 


Archean Eon 

Herve Martin 1 and Daniele L. Pinti 2 
^aboratoire Magmas et Volcans, Universite 
Blaise Pascal, OPGC, CNRS, IRD, Clermont- 
Ferrand, France 

2 GEOTOP Research Center for Geochemistry 
and Geodynamics, Universite du Quebec a 
Montreal, Montreal, QC, Canada 

Keywords 

Continental crust; Greenstone belts; Komatiite; 
Plate tectonics; TTG 

Synonyms 

Precambrian 


Definition 

The Archean (Archaean in British English) is the 
second major period in geological history. Pre¬ 
ceded by the ► Hadean and followed by the Pro¬ 
terozoic, its start is usually taken as the age of the 
oldest preserved rocks, either the 4.0 Ga-old 
(Ga = 10 9 years = billion years) ► Acasta 
gneisses (Canada) or the 3.85-3.80 Ga-old 
Amitsoq gneisses (► Greenland). The Interna¬ 
tional Commission on Stratigraphy (ICS, Jan. 
2013) sets its beginning at the Global Standard 
Stratigraphic Age of 4.0 Ga. The transition to the 
Proterozoic is typically taken at 2.5 Ga, which 
was thought to mark a major change in the 
Earth’s geodynamic style and corresponds 
roughly to the ► Great Oxygenation Event. The 
Archean thus encompasses an approximately 1.5- 
Ga-long period during which the oldest well- 
preserved rocks formed and life likely originated. 
Its tectonic style was different from today, with 
more abundant mantle plumes, greatly 
fragmented tectonic plates, and longer 




126 


Archean Eon 


mid-oceanic ridges. It is commonly believed that 
► plate tectonics started in this period. 

Overview 

Geographical and Temporal Distribution of 
Archean Terranes 

The Archean eon is characterized by the extrac¬ 
tion from the mantle and the subsequent differ¬ 
entiation of significant amounts of ► continental 
crust. Indeed, at the end of the Archean eon, 
probably about 75 % of the juvenile continental 
crust had formed. Large parts of this Archean 
crust, named ► cratons or shields, have been pre¬ 
served on all continents (Condie 1994; Fig. 1), 
including: 

• In Europe, the 3.1-2.5 Ga Baltic (sometimes 
referred to as Fennoscandian) and 3.8-3.2 Ga 
Ukrainian shields as well as a few outcrops in 
northern Scotland (Lewisian gneisses in the 


Hebrides with a debated age of 

3,520 ± 160 Ma) 

• In Asia, the Siberian Aldan ► Shield 

(3.5-3.0 Ga), the Indian Dharwar 

(3.6-2.5 Ga), and the Sino-Korean cratons 
(3.8-3.0 Ga) 

• In Australia, the Pilbara (3.6-2.5 Ga), Yilgarn 
(2.94-2.63 Ga), Gawler (2.5 Ga), and North¬ 
ern Australia cratons 

• In Antarctica, the Napier complex 

(orthogneisses dated at 3.95-2.46 Ga) 

• In Africa, the Kaapvaal (3.6-2.5 Ga), Zimba¬ 
bwe (3.5-2.5 Ga), and Madagascar 

cratons, as well as the Central and West Africa 
cratons 

• In South America, the Sao Francisco and 
Amazonian cratons (3.5-2.4 Ga) in Brazil 
and the 3.4 Ga Guyana Shield 

• In North America, the Wyoming Province, 
USA (3.5-2.5 Ga); the Superior Province 
(3.7-2.7 Ga); the Slave Province (dominated 
by 2.73-2.63 Ga greenstone sequences but 


180 ° 120 ° 60 ° 0 ° 60 ° 120 ° 180 ° 



180 ° 120 ° 60 ° 0 ° 60 ° 120 ° 180 ° 
Archean terranes Outcropping []|[[||[| Covered by sedimentary rocks 


Archean Eon, Fig. 1 Geographical distribution of the 
Archean provinces (After Condie 1994; redrawn). 1 Baltic 
Shield, 2 Ukrainian Shield, 3 Scotland Shield, 4 Siberian 
Shield, 5 Indian Craton, 6 Sino-Korean Craton, 7 Pilbara 
craton, 8 Yilgarn craton, 9 Northern Australia craton, 10 
Napier complex, 11 Kaapvaal craton, 12 Zimbabwe Cra¬ 
ton, 13 Madagascar Craton, 14 Central Africa Craton, 15 


West Africa Craton, 16 Sao Francisco and Amazonian 
Cratons, 17 Guyana Shield, 18 Wyoming Province, 19 
Superior Province, 20 Slave Province, 21 Labrador Shield, 
and 22 Greenland Shield. Dotted areas represent exposed 
Archean terranes, while striped areas represent regions 
underlain by Archean rocks 



































Archean Eon 


127 


with the ► Acasta gneisses dated to 4.03 Ga); 
the Labrador Shield (Canada) and the 
► Greenland Shield (3.8-2.6 Ga with older 
units at ► Akilia and Isua up to 3.88 Ga) 

The largest continuously exposed outcrop of 
Archean rocks is the Amitsoq gneiss in Green¬ 
land with an area of 3,000 km 2 . The protolith of 
these rocks consists of older granitoids, metamor¬ 
phosed into gneisses with emplacement ages of 
3.822 zb 0.005 Ga. The oldest supracrustal rocks 
(volcaniclastic and sedimentary) are in Akilia 
island and the Isua Supracrustal belt with older 
ages at 3.872 zb 0.010 Ga, together with banded 
iron formation of the Nuvvuagittuq greenstone 
belt (3.817 zb 0.016 Ga or older). The recognized 
oldest rocks on the Earth (covering a surface of 
about 20 km 2 ) are the ► Acasta gneisses in Can¬ 
ada (Slave Province) with an age of 
4.030 zb 0.003 Ga (Bowring and Williams 
1999), while the oldest known minerals are the 
famous Jack Hills detrital zircons (Western Aus¬ 
tralia) with recorded ages as old as 4.404 Ga 
(Wilde et al. 2001). Similarly, inherited cores in 
zircons from Acasta provided an age of 
4.20 zb 0.06 Ga (Isuka et al. 2006). These zircon 
crystals are thus the only records of Hadean crust 
existing on Earth. Recently, a model age of 
4.28 Ga has been proposed for an amphibolitic 
rock (Faux amphibolite), outcropping in the 
Nuvvuagittuq greenstone belt (O’Neil 
et al. 2008), though this age is strongly debated. 

Geology of Archean Terranes 

Archean terranes all show similar lithological 
associations, independent of their age: (1) granite- 
gneiss, (2) ► greenstone belts, and (3) late gran¬ 
itoids. In addition, some show a cratonal cover. 

The granitic gneisses are the most abundant, 
composing up to 80 % of the Archean continental 
crust. Better known under the acronym TTG for 
► Tonalite-Trondhjemite-Granodiorite associa¬ 
tion (Jahn et al. 1981), these rocks are coarse¬ 
grained, gray orthogneisses (which means 
derived from magmatic rocks, in this case gran¬ 
itoids) with well-developed banding consisting in 
the alternation of whitish quartz-plagioclase 
layers with gray to black biotite- and 




Archean Eon, Fig. 2 Photo of typical gray gneisses 
(TTG) from Sand River, Limpopo, South Africa. These 
3.283 =b 0.008 Ga-old rocks consist in the alternation of 
whitish quartz-plagioclase layers with biotite and 
amphibole-richer gray layers (Photo H. Martin) 

amphibole-rich layers (Fig. 2). Contrary to typi¬ 
cal modern granites, the TTG contain very low 
proportion of potassic feldspar (KAlSi 3 0 8 ). 

The parent magma from which TTG derived 
results from the melting at high pressure of a 
hydrated mafic rock of basaltic composition 
(Fig. 3a). Indeed, when the pressure increases, 
basalt is transformed into amphibolite 
(amphibole zb garnet zb plagioclase feldspar- 
rich rock) and then into eclogite 
(pyroxene + garnet rock). These products are 
melted to give the parental magmas of TTG 
(e.g., Martin and Moyen 2002). Although all 
geologists agree on the basaltic source of TTG, 
the geodynamic environment where melting took 
place is still debated: (1) ► basalts from a 
subducted oceanic crust (Fig. 3; Martin 1995; 
Martin and Moyen 2002); or (2) underplated 
basalts melted during the passage of a mantle 
plume (Smithies 2000). The first hypothesis can 



128 


Archean Eon 




Archean Eon, Fig. 3 (a) Pressure-temperature (P-T) 
diagram and schematic cross section of both Archean (b) 
and modern (c) subduction zones, (a) The P-T diagram 
shows the dry and 5 % hydrous solidus of tholeiite as well 
as main dehydration reactions of oceanic lithosphere. 
Abbreviations: H is hornblende out, A is anthophyllite 
out, C is chlorite out, Ta is talc out, Tr is tremolite out, 
Z is zoisite out. G outlines stability field of garnet. The 
grey field is the P-T domain where slab melts can coexist 
with hornblende- and gamet-bearing residue. In the 
Archean (inset b), the geothermal gradient along the 

be explained if we assume a hotter Archean man¬ 
tle, as inferred by the occurrence in Archean 
times of Mg-rich magmas called ► komatiites. 
It can also be explained by the subduction of 
young and consequently hotter oceanic plates. 
In modem tectonic regimes, the subducted plate 
is old and cold, such that it dehydrates during its 
descent into the mantle; indeed, there, the oceanic 
plate is subjected to both higher pressure and 
temperature, such that it dehydrates. Volatiles, 
mainly water, are liberated and ascend through 
the mantle wedge, thus lowering its melting tem¬ 
perature (the mantle wedge lies between the 
descending or subducting oceanic plate and the 
continental (or oceanic) plate). Mantle wedge 
melting generates magmas with andesitic to gra¬ 
nitic composition that are accreted to form new 
continental crust (Fig. 3b). Modern subduction 
systems (both mantle and oceanic crust) are nor¬ 
mally too cold to allow subducted basalt melting. 
If we assume a hotter Archean mantle associated 


Benioff plane was very high; the subducted slab melted 
at shallow depth before dehydration could take place. 
After 2.5 Ga, Earth was cooler and the geothermal gradi¬ 
ent along the Benioff plane was lower (inset c) such that 
slab dehydration generally occurred before its melting 
began. The liberated volatiles (mainly water) ascended 
through the mantle wedge, thus lowering its solidus tem¬ 
perature, which induced its melting. Abbreviations: OC is 
oceanic crust, CC is continental crust, MS is solidus of 
hydrated mantle, black teardrops indicate magma 


or not to the subduction of a younger oceanic 
crust, then the latter cannot rapidly dehydrate 
and consequently, direct melting of hydrated 
basalts is possible, resulting in TTG magma gen¬ 
esis (Fig. 3c). 

► Greenstone belts represent only 5-10 % of 
the Archean terrains. These elongated structures 
(typically >100 x 20 km) contain variable 
amounts of metamorphosed mafic to ultramafic 
volcanic sequences associated with sedimentary 
rocks. The name “greenstone” comes from the 
green hue imparted by the color of the metamor- 
phic minerals within the mafic rocks. Chlorite, 
actinolite, and other green amphiboles are the 
usual green minerals. In some cases, greenstone 
belts show a specific stratigraphic sequence, with 
ultramafic lavas (komatiites) at the base of the 
sequence, followed by basalts (often erupted 
subaqueously with typical pillow structures). 
Variably metamorphosed sedimentary rocks 
(► metasediments) are emplaced at the top of 




















Archean Eon 


129 


Archean Eon, 

Fig. 4 Pillow lavas of 
2.65 Ga-old tholeiitic basalt 
from Kuhmo (Finland) 
(Photo H. Martin) 



Archean Eon, 

Fig. 5 Clastic sediments 
(conglomerate) from the 
base of the 3.22 Ga-old 
Moodies group, Barberton, 
South Africa (Photo 
H. Martin) 



the sequence. Greenstone belts are in complex 
contact relationships with adjacent plutons or 
metamorphic rocks: Commonly, the contacts are 
structurally modified (thinned or thickened) 
contactmetamorphic aureoles; brittle-ductile 
fault planes are also common. 

► Komatiites are ultramafic volcanic rocks 
(Arndt et al. 2008), almost exclusively restricted 
to the Archean eon, which are distinguished from 
the more common basalts by a higher content of 
MgO (>18 %) and correlated low contents of 
most other elements. The high Mg content is 
explained by a higher degree of melting of the 
mantle; the emplacement temperatures of 
komatiites ranges between 1,400 °C and 
1,650 °C (Amdt et al. 2008) compared to 
1,100-1,300 °C for modern basalts. They 


demonstrate that the internal Earth heat produc¬ 
tion in the Archean was higher than today. After 
emplacement, these magmas cooled very rapidly, 
resulting in acicular and dendritic textures, 
referred to as “spinifex” textures, which are typ¬ 
ical of komatiites. Earth almost totally ceased to 
produce komatiites after 2.5 Ga. Archean mafic 
volcanics are mainly tholeiitic basalts (Fig. 4), 
while calc-alkaline lavas are rare. In contrast to 
modern Earth, Archean andesites are rare. At the 
top of the sequence, more felsic rocks (dacites to 
rhyolites) can occur interbedded within the sedi¬ 
mentary successions. 

Sedimentary successions include thick 
litharenites deposited in deep water as turbidites 
(Fig. 5) and subordinates conglomerates. Well- 
preserved 3.5 Ga old turbidites can be observed in 





130 


Archean Eon 


Archean Eon, 

Fig. 6 Banded Iron 
Formation (BIF) from 
Copping Gap (Australia). 
These rocks consist of 
alternating silica- and iron- 
rich layers (Photo 
H. Martin) 



Archean Eon, 

Fig. 7 Dyke of high-Mg 
granodiorite (sanukitoid) 
intrusive into the 2.65 Ga- 
old Kuhmo greenstone belt 
(Finland) (Photo H. Martin) 



the Komati River valley of the Barberton Green¬ 
stone Belt, South Africa. They are overlain by 
and interbedded with siltstones, shales, chert, and 
banded iron formations (BIF; Fig. 6). Cherts and 
BIF are common lithologies in Archean green¬ 
stone belts and are likely the result of intense 
hydrothermal activity on the ocean floor 
(Westall 2005; Van Kranendonk 2006). 

Both the TTG basement and the greenstone 
belts were later intruded by high-magnesium 
granitoids or sanukitoids (Fig. 7). These calc- 
alkaline granites are rich in potassic feldspars 
and magnesium and they might derive by melting 
of a mantle peridotite, whose initial composition 


was modified by assimilation of TTG (Martin 
et al. 2009). 

Archean Geodynamics 

Modern plate tectonics induces horizontal forces 
that cause thrusting during orogenesis. These 
structures are known in most Archean terranes, 
indicating that tectonics similar to modem plate 
tectonics was operating since at least 4.0 Ga ago. 
However, Archean terranes also show large evi¬ 
dence of major vertical deformation that produce 
dome-and-basin structures (Fig. 8) which are 
exclusive to Archean times. This type of tectonics 
is driven by gravity (as opposed to plate tectonics 






Archean Eon 


131 



Archean Eon, Fig. 8 (Left) Sketch depicting the three 
main steps of sagduction: (1) In a greenstone belt, high- 
density komatiites (d = 3.3 g/cm 3 ) emplace over lower 
density (d = 2.7 g/cm 3 ) TTG basement rocks, thus gen¬ 
erating an inverse density gradient; (2) komatiites sink 
downward into the TTG basement which favor a relative 
upward motion of the TTG; (3) the movement is amplified 


creating a sedimentation basin at the center of the green¬ 
stone belt. Dark gray is komatiites, light gray is TTG 
basement, and white are sediments. (Right) Satellite 
photo of the sagduction structures at the Pilbara craton, 
Western Australia. The greenstone belts (in dark gray) are 
localized between TTG domes (white). The width of the 
photo is ~300 km 


which is driven by mantle convection) and this 
process has been known as sagduction since the 
1970s (Gorman et al. 1978). Sagduction struc¬ 
tures result from the down motion of high 
density greenstones (such as komatiites; 
density = 3.3 g/cm 3 ) into the TTG basement 
(density = 2.7 g/cm 3 ) and the concomitant 
upward motion of low-density TTG into the 
greenstones creating inverse diapirs. At the top 
of the inverted diapirs, a basin is created allowing 
deposition of sedimentary rocks. Several author¬ 
ities have suggested that horizontal forces acted 
mainly at the plate boundaries (as today) while 
sagduction processes were concentrated within 
plates. 

Another difference compared with today is the 
supposed length of the mid-ocean ridges, i.e., the 
divergent boundaries between two plates. Indeed, 
the large amounts of internal heat produced dur¬ 
ing Archean times has necessarily been released, 
otherwise, the accumulated heat should have 
resulted in melting the external part of our planet, 
which is not attested by geological record. As 
conduction is not efficient at all to evacuate inter¬ 
nal heat, Archean convection should have played 
this role and, as today, heat must have been 
released by ocean-ridge systems. As the amount 


of heat to evacuate was greater, it can be con¬ 
cluded that the excess of heat has been released 
through convective processes. Convection rate 
could have been slightly greater, but mainly the 
ridge length was significantly greater than today. 
The amount of heat dissipated is correlated with 
cubic square of the ridge length (Hargraves 
1986). Because the Earth volume and surface 
did not significantly change since 4.5 Ga, a 
greater ridge length should result in smaller 
plates (Fig. 9). The greater ridge length can also 
account for the abundance of cherts and BIFs in 
Archean greenstone belts. 

Hydrosphere, Atmosphere, and Climate 

There is good evidence that oceans were present 
on the Earth already in the Early Archean 
(~3.8 Ga ago) after the ► Late Heavy Bombard¬ 
ment (Abe 1993; Sleep et al. 2001). The convinc¬ 
ing evidence comes from one of the oldest areas 
of volcanic and sedimentary rocks - the ► Isua 
Supracrustal Belt, West Greenland. The ages of 
the rocks have been established at about 
3.7-3.8 Ga (for Nuvvuagittuq a date of 4.28 Ga 
has been proposed; O’Neil et al. 2008). In the 
Isua Supracrustal Belt, pillow basalts provide 
evidence of underwater eruption and 















132 


Archean Eon 



Today Archean 


Archean Eon, Fig. 9 Sketch representing the size of the tectonic plates that presently cover the surface of the Earth 
(left) and that supposed for the Archean plates (right) 


metasedimentary rocks (banded iron formations, 
metapelite, and ferruginous quartzite) are the 
products of erosion, fluvial transport, and sub¬ 
aqueous deposition (Rosing et al. 1996). 

Primary fluid inclusions were found in quartz 
crystals in iron oxide structures from the 3.5 to 
3.2 Ga ► Barberton greenstone belt, South Africa 
(Channer et al. 1997), intra-pillow quartz from 
the Dresser Formation (3.49 Ga), ► Pilbara era- 
ton, Western Australia (Foriel et al. 2004), and in 
the 2.7 Ga Abitibi Greenstone Belt, Ontario, Can¬ 
ada (Weiershauser and Spooner 2005). The anal¬ 
ysis of major cations and anions indicates that the 
chemistry of the seawater was similar to today, 
with some noticeable differences in iron, iodine, 
and bromine abundances indicating a larger influ¬ 
ence of hydrothermal fluids (today, the chemistry 
of seawater is mainly controlled by weathering of 
continents with a minor role for hydrothermal 
fluids). Salinity was basically NaCl-dominated, 
though salinities up to ten times the present 
values have been measured, possibly related to 
seawater evaporation in closed basins (Foriel 
et al. 2004). 

The atmosphere was possibly mildly reducing. 
The amount of N 2 was likely close to the present 
level (Kasting 1993); C0 2 might have been pre¬ 
sent in larger amounts (up to 1 % in volume or 
higher; Kasting 1987), while oxygen was likely 


~1 ppmv against the 21 % by volume today. 
Oxygen concentrations rose only at the end of 
Archean to values close to 1 % of their present- 
day level, probably because of shifts in the com¬ 
petition between the production of oxygen 
derived from cyanobacteria photosynthesis and 
the rate of consumption of oxygen by different 
geological processes. The amount of C0 2 in the 
atmosphere is still a matter of debate, but the 
occurrence of larger amounts of greenhouse 
gases (C0 2 , CH 4 ) may have been needed in the 
Archean atmosphere to counterbalance the lower 
radiation from the faint young Sun, which was 
~30 % less than the present-day value. Archean 
terranes do not contain evidence for major glaci¬ 
ations during the first two billion years of the 
Earth’s history indicating that a warmer climate 
(as suggested by high ocean temperatures; Robert 
and Chaussidon 2006) dominated during the eon. 

Life 

Though the timing of the origin of life is 
unknown, the Archean world likely saw the 
emergence of the first organisms. Several mor¬ 
phological, molecular, and chemical traces of life 
punctuate the Archean sedimentary record. Cur¬ 
rently, it is difficult to declare with certainty what 
the oldest trace of life is, and importantly what its 
nature and habitat were. Life can be traced 







Archean Eon 


133 


Archean Eon, 

Fig. 10 3.5 Ga-old 
stromatolites from North 
Pole (Pilbara, Australia) 



unambiguously to approximately 2.7-3.0 Ga ago 
(Lopez-Garcia et al. 2006). Beyond this point 
many claims for biological processes have been 
made, and all of them have to some degree been 
questioned. Some of the intriguing but controver¬ 
sial early Archean traces include (1) isotopically 
light graphite inclusions in rocks older than 
3.8 Ga from Akilia island and the Isua 
Supracrustal Belt in southwest Greenland 
(Mojzsis et al. 1996; Van Zuilen et al. 2002); 
(2) kerogenous microstructures, stromatolites, 
and diverse stable isotope ratio anomalies in 
3.5 Ga cherts from the Pilbara Granitoid- 
Greenstone Belt in Western Australia (Schopf 
1993; Brasier et al. 2002; Ueno et al. 2006; Pinti 
et al. 2009) (Fig. 10); (3) kerogenous microstruc¬ 
tures, stromatolites, and diverse stable isotope 
ratio anomalies in cherts, as well as microscopic 
tubes in altered pillow basalts from the 3.4 to 
3.2 Ga Barberton Greenstone Belt in South 
Africa (Staudigel et al. 2008). 

See Also 

► Acasta Gneiss 

► Akilia 

► Amphibolite Facies 

► Archean Traces of Life 

► Barberton Greenstone Belt 

► Basalt 

► Canadian Precambrian Shield 


► Craton 

► Earth, Formation and Early Evolution 

► Earth’s Atmosphere, History of the Origins 

► Granite 

► Greenstone Belts 

► Igneous Rock 

► Isua Supracrustal Belt 

► Metamorphic Rock 

► Metamorphism 

► Metasediments 

► Pilbara Craton 

► Pillow Lava 

► Shield 

► Volcaniclastic Sediment 


References and Further Reading 

Abe Y (1993) Physical state of the very early Earth. Lithos 
30:223-235 

Amdt N, Lesher MC, Barnes SJ (2008) Komatiite. 
Cambridge University Press, New York, 488 pp 

Bowring SA, Williams IS (1999) Priscoan (4.00-4.03 Ga) 
orthogneisses from northwestern Canada. Contrib 
Mineral Petrol 134:3-16 

Brasier M, Green O, Lindsay J, Mcloughlin N, Steele A, 
Stoakes C (2005) Critical testing of Earth’s oldest 
putative fossil assemblage from the ~3.5 Ga Apex 
chert, Chinaman Creek, Western Australia. Precam¬ 
brian Res 140(l-2):55-102 

Channer DMDR, de Ronde CEJ, Spooner ETC (1997) The 
Cl-Br-I composition of ~3.23 Ga modified seawater: 
implications for the geological evolution of 




134 


Archean Mantle 


ocean halide chemistry. Earth Planet Sci Lett 
150:325-335 

Condie KC (1994) The Archean crustal evolution. Devel¬ 
opments in Precambrian geology. Elsevier, Amster¬ 
dam, 528 pp 

Foriel J, Philippot P, Rey P, Somogyi A, Banks D, Menez 
B (2004) Biological control of Cl/Br and low sulfate 
concentration in a 3.5-Gyr-old seawater from North 
Pole, Western Australia. Earth Planet Sci Lett 
228:451—463 

Gorman BE, Pearce TH, Birkett TC (1978) On the struc¬ 
ture of Archean greenstone belts. Precambrian Res 
6:23-41 

Hargraves RB (1986) Faster spreading or greater ridge 
length in the Archean. Geology 14:750-752 

Jahn B-M, Glikson AY, Peucat JJ, Hickman AH 
(1981) REE geochemistry and isotopic data of 
Archean silicic volcanics and granitoids from the 
Pilbara Block, Western Australia: implications for 
the early crustal evolution. Geochim Cosmochim 
Acta 45:1633-1652 

Kasting JF (1993) Earth’s early atmosphere. Science 
259:920-926 

Lopez-Garcia P, Moreira D, Douzery E, Forterre P, van 
Zuilen MA, Claeys P, Prieur D (2006) Ancient fossil 
record and early evolution (ca. 3.8 to 0.5 Ga). Earth 
Moon Planet 98:248-268 

Martin H (1995) The Archean grey gneisses and the gen¬ 
esis of the continental crust. In: Condie KC (ed) The 
Archean crustal evolution. Elsevier, Amsterdam, 
pp 205-259 

Martin H, Moyen J-F (2002) Secular changes in TTG 
composition as markers of the progressive cooling of 
the Earth. Geology 30:319-322 

Martin H, Moyen J-F, Rapp R (2009) The sanukitoid 
series: magmatism at the Archean-Proterozoic transi¬ 
tion. Earth Environ Sci Trans R Soc Edinb 100:15-33 

Mojzsis SL, Arrhenius G, Friend CRL (1996) Evidence 
for life on Earth before 3,800 million years ago. Nature 
384:55-57 

O’Neil J, Carlson RW, Francis D, Stevenson RK (2008) 
Neodymium-142 evidence for Hadean Mafic crust. 
Science 321:1828-1831 

Pinti DL, Hashizume K, Sugihara Y, Massault M, 
Philippot P (2009) Isotopic fractionation of 
nitrogen and carbon in Paleoarchean cherts from 
Pilbara Carton, Western Australia: origin of 15 N- 
depleted nitrogen. Geochim Cosmochim Acta 
73(13):3819—3848 

Robert F, Chaussidon M (2006) A palaeotemperature 
curve for the Precambrian oceans based on silicon 
isotopes in cherts. Nature 443:969-972 

Rosing MT, Rose NM, Bridgwater D, Thomsen HS 
(1996) Earliest part of Earth’s stratigraphic record: a 
reappraisal of the >3.7 Ga Isua (Greenland) 
supracrustal sequence. Geology 24:43-46 

Schopf JW (1993) Microfossils of the early Archean apex 
chert: new evidence of the antiquity of life. Science 
260(5108):640-646 


Sleep NH, Zahnle K, Neuhoff PS (2001) Initiation of 
clement surface conditions on the earliest Earth. Proc 
Natl Acad Sci U S A 98(7):3666-3672 
Smithies RH (2000) The Archean tonalite-trondhjemite- 
granodiorite (TTG) series is not an analogue of Ceno- 
zoic adakite. Earth Planet Sci Lett 182:115-125 
Staudigel H, Furnes H, Mcloughlin N, Banerjee N, 
Connell L, Templeton A (2008) 3.5 billion years of 
glass bioalteration: volcanic rocks as a basis for micro¬ 
bial life? Earth Sci Rev 89:156-176 
Ueno Y, Yamada K, Yoshida N, Maruyama S, Isozaki 
Y (2006) Evidence from fluid inclusions for microbial 
methanogenesis in the early Archean era. Nature 
440:516-519 

Van Kranendonk MJ (2006) Volcanic degassing, 
hydrothermal circulation and the flourishing of early 
life on Earth: a review of the evidence from 
c. 3490-3240 Ma rocks of the Pilbara Supergroup, 
Pilbara Craton. West Aust Earth Sci Rev 
74(3-4): 197-240 

van Zuilen MA, Lepland A, Arrhenius G (2002) 
Reassessing the evidence for the earliest traces of 
life. Nature 418(6898):627-630 
Weiershauser L, Spooner E (2005) Seafloor hydrothermal 
fluids, Ben Nevis area, Abitibi Greenstone Belt: impli¬ 
cations for Archean (~2.7 Ga) seawater properties. 
Precambrian Res 138(1—2):89—123 
Westall F (2005) The geological context for the 
origin of life and the mineral signatures of fossil 
life. In: Gargaud M, Barbier B, Martin H, Reisse 
J (eds) Lectures in astrobiology. Springer, Berlin, 
pp 195-226 

Wilde SA, Valley JW, Peck WH, Graham CM (2001) Evi¬ 
dence from detrital zircons for the existence of conti¬ 
nental crust and oceans on the Earth 4.4 Ga ago. Nature 
409:175-178 


Archean Mantle 

Nicholas Arndt 1 and Daniele L. Pinti 2 
^STerre, Universite Grenoble Alpes, France 
2 GEOTOP Research Center for Geochemistry 
and Geodynamics, Universite du Quebec a 
Montreal, Montreal, QC, Canada 

Definition 

Archean mantle refers to the terrestrial mantle 
during the Archean eon, which differed both 
physically and chemically from the modem-day 
mantle. 



Archean Tectonics 


135 


Overview 

The mantle is that part of Earth or other planets 
between the ► crust and the core. The upper 
mantle, from the base of the crust at about 9 km 
(oceanic) or 30 km (continental) to the transition 
zone at 660 km, is composed mainly of ► peri- 
dotite, an ultramafic rock mainly composed of 
► olivine, pyroxene, and minor garnet. In the 
lower mantle, which extends to the core at 
2,990 km, the minerals are mainly Mg- and 
Ca-perovskite ((Mg, Ca)Ti0 3 ) and 
magnesiowiistite ((Mg, Fe)0). The mantle is 
solid except for localized zones of partial melt¬ 
ing, but it convects with velocities of a few tens of 
centimeters per year. 

The Archean mantle differed from the modern 
mantle in several important ways. Because the 
main sources of heat - ► radioactivity, residual 
heat from accretion, and core 
crystallization - were more active than today, 
the mantle was hotter and it convected more 
vigorously. Higher temperatures in mantle 
upwelling beneath ► mid-ocean ridges produced 
larger melt volumes and a thicker oceanic crust. 
Higher temperatures at depth may have resulted 
in larger and hotter mantle plumes. The abun¬ 
dance of ► komatiite only in the Archean pro¬ 
vides evidence of higher mantle temperatures. 

The composition may also have been differ¬ 
ent, if, as many authors believe, the continental 
crust was less voluminous through the Archean. 
Continental crust contains far higher concentra¬ 
tions of elements such as Si, Al, K, and the 
“incompatible” trace elements, and the segrega¬ 
tion of this crust has left the upper part of the 
modem mantle depleted in these elements. If 
crustal growth were incomplete in the Archean, 
either the volume of depleted mantle or the 
degree of depletion would have been less. The 
isotopic composition of rocks from the Archean 
mantle should, in theory, cast some light on the 
problem but at present the message is ambiguous. 
The Hf isotope compositions of ► zircons show 
evidence of extraction prior to 4 Ga ago of 
enriched material, perhaps continental crust; the 
Nd isotopic compositions of rocks from the oldest 


areas of West Greenland have been interpreted to 
indicate derivation from strongly depleted man¬ 
tle. Either these rocks were extracted from a small 
and localized volume of mantle or a large volume 
of continental crust had formed at this time. 

If the mantle were significantly hotter, it 
would have been drier because the reactions that 
liberate water in upwelling mantle, where 
degassing takes place, or in subduction zones, 
where the mantle is rehydrated, are temperature- 
dependent. The proportion of water on the sur¬ 
face was larger and therefore the volume of the 
oceans may have been greater. The oxidation 
state of the Archean mantle has been investigated 
using redox-sensitive elements such as vana¬ 
dium; no significant difference from that of the 
modern mantle has been established. 


See Also 

► Archean Environmental Conditions 

► Archean Eon 

► Archean Tectonics 

► Isua Supracrustal Belt 

► Jack Hills (Yilgarn Craton, Western Australia) 

► Komatiite 

► Mantle, Oxidation of 

► Peridotite 

► Ultramafic Rocks 


Archean Tectonics 

Martin J. Van Kranendonk 

School of Biological, Earth and Environmental 

Sciences, University of New South Wales, 

Australia 


Keywords 

Archean; Continents; Crust; Lithosphere; Non- 
uniformitarian; Plate tectonics; Tectonics; Ther¬ 
mal evolution of the Earth; TTG 




136 


Archean Tectonics 


Synonyms 

Crustal deformation; Early earth 

Definition 

Archean tectonics is the study of the formation, 
interaction, and deformation of the Earth’s conti¬ 
nental and oceanic crust during early Earth his¬ 
tory (the Archean Eon; ca. 4.0-2.5 Ga) and the 
driving forces behind these processes, including 
mantle plumes, subduction, and accretion/colli¬ 
sion. This topic remains highly controversial due, 
in part, to a fragmentary rock record, but also to 
nonunique interpretations of complex geological 
datasets in the absence of actualistic plate config¬ 
urations. Historically, Archean tectonics has been 
polarized into uniformitarian (i.e., analogous 
with modern, or Phanerozoic Earth) and 
non-uniformitarian views, but recent studies 
have favored modern Earth processes in the 
Archean, complicated by problems arising 
mainly from greater heat production and higher 
mantle temperatures (Condie 1994; Benn 
et al. 2006; Brown and Rushmer 2006). The dis¬ 
cussion revolves around the basic question if and 
how tectonics in the Archean was different from 
modem-style plate tectonics. 

History 

Although the relative antiquity of some parts of 
the continental crust was recognized more than 
150 years ago (Logan 1857), it was not until the 
advent of radiometric dating, 100 years later, that 
the antiquity of much of the continental crust was 
fully appreciated (Stockwell 1961). Only in the 
past decade it has been discovered that the pre¬ 
served crustal record on Earth extends back to 
within 150 Ma of the age of formation of the 
Solar System (Wilde et al. 2001). Early geologi¬ 
cal studies found that continental crust older than 
about 2.5 Ga was different from younger crust. 
Archean crust showed distinct regional patterns 
defined by overlapping, elliptical areas of granitic 
rocks (gregarious batholiths; Macgregor 1951); 


steeply dipping, generally synclinal, greenstone 
keels (granite-greenstone crust: Hickman 1984; 
Chardon et al. 1996); and a unique type of ultra- 
mafic lava known as ► komatiite derived from 
high-temperature mantle melts (Viljoen and 
Viljoen 1969; Arndt 2003). Many authors also 
noted that Archean granite-greenstone crust 
lacked the diagnostic features of modem subdue- 
tion/collision zones, including accretionary tec¬ 
tonic melange, ophiolites, and high-pressure/ 
low-temperature metamorphism, leading some 
to suggest - even recently - that plate tectonics 
either did not operate in the Archean (Hamilton 
1998; McCall 2003; Stern 2005) or operated in 
conjunction with other processes (e.g., Rey 
et al. 2003; Sandiford et al. 2004). 

Overview 

The Archean ► mantle was probably 100-300 K 
hotter than today, which significantly affected the 
dominant tectonic style. Geochemical, geophysi¬ 
cal, and modeling evidence suggests some form 
of ► plate tectonics in the Archean, although the 
absence of key characteristics such as ophiolites 
and blueschists implies that it probably differed 
from modern ► plate tectonics. Evidence for 
Archean plate tectonics was recognized quite 
early on in the type of Archean ► crust known 
as high-grade gneiss terranes. This evidence 
included the presence of large-scale recumbent 
isoclinal folds associated with crustal thickening 
(Bridgwater et al. 1974; Myers 1976; Wilks 
1988; Hanmer and Greene 2002), voluminous 
sodic granitoids derived from high-pressure melt¬ 
ing of basalt (Martin et al. 2005; 
Rapp et al. 1991), high-pressure metamorphism 
(Riciputi et al. 1990; Harley 2003), and structures 
consistent with terrane accretion (Nutman 
et al. 2002; Windley and Garde 2009). Over the 
past three decades, abundant evidence for 
Archean plate tectonics has also been found in 
some Archean granite-greenstone terrains in the 
form of thrusts and recumbent isoclinal folds, 
coupled high-pressure-low-temperature meta¬ 
morphism, fossil subduction zones, accreted ter¬ 
ranes, rift sequences, and subduction-zone 



Archean Tectonics 


137 


magmatism (Card 1990; Heubeck and Lowe 
1994; Calvert et al. 1995; Smithies et al. 2005; 
Moyen et al. 2006; Wyman et al. 2006; Van 
Kranendonk 2007; Van Kranendonk 
et al. 2010). However, an absence of hallmark 
characteristics of modern subduetion-accretion 
zones in many granite-greenstone terrains 
(Hamilton 1998; McCall 2003; Stern 2005), the 
autochthonous nature of some major greenstone 
successions, and suggestions that mantle roots 
form through in situ melting events rather than 
through subduction stacking indicates local 
crustal development as volcanic plateaus devel¬ 
oped on top of older continental basement (e.g., 
Blenkinsop et al. 1993; Bleeker et al. 1999; Van 
Kranendonk et al. 2007). Indeed, many studies 
suggest that some pieces of Archean crust contain 
features that cannot be ascribed to uniformitarian, 
Phanerozoic-type, plate tectonics, but rather 
formed as a result of large-scale infra-crustal 
differentiation accompanying periods of mantle- 
plume-related magmatism (Stein and Hofmann 
1994; Whalen et al. 2002; Rey et al. 2003; Smith¬ 
ies et al. 2009; Van Kranendonk et al. 2009). The 
fact that different processes have been recognized 
from studies of different pieces of Archean crust 
indicates that there was no single Archean tec¬ 
tonic process, but rather that - as with modern 
Earth - Archean continental crust formed through 
a variety of processes, including plate tectonics 
and mantle-derived upwellings, and probably 
through the interaction between these two 
end-member processes. 

Basic Methodology 

Direct field evidence from Archean continental 
lithosphere provides a record of Archean tectonic 
processes. Geophysical methods include paleo- 
magnetism and seismic evidence. Solidifying 
magma registers the paleo-latitude and thus can 
record (relative) continental motion. Seismic pro¬ 
files through Archean crust indicate the presence 
of dipping seismic reflectors, which could be 
interpreted as the remnants of a fossil subduction 
zone. Among the geological evidence, ophiolites 
(slivers of oceanic lithosphere that escaped 


subduction), blueschists, and ultrahigh-pressure 
metamorphic rocks (partly subducted rocks that 
emerged again at the Earth’s surface) are all well- 
understood features associated with modem plate 
tectonics. Their occurrence throughout Earth’s 
history is thought to provide clear indicators of 
plate-tectonic activity. Large-scale tectonic 
structures can be indicative as well: linear struc¬ 
tures are often interpreted as remnants of subduc¬ 
tion trenches, whereas large oval-shape structures 
are thought to be diapir- or dome-related that 
might not need any plate-tectonic activity. 

Geochemical and petrologic techniques pro¬ 
vide the “fingerprints” of the chemical processes 
associated with Archean tectonics. Mantle melt¬ 
ing will deplete the mantle of “incompatible” 
elements (Rollinson 2007). Another form of ele¬ 
ment separation occurs due to differences in fluid 
mobility, so that some elements will preferen¬ 
tially move with any pore fluids, while others 
will stay in the residue. These processes will 
leave geochemical fingerprints that can be used 
to recognize ancient subduction processes (e.g., 
Shirey et al. 2008). In addition, geochemical dat¬ 
ing of crustal rocks and mantle material shows 
how mantle material was depleted through time 
by continent formation. Since continents today 
are formed primarily at subduction zones, this 
has been interpreted as another indication for 
the presence of ancient subduction and therefore 
plate tectonics. 

Various modeling techniques are used to fur¬ 
ther constrain the range of dynamically viable 
tectonic processes during the Archean. Tectonic 
vigor is related to mantle convection and inti¬ 
mately couples to the cooling rate of the Earth: 
tectonic activity leads to increased heat loss from 
the mantle, and mantle temperature influences the 
vigor of tectonic activity. Mantle temperature 
through time therefore provides an important 
constraint, and parameterized and numerical 
modeling techniques provide a means to link 
mantle temperature and tectonic activity. 
Today’s plate tectonics is primarily driven by 
the subduction process, and subduction dynamics 
is, to a large extent, influenced by mantle temper¬ 
ature due to melting events and the temperature- 
dependent strength of the lithosphere. 



138 


Archean Tectonics 


The viability and style of subduction in an early, 
hotter Earth is investigated using parameterized 
and numerical modeling techniques. 

Key Research Findings 

Field evidence has been used to argue for or 
against modem-style plate tectonics in the 
Archean. Ophiolites are preserved pieces of old 
oceanic lithosphere that escaped subduction, and 
the occurrence of old ophiolites is therefore a 
clear indicator of plate-tectonic activity. They 
are widespread since ~ 1 Ga, but are much rarer 
before that. Recently, Furnes et al. (2007) 
reported a 3.8 Ga-old ophiolite in Isua, West 
Greenland, although their interpretation has 
been disputed. Other direct types of evidence 
for plate tectonics are blueschists and ultrahigh- 
pressure metamorphic rocks, which are both gen¬ 
erally believed to form within subduction zones, 
where they are brought down to large pressures 
and temperatures, and subsequently make it back 
to the surface. The oldest blueschists are 
ca. 850-700 Ma old, while the oldest UHP local¬ 
ities are ~600 Ma old. These data could indicate 
that modern-style plate tectonics did not start 
until the Neoproterozoic (Stern 2005) or that the 
appearance of plate tectonics evolved over time 
(van Hunen and van den Berg 2008). 

Earth’s thermal evolution provides further 
constraints. Today, plate tectonics forms the 
dominant cooling mechanism for the Earth and 
is therefore closely linked to the thermal evolu¬ 
tion of the Earth. The Archean Earth had an 
amount of radiogenic heat production two to 
three times larger than today due to the gradual 
decay of the dominant heat-producing elements 
uranium, thorium, and potassium in the mantle. 
Today, the surface geothermal heat flux (heat 
escaping the Earth’s interior) is ~30 % provided 
by internal radiogenic heating while the 
remaining 70 % comes from cooling of the 
Earth (Turcotte and Schubert 2002; Korenaga 
2006). This shows that surface heat flow from 
radiogenic heating was a lot more important in 
the Archean which implies that either surface 
tectonics were such that the total surface heat 


flux was higher or that Earth was not cooling 
(significantly) or was perhaps even heating 
up. Inferred liquidus temperatures from 
ophiolites and greenstone belts suggest a gradual 
mantle temperature drop of ~200 K since the 
Archean. Komatiitic melt data suggest a mantle 
potential temperature (i.e., mantle T extrapolated 
to surface P, T-conditions) reduction by~300 K 
for dry melting to ~ 100 K if melting took place 
under much wetter conditions. Jaupart 
et al. (2007) provide a recent overview of the 
thermal evolution of the Earth. 

The dynamical viability of subduction in the 
Archean has been questioned. Today, plate tec¬ 
tonics is primarily driven by dense slabs sinking 
into the mantle, and thereby pulling the trailing 
lithosphere across the surface. Archean plate tec¬ 
tonics would require a similar driving mecha¬ 
nism. A hotter mantle provides more melt and 
therefore a thicker, low-density mafic crust (up to 
20 km thick instead of today’s 5-8 km) that 
doesn’t easily subduct. Although dehydration 
during melting will make the plate composition- 
ally stronger and could allow for similar plate- 
tectonic rates in the Archean as today (Korenaga 
2006), thermal weakening would probably dom¬ 
inate if the mantle was substantially hotter and 
would result in weaker plates. The combined 
buoyancy and plate strength effects make sub¬ 
duction inefficient for mantle temperatures more 
than 150 K hotter than today (van Hunen and van 
den Berg 2008). 

Today’s continental crustal rocks (loosely 
termed andesites) differ significantly in trace- 
element composition from their Archean coun¬ 
terparts (trondhjemite-tonalite-granodiorite, or 
TTGs). Whereas andesites are thought to ulti¬ 
mately derive from melting in the hydrated 
supra-subduction mantle wedge, TTGs seem to 
form from wet melting of oceanic basalts at 
sometimes >50 km depth, and the most popular 
formation model is melting of subducting oceanic 
crust (Foley et al. 2002). So the differences 
between modern and Archean continental crust 
suggest a secular evolution of the subduction 
process. But at the same time, it indicates the 
need for a process to bring fluids to 50-100 km 
depth throughout the Earth’s history. At present, 



Archean Tectonics 


139 


no other mechanism than subduction seems capa¬ 
ble of doing that, which is regarded as one of the 
strong arguments in favor of Archean plate 
tectonics. 

However, although most studies support 
Archean plate tectonics, perhaps in some modi¬ 
fied form, the possibility of other dominant tec¬ 
tonic processes should not be excluded. If indeed 
plate tectonics were absent in the Archean, such 
alternative tectonic models were probably essen¬ 
tial to provide a mechanism for the observed 
steady mantle cooling of 50-100 K/Gyr. One 
popular model is the crustal delamination model 
(e.g., Zegers and van Keken 2001), in which 
mantle melting events would thicken the conti¬ 
nental crust until its base becomes gravitationally 
unstable and would cause lithospheric overturn. 
Such models would explain observations from 
early Archean rocks such as the ovoid-shaped 
intrusions in the eastern Pilbara craton. 


Applications 

The style and vigor of tectonics in the Archean 
has important consequences for many aspects of 
the evolution of the Earth. Tectonic style directly 
influences (a) how and when continents formed 
and why cratons remained stable and preserved 
over much of the Earth’s history (Lenardic 
et al. 2003); (b) how tectonics-related events 
such as melting, remelting, and fluid-related 
alteration has changed the composition of the 
mantle from its primitive composition shortly 
after core formation to its modern composition 
(Shirey et al. 2008); and (c) the composition of 
the atmosphere and oceans through ► degassing 
(during volcanism) and regassing (at subduction 
zones) of volatiles and surface weathering (Lowe 
and Tice 2007; Rollinson 2007), and through that 
the emergence and evolution of life on Earth. 
Furthermore, if plate tectonics has been operative 
throughout the changing conditions of the Earth 
during its history, how does that relate to the 
viability of plate tectonics on the other terrestrial 
planets of our solar system, such as on Mars 
(which has no plate tectonics today, but might 
have had some during its earliest history) or 


Venus (which doesn’t have plate tectonics, prob¬ 
ably because of the lack of liquid water, but 
perhaps experiences episodic large-scale mantle 
overturns). 

Future Directions 

Integrated, four-dimensional lithospheric studies 
of Archean lithosphere are the key future research 
directions, particularly in poorly studied regions. 
Detailed geochronology within a well- 
established map framework continues to be key 
to understanding formation processes of ancient 
crust, particularly when coupled with ongoing 
reevaluation of uniformitarian assumptions 
given known aspects of secular change. Hf iso¬ 
tope determination of zircon can help discrimi¬ 
nate juvenile crustal growth through subduction 
from volcanism and crustal recycling during epi¬ 
sodes of plume magmatism. Further understand¬ 
ing of crustal growth processes will be aided by 
more complete knowledge on the origin of sub¬ 
continental lithospheric mantle: detailed studies 
of primary dunite-harzburgite xenoliths are 
required to determine the age, composition, and 
history of these more depleted rocks, and their 
properties tied into detailed regional seismic 
studies, including physical modeling of their geo¬ 
physical response. Additional work is also 
required on the ► metamorphism of granite- 
greenstone terranes, specifically precise dating 
of mineral assemblages related to magmatic and 
deformational events and P-T studies of granitic 
rocks as a counterpart to greenstones, to test 
models of cold greenstone diapirs in hot rising 
granites (partial convective overturn; Smithies 
et al. 2009). Additional studies are required on 
the origin of Archean calc-alkaline felsic volca¬ 
nic rocks and high-Mg diorites to establish 
whether they are really the products of volcanic 
arc magmatism over an active subduction zone, 
as widely assumed, or the products of fraction¬ 
ation and crustal contamination of large tholeiitic 
magma chambers derived from mantle plumes. 
Additional research is required across the interval 
3.3-2.9 Ga, in order to assess the tantalizing 
clues that there may have been a global change 



140 


Archean Tectonics 


in crust-formation processes at this time, perhaps 
due to an increase in plate size and concomitant 
cooling of oceanic lithosphere and steepening of 
the angle of subducting oceanic lithosphere. Key 
open questions include the following: How did 
subduction initiate, and did plate tectonics remain 
operative from its first onset until today, or was it 
once more episodic (Sleep 2000)? Is the onset of 
plate tectonics related to any atmospheric and 
oceanic changes in the Archean, to the habitat 
that provided early life and its evolution, and to 
the presence of the Earth’s magnetic field? How 
does Archean tectonics relate to the observed 
peaks in continental crust formation at 3.3, 2.7, 
1.9, and 1.2 Ga (Condie 1998; Parman 2007)? 

See Also 

► Continental Crust 

► Degassing 

► Early Archean 

► Komatiite 

► Ophiolite 

► Plate Tectonics 


References and Further Reading 

Arndt N (2003) Komatiites, kimberlites, and boninites. 
J Geophys Res 108(B6):ECV 5-1-ECV 5-11 

Benn K, Mareschal J-C, Condie KC (2006) Archean 
geodynamics and environments. Geophysical mono¬ 
graph series, vol 164. American Geophysical Union, 
Washington, DC, p 320 

Bleeker W, Ketchum J, Jackson V, Villeneuve M (1999) 
The central slave basement complex, part I: its struc¬ 
tural topology and autochthonous cover. Can J Earth 
Sci 36:1083-1109 

Blenkinsop TG, Fedo CM, Bickle MJ, Eriksson KA, 
Martin A, Nisbet EG, Wilson JF (1993) Ensialic origin 
for the Ngezi Group, Belingwe greenstone belt, Zim¬ 
babwe. Geology 21:1135-1138 

Bridgwater D, McGregor VR, Myers JS 
(1974) A horizontal tectonic regime in the Archean 
of Greenland and its implications for early crustal 
thickening. Precambrian Res 1:179-197 

Brown M, Rushmer T (2006) Evolution and differentia¬ 
tion of the continental crust. Cambridge University 
Press, Cambridge 

Calvert AJ, Sawyer EW, Davis WJ, Ludden JN 
(1995) Archean subduction inferred from seismic 


images of a mantle suture in the Superior Province. 
Nature 375:670-674 

Card KD (1990) A review of the superior province of the 
Canadian shield, a product of Archean accretion. Pre¬ 
cambrian Res 48:99-156 

Chardon D, Choukroune P, Jayananda M (1996) Strain 
patterns, decollement and incipient sagducted green¬ 
stone terrains in the Archean Dharwar craton (southern 
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Archean Traces of Life 

Nicola McLoughlin 

Department of Earth Science and Centre for 
Geobiology, University of Bergen, Bergen, 
Norway 

Keywords 

Earliest evidence of life on earth; Emergence of 
life; Oldest fossils 


Synonyms 

Archean biosignatures; Trace of life 


Definition 

The ► Archean is the period of geological time 
between 3.8 and 2.5 billion years ago when life is 
thought to have emerged on Earth. Traces of 
Archean life are preserved in rare, fragmentary, 
and often highly altered rock sequences. Morpho¬ 
logical evidence for Archean life is provided by 
► microfossils, microborings, ► stromatolites, 
and wrinkle mats. Chemical evidence for life is 
recorded by stable isotope ratios of C and 


S especially. These different biosignatures are 
yet to provide a consistent and complete picture 
of early Archean ecosystems, and there is cur¬ 
rently little scientific consensus about when and 
where life first emerged on Earth. Refining our 
understanding of microbial biosignatures in the 
Archean rock record is essential to designing 
strategies for seeking life elsewhere in our uni¬ 
verse and for ratifying this evidence. 

Overview 

This entry first explains where to look for 
Archean traces of life, what evidence astrobiolo- 
gists seek, and how these rocks are investigated, 
especially the techniques and approaches 
involved. Then a review of current research find¬ 
ings is given focusing on selected case studies of 
microfossils, stromatolites, and microborings 
along with stable isotope evidence from the 
early Archean. Lastly, new frontiers in early 
earth research are described with the aim of better 
understanding the nature of Archean life and 
environments and how this translates to recogniz¬ 
ing signatures of life beyond earth. 

Basic Methodology 

Locating Well-Preserved Archean Rocks from 
Habitable Environments 

The search for Archean traces on life relies upon 
geological mapping and radiometric dating to 
locate rocks of Archean age. Worldwide, there 
are two ► cratons that preserve intact sequences 
of early Archean age where now metamorphosed 
volcanic and sedimentary rocks are preserved in 
► greenstone belts - so called because of the 
green color conferred by their typical metamor- 
phic minerals. The first of these is the Pilbara of 
Western Australia and the second is the Kaapvaal 
Craton of South Africa and the ► Barberton 
Greenstone Belt. In recent years, there have 
been several Archean scientific drilling projects 
that have targeted these sequences to seek the 
earliest evidence for life. Scientific drilling yields 
continuous sequences of rock unaffected by 




Archean Traces of Life 


143 


alteration at the earth’s surface allowing more 
complete investigation of well-preserved 
biosignatures within their geological context. 
Older Archean rocks between 3.8 and 3.7 Ga 
from the ► Isua supracrustal belt of Western 
Greenland and also Labrador are of much higher 
metamorphic grade and more intensely 
deformed. Thus, any morphological traces of 
life have been almost completely destroyed in 
these earliest rocks, and discussions regarding 
the evidence for life center on chemical evidence 
alone. 

The search for Archean life has traditionally 
centered on metasedimentary rocks, in particular 
cherts and carbonates. Geological environments 
where microbial remains are most likely to be 
preserved are those where rapid, contemporane¬ 
ous mineralization entombs and permineralizes 
living organisms. Precipitation of microcrystal¬ 
line silica is a good example and can preserve 
cellular remains with exceptionally high fidelity. 

► Cherts are formed in the vicinity of hydrother¬ 
mal vents, hot springs, and as chemical sediments 
on the Archean seafloor. The retention of fossil¬ 
ized biosignatures over geological time frames is 
increased if the host rock comprises phases that 
are resistant to postdepositional alteration pro¬ 
cesses such as diagenetic recrystallization, disso¬ 
lution, or replacement. In recent years, a new 
approach to seeking traces of Archean life has 
come to prominence, and this involves seeking 
“footprints” of life or tunnels created by microbes 
that etch rocks rather than the organic remains of 
the microorganisms themselves. Meta-volcanic 
glass from Archean seafloor ► pillow lavas has 
been found to contain such “microbial foot¬ 
prints,” and Archean carbonate sequences are 
now also being reexamined for evidence of such 
rock-tunneling microorganisms. 

An important criterion for establishing the 

► biogenicity of candidate Archean traces of 
life is the demonstration that the geological envi¬ 
ronment was viable for life. This translates to the 
assessment of habitability or, in other words, 
mapping out the environmental limits to life. 
There are a number of first-order differences 
between the Archean world and recent Earth 
that should be borne in mind. Firstly, Archean 


surface environments were largely anoxic, the 
atmosphere was probably rich in carbon dioxide 
and methane, and there was no ozone layer. Sec¬ 
ondly, seawater was supersaturated with silica, 
and its pH, temperature, and salinity are widely 
debated and certainly differed from today, with 
the ocean temperatures likely being higher. 
Thirdly, exactly when Archean ► plate tectonics 
began, the nature of early tectonic processes is 
unclear with profound implications for the 
cycling of nutrients on Earth and the oxidation 
of key geological reservoirs. A comprehensive 
review of the latest research investigating early 
Archean rocks can be found in Van Kranendonk 
et al. (2007). 

Textural Evidence of Life: Investigating 
Morphological Complexity 

Morphological ► complexity is often regarded as 
a diagnostic criterion for life. But it must be 
remembered that complex shapes do not require 
complex causes and can arise naturally in 
physiochemical systems as shown, for example, 
by snowflakes growth. There are three key mor¬ 
phological traces of life: ► microfossils, ► stro¬ 
matolites, and microborings, and interpretation of 
this morphological evidence proceeds hand in 
hand with studies of modem analogs and explo¬ 
ration of potential abiological mimics as 
explained below. 

Chemical Evidence of Life: Elemental and 
Isotopic Signatures 

► Isotopic ratios preserved in ancient rocks may 
record past biological activity and can be mea¬ 
sured by mass spectrometry to test for the pres¬ 
ence of life and sometimes identify the 
metabolisms involved. Carbon and sulfur are the 
main isotopic tools used in the search for Archean 
life, and these are introduced below. Elemental 
mapping in the vicinity of microbial remains 
can also be highly informative as the life 
activity and/or the subsequent decay of a micro¬ 
organism can modify the composition of the sur¬ 
rounding minerals. Examples are given below 
along with the techniques and instruments capa¬ 
ble of undertaking such isotopic and elemental 
mapping. 





144 


Archean Traces of Life 


Carbon Isotopes 

Carbon isotopes are probably the most studied 
isotopic tracer of life on Earth. Carbon isotope 
systematics is described elsewhere in this vol¬ 
ume, and rather here the focus is on their appli¬ 
cation to seeking traces of Archean life. The 5 13 C 
of the biosphere through time has been measured 
directly from carbonaceous material found in 
ancient sediments, and if this can be shown to 
be both syngenetic and endogenetic, then it 
records the microbial metabolisms employed at 
that time. Typical Archean organic matter is 
found to have a 5 13 C value of —20 %o relative 
to inorganic carbonate leading many researchers 
to claim that biological activity began 3.8 billion 
years ago (Schidlowski 2001). Specific microbial 
metabolisms have also been inferred on the basis 
of the magnitude of carbon isotopic fraction¬ 
ations measured from Archean rocks, and several 
examples will be discussed below. 

Sulfur Isotopes 

Microorganisms that metabolize sulfur com¬ 
pounds are one of the most deeply rooted groups 
in the tree of life. ► Sulfur isotopes preserved in 
ancient sulfides especially pyrite along with sul¬ 
fate minerals like barite are used to trace ancient 
microbial metabolisms. A review of sulfur iso¬ 
topes in early Archean rocks can be found in Van 
Kranendonk et al. (2007). The baseline for 
interpreting such data is provided by studies of 
modem microbes that employ sulfur-based 
metabolisms including sulfur oxidation, sulfate 
reduction, and sulfur disproportionation 
(Canfield 2001). ► Sulfur cycling and isotope 
systematics are explained in detail elsewhere in 
this volume. Of particular interest to Archean 
studies is the development of mass spectrometry 
techniques that can measure mass-independent 
sulfur isotope fractionations (MIF) as will be 
explained below. Sulfur isotopes have also pro¬ 
vided a hotly debated tracer for the rise of atmo¬ 
spheric oxygen (e.g., Farquhar et al. 2000), and 
this will not be discussed further here. 

The S isotope record from ~2 Ga onward 
shows 5 34 S fractionations of 50-60 %o between 
sulfides that are depleted relative to coexisting 
sulfates, and this has been attributed to microbial 


sulfate reduction (Canfield and Rais well 1999). 
In older rocks such fractionations are much 
smaller with most sedimentary sulfides older 
than ~2.7 Ga showing a narrow 5 34 S range, and 
this has several possible explanations. Firstly, a 
nonbiological origin from H 2 S derived from 
hydrothermal or volcanogenic processes always 
needs to be tested. Secondly, sulfate reducers 
only discriminate sulfur isotopes when seawater 
sulfate concentrations are above millimolar. 
Thus, the absence of a large 5 34 S signal before 
~2.7 Ga could mean that either seawater sulfate 
levels were low or that sulfate reduction had not 
yet evolved. Evidence in support of the former 
explanation is discussed below. 

Additional Stable Isotope Systems 
Additional isotopic systems that have been uti¬ 
lized to investigate Archean environments and 
traces of life are explained in a rich literature 
that includes silicon, oxygen, and ► deuterium 
isotopes measured on cherts to investigate sea¬ 
water temperatures (e.g., Hren et al. 2009), 

► nitrogen isotopes measured especially on 

► kerogen (e.g., Godfrey and Falkowski 2009), 
and ► iron isotopes in a range of rock types (e.g., 
Dauphas et al. 2004). 

Instrumental Techniques for Seeking Traces 
of Archean Life 

Having outlined the morphological and chemical 
basis for seeking Archean traces of life, the tech¬ 
niques used for deciphering these traces are 
reviewed. All such investigations begin with geo¬ 
logical mapping to identify the nature of the host 
rocks, to determine if the context was plausible 
for life, and to establish age relationships with 
other rock units. The key techniques are: 

Optical microscopy : Examines the morphology 
of the putative biosignature in two dimensions 
and if z-plane stacking is available in three 
dimensions and also the mineralogy of the 
enclosing rock and relative age of the candi¬ 
date biosignature with respect to other fabrics 
in the rock. 

Scanning electron microscopy - with energy- 
dispersive X-rays (SEM-EDX): Examines the 



Archean Traces of Life 


145 


shape and surface morphology of a putative 
biosignature. Accompanying element distri¬ 
bution maps can be created using EDX. 

Focused ion beam milling - transmission elec¬ 
tron microscopy (FIB-TEM): FIB is used to 
mill a very thin ^100 nm wafer from a chosen 
site within a sample targeting, for example, 
fossilized cell walls. This can then be imaged 
by TEM at the nanometer scale to reveal cel¬ 
lular and crystalline structures. Electron dif¬ 
fraction patterns can also be generated to 
identify crystalline phases. 

Electron microprobe : Is used for nondestructive 
analysis of the chemical composition of a 
biosignature including the quantification of 
elements present at levels as low as 100 ppm. 

Confocal laser Raman microspectroscopy : Gen¬ 
erates spectra that are diagnostic of different 
mineral and organic polymorphs and can be 
used for rapid mineral identification. Also the 
spectra can be used for nondestructive 2-D and 
3-D morphological mapping of, for instance, 
microfossils. Raman microspectroscopy is 
also useful for thermometry, providing crucial 
assessment of the thermal maturity of 
organics, important to evidence their 
► syngenicity. 

Atomic force microscopy (AFM): Can be used to 
image and measure the atomic surface struc¬ 
ture of a sample at the nanoscale by “feeling” 
the surface with a cantilever tip (can be 
coupled to a Raman microscope). 

Laser ablation inductively coupled plasma mass 
spectrometry (LA-ICP-MS) of stable isotopes 
C and S: Can measure isotopic ratios for a 
target spot several microns across to detect 
potential biological processing of these 
elements. 

Secondary ion mass spectrometry (► SIM S and 
nanoSIMS): A surface analytical technique 
that enables in situ elemental mapping of 
major and trace elements and measurement 
of isotopic ratios at the micron scale or sub¬ 
micron scale in the case of nanoSIMS. Can 
detect elements present in the parts per billion 
range. 

Gas chromatography - mass spectrometry 
(► GC/MS): Used to identify organic 


molecules that are ► biomarkers for specific 
groups of organisms, for example, 
► cyanobacteria. 

Radiogenic isotopes : The abundances of natu¬ 
rally occurring radioactive elements are mea¬ 
sured to calculate absolute ages of rocks. 

Synchrotron X-ray tomography : Nondestructive 
3-D morphological images created from a 
series of 2-D X-ray images taken around a 
single axis of rotation. It yields spectacular 
images of paleontological samples. 

Synchrotron X-ray spectroscopy and microscopy : 
Uses the absorption of X-rays to image sam¬ 
ples at the micron to nanometer scale and to 
investigate, for example, the redox state or 
coordination chemistry of the sample. There 
are many astrobiological applications, for 
instance, to investigate microbe-mineral 
interfaces. 


Microfossils 

► Microfossils are the permineralized remains of 
carbonaceous microbial cells and display a range 
of shapes that in the Archean include coccoids or 
simple spheres and filaments that may be septate 
and/or branched. An instructive example of how 
the ► biogenicity of candidate Archean microfos¬ 
sils is assessed comes from the ~3.45 Ga ► Apex 
Chert of Western Australia that is now famous for 
engendering a vigorous debate regarding the 
oldest microfossil-like objects (Fig. lc). In the 
20 years since their discovery, these “microfos¬ 
sils” have become the cornerstone of textbook 
descriptions of an early Archean biosphere. This 
changed, however, when a reexamination of the 
“microfossils” called into question their 
biogenicity (Brasier et al. 2002). These authors 
argued that the geological context, morphology, 
and distribution of the “microfossils” are more 
consistent with an origin as ► abiotic graphite 
artifacts, produced by the recrystallization of 
amorphous silica to spherulitic chert. The princi¬ 
pal lines of evidence from Brasier et al. (2005) 
are summarized in Table 1 and contrasted with 
the original interpretation of Schopf and Packer 


Key Research Findings 



146 


Archean Traces of Life 



Archean Traces of Life, Fig. 1 Precambrian morpho¬ 
logical traces of life, (a) Photomicrograph of microbial 
biotextures in an inter-pillow breccia from the 
Hooggenoeg Formation of the Barberton Greenstone 
Belt, South Africa, and the meta-volcanic glass comprises 
a greenschist facies assemblage of chlorite and quartz with 
titanite-filled tubular texture, and these are curvilinear and 
unbranched, radiate from a central “root zone,” and are 
segmented by crosscutting chlorite; (b) scanning electron 
micrograph of a twisted filamentous pseudofossil made 
experimentally by precipitating barium-carbonate crystals 
in sodium silicate gel; (c) branched, septate “microfossil” 


composed of carbonaceous material ( orange ) in a silica 
matrix ( yellow ) from the ~3.45 Ga Apex Chert of West 
Australia; (d) transmitted light image of coccoid micro¬ 
fossils from the ~1 Ga Boorthana Chert of South Austra¬ 
lia; (e) putative microbial mat layer from the ~3.5 Ga 
Buck Reef Chert of South Africa; a lower layer of 
rounded, composite, carbonaceous grains is overlain by 
putative microbial mat rip-up fragments that show plastic 
deformation features; (f) automontaged, transmitted light 
image of intertwined filamentous microfossils from the 
3.2 Ga Sulphur Springs Group of West Australia. Scale 
bars: (a) 50, (b) 20, (c) 10, (d) 50, (e), and (f) 50 pm 
















Archean Traces of Life 


147 


Archean Traces of Life, Table 1 Contrasting lines of evidence and their interpretation collected from the ~3.45 Ga 
Apex Chert of Western Australia and contained “microfossil” structures 


Lines of 
evidence 

Brasier et al. 

Schopf et al. 

Environment 
of deposition 

Deep-marine seafloor cherts with intrusive 
hydrothermal dike cherts 

Shallow-marine silicified sediments 

“Microfossil” 

morphology 

Sheets and wisps of carbonaceous material 
concentrated around the rims of silica 
spherulites and rhombic crystal inclusions 

Eleven taxa of filamentous “microfossils” 

Laser Raman 
analysis 

The carbonaceous material has a graphitic 

Raman signature, and the “microfossil” 
signature is indistinguishable from the matrix 
carbonaceous material 

The “microfossils” have a Raman signature that 
is argued to be comparable to disordered 
kerogenous carbon from younger biogenic 
assemblages 

Carbon 

isotopes 

6 13 Corg of —30 %o to —26 %o which cannot 
exclude abiotic Fischer-Tropsch synthesis 

5 13 Corg of —30 %o to —23 %o lies within the 
range of biological fractionation 

Interpretation 

Abiotic artifacts created by the recrystallization 
of amorphous silica that displaced graphitic 
margins forming a spectrum of arcuate to 
dendritic artifacts 

Silica permineralization of filamentous 
“microfossil” cells that could have included 
oxygen-producing cyanobacteria and possibly 
larger, beggiatoacean microfossils 


(1987) and Schopf (2002). An origin for 
these “microfossils” as oxygen-producing 
cyanobacteria-like organisms now seems highly 
unlikely. 

There have been several subsequent studies 
that have investigated the morphology of the 
Apex microfossil-like structures and compared 
them to younger less metamorphosed samples 
and also studies that have looked at the carbon 
ultrastmcture and likened this to younger biogenic 
microfossils. But no studies have yet investigated 
the correlation between seafloor-hydrothermal 
depositional gradients within the Apex Chert and 
changes in the candidate chemical and/or morpho¬ 
logical biosignatures to conclusively reconstmct a 
microbial ecosystem. Moreover, SEM investiga¬ 
tions of the Apex Chert have revealed multiple 
episodes of hydrothermal alteration at tempera¬ 
tures >250 °C and also recent groundwater alter¬ 
ation that have generated micrometer-sized silica 
structures resembling microbial ► exopolymers 
and textures formed by the partial dissolution of 
tubular minerals that mimic some fossilized 
microbial mat textures (Pinti et al. 2009). In addi¬ 
tion, there is evidence for postdepositional coloni¬ 
zation of micro-cracks in the Apex Chert, and 
taken together these processes point to several 
sources of nonindigenous carbonaceous material 
within this unit. In summary, the Apex Chert has 
proven to be a highly controversial, but also 


instructive example of how the biogenicity and 
antiquity of microfossil-like structures can be 
tested. 

Further examples of putative Archean micro¬ 
fossils including spheroids, ellipsoids, and fila¬ 
ments have been reported from the ~2.6 Ga 
Ghaap Subgroup of South Africa, the ~2.7 Ga 
Tumbiana Formation of West Australia, the 
~3 Ga Farrell Quartzite of West Australia, 
the ~3.2 Ga Dixon Island Fm of West Australia, 
the ~3.41 Ga Kromberg Fm of South Africa, 
and the ~3.5 Ga Dresser Formation of the Pilbara; 
these are illustrated and discussed in Wacey 
(2009). The perennial difficulty with interpreting 
all such structures is that they comprise shapes that 
can be difficult to distinguish from natural abiotic, 
crystal habits that could grow under similar con¬ 
ditions and develop complex self-organized mor¬ 
phologies (Brasier et al. 2006). This has been 
illustrated by “crystal-garden”-type experiments 
that precipitate microfossil-like biomorphs in 
sodium silicate gels (Garcia-Ruiz et al. 2003; 
Fig. lb). Moreover, organic compounds produced 
by the abiogenic breakdown of iron carbonate can 
condense onto these biomorphs during mild 
heating, thereby mimicking both the morphologi¬ 
cal and chemical signatures of ~3.5 Ga “micro¬ 
fossils” (Garcia-Ruiz et al. 2003). Perhaps more 
robust microfossil evidence may come from the 
younger Sulphur Springs Group at ~3.24 Ga in the 












148 


Archean Traces of Life 


form of pyritic filaments from a deep-sea, 
volcanogenic, massive sulfide deposit, interpreted 
as the fossilized remains of thermophilic, 
chemotrophic prokaryotes (Rasmussen 2000; 
Fig. If). These straight, curved, or sinuous fila¬ 
ments exhibit putative biological behavior includ¬ 
ing preferred orientations, clustering, and 
intertwining. They are found in an early chert 
fabric in a subsurface drill core that is crosscut 
by later fractures. Thus, these filaments appear to 
satisfy criteria for the ► syngenicity and 

► biogenicity of candidate microfossils and 
await supporting lines of geochemical evidence. 

Siliciclastic sediments such as sandstones, 
siltstones, and mudstones have also been some¬ 
what overlooked in the search for Archean traces 
of life. A recent study by Javaux et al. (2010) 
reports large, hollow spherical organic-walled 
microfossils known as ► acritarchs from the 
~3.2 Ga ► Moodies Group of South Africa. 
These structures pass syngenicity and 
endogenicity tests and appear to be the oldest 
and largest organic-walled spheroidal microfos¬ 
sils reported to date. They may record a plank¬ 
tonic ecosystem contemporaneous with benthic 

► microbial mat textures described by Noffke 
et al. (2006) and will reinvigorate the search for 
traces of Archean life in siliciclastic sediments 
with low-organic carbon contents. 

Microborings 

Microborings are micron-sized cavities created by 
the activities of rock-dwelling microorganisms 
termed endoliths. Microborings have long been 
known from Precambrian silicified carbonates and 
have more recently been reported from the glassy 
margins of pillow lavas from modem to Archean 
volcanic rocks (Staudigel et al. 2008). A rock¬ 
dwelling mode of life in the Archean subseafloor 
may have offered many attractions including prox¬ 
imity to geothermal heat, a source of reductants, 
principally Fe and Mn which are abundant in 
basalts, and access to both oxidants and carbon 
sources carried by circulating fluids. Such habitats 
would also have offered protection from the ele¬ 
vated UV radiation and meteoritic and cometary 
impacts on the early earth. First, a brief overview of 
what is known about these organisms in the modem 


subseafloor is given (for a more complete review, 
see Thorseth 2011), and then these are compared to 
mineralized, tubular stmctures from the Archean. 
Given that pillow lavas constitute an estimated 99% 
of Archean greenstone belts, they represent perhaps 
the largest potential habitat for seeking traces of 
early Archean life. 

Trace of ► endolithic microbes has been 
reported from both the modern oceanic crust 
and older seafloor fragments; for a comprehen¬ 
sive review, see Furnes et al. (2008). These are 
microtubular and granular cavities found at the 
interface of fresh and altered glass, along frac¬ 
tures in the rims of pillow basalts and around the 
margins of volcanic glass fragments. These are 
both texturally and chemically distinct from abi¬ 
otic alteration textures found in ► basalts and 
include diverse tubular shapes such as spiraled, 
annulated, and branched forms (McLoughlin 
et al. 2009). Studies of recent material have 
found nucleic acids and bacterial and archaeal 
RNA concentrated within these microborings. 
These textures may later be mineralized by 
► clays and iron oxyhydroxides that can preserve 
localized enrichments in C, N, and P along the 
margins that are interpreted as decayed cellular 
remains. Quantitative studies of the distribution 
and abundance of these alteration textures with 
depth in the modem oceanic crust have found that 
in the upper ~350 m of the crust the granular type 
is dominant. Meanwhile, the tubular alteration 
textures constitute only a small fraction of the 
total zone of alteration and show a clear maxi¬ 
mum at ~ 120-130 m depth corresponding to 
lower temperatures of ~70°C and thermophilic 
metabolisms. Comparisons of seafloor and drill 
core samples of different ages suggest that 
bioalteration commences early soon after crystal¬ 
lization of the basalt flows. 

In the Archean tubular bioalteration, textures 
have been reported from the formerly glassy rims 
of pillow basalts and inter-pillow breccias from 
both South Africa (Fig. la) and West Australia 
(Furnes et al. 2007). Some of the best examples 
come from the ^3.46 Ga Hooggenoeg Complex 
of South Africa and are mineralized by titanite 
(CaTi0 3 ) that ensured preservation of the tex¬ 
tures when the host glass was transformed to a 



Archean Traces of Life 


149 


greenschist facies metamorphic mineral assem¬ 
blage. These mineralized tubular structures are 
1-10 pm wide, up to 200 pm long, and extend 
away from “root zones” of fine-grained titanite 
that is associated with fractures in the basaltic 
glass (Fig. la). These microtubes can have a 
segmented appearance caused by overgrowths 
of metamorphic chlorite. Morphologically com¬ 
parable microtubular structures have also been 
reported from inter-pillow breccias within the 
~3.35 Ga Euro Basalt Fm of West Australia 
(Fumes et al. 2007). These are also infilled with 
titanite that has been dated directly using U-Pb 
systematics, which confirm that the microborings 
formed prior to an Archean ~2.7 Ga phase of 

► metamorphism (Banerjee et al. 2007). Late 
Archean microborings have now also been 
described from ~2.5 Ga pillow lavas of Wutai, 
China. 

In summary, microborings provide an impor¬ 
tant tool for mapping the deep subseafloor bio¬ 
sphere that may represent one of the earliest 
habitats for life on earth and perhaps other plan¬ 
etary surfaces. 

Stromatolites and Wrinkle Mats 

► Stromatolites are the most abundant macrofos¬ 
sil in the Precambrian rock record and are a 
volumetrically significant component of Precam¬ 
brian carbonate platforms. Stromatolites com¬ 
prise laminated, centimeter-to-decimeter-scale 
domes, cones, columns, and planiform surfaces 
that are built through a complex interplay of 
physical, chemical, and biological processes pro¬ 
ducing an array of micro-fabrics and laminar 
geometries. The processes that lead to the growth 
of stromatolites and how these can be identified 
in the ► fossil record are reviewed in detail else¬ 
where in this volume. Here a nongenetic defini¬ 
tion of a stromatolite is adopted because it can be 
difficult to demonstrate active biological partici¬ 
pation in stromatolite growth. There have been 
many attempts to develop stromatolite 
biogenicity criteria in an effort to distinguish 
laminated seafloor precipitates formed by purely 
chemical processes from microbially mediated 
deposits. Most of these biogenicity criteria are 
so exacting, however, that the majority of 


Precambrian stromatolites of widely regarded 
biogenic origin fail to qualify. The task of 
distinguishing biogenic from abiogenic stromat¬ 
olites is unfortunately, especially, difficult in the 
Archean where diagenetic recrystallization and 
low-grade metamorphism can destroy any 
organic micro-textures that were once present. 

The oldest putative stromatolites are reported 
from the ~3.49 Ga Dresser Formation of the 
West Australia, including wrinkled planiform 
surfaces, broad domes, and columnar forms. 
These occur at several localities in the North 
Pole Dome both in syn-depositional barite 
mounds and hydrothermal dikes and in silicified 
and hydrothermally altered ferruginous carbon¬ 
ates (Wacey 2009). They are of disputed biolog¬ 
ical origin and are discussed elsewhere in this 
volume. Some of the next oldest putative stro¬ 
matolites are described from the ~3.4 Ga Strelley 
Pool Chert of West Australia. The discovery of 
large coniform stromatolites with rare flank struc¬ 
tures and domal and laterally linked 
pseudocolumnar morphologies leads to a biolog¬ 
ical origin for these structures being advanced 
(Hofmann et al. 1999). Subsequently, detailed 
mapping of the stromatolites and investigation 
of rare outcrops with good micro-textural preser¬ 
vation have found evidence for a spatiotemporal 
correlation between stromatolite morphology, 
micro-fabric, and depositional environment 
(Allwood et al. 2009). Regionally, however, the 
more typical, small, unbranched coniform stro¬ 
matolites of the Strelley Pool Chert do not show 
unambiguous biological characteristics or depth- 
controlled distribution and/or changes in mor¬ 
phology with depth (Wacey 2010). In short, the 
Strelley Pool Chert includes a spectrum of stro- 
matolitic structures, some of which are biogenic, 
but we are still a way from confidently 
distinguishing those that are undoubtedly bio¬ 
genic from those that are not microbially 
mediated. 

A morphological biosignature related to stro¬ 
matolites is that of wrinkle-mat textures or 
microbially induced sedimentary structures 
(MISS). These are formed by the interaction of 
benthic microbiota with physical sediment 
dynamics, and some of the oldest come from the 



150 


Archean Traces of Life 


—3.2 Ga Moodies Group of South Africa (Noffke 
et al. 2006). These types of structures have been 
described as orange-peel textures on bedding sur¬ 
faces with microscopic reticulated filaments of 
carbonaceous material among the sediment 
grain that have carbon isotopic signatures that 
are consistent with a biological origin. Older 
putative wrinkle-mat horizons are described 
from cherts of the Barberton (e.g., Walsh and 
Lowe 1999). These comprise carbonaceous lam¬ 
inae and wisps with examples of plastically 
deformed carbonaceous fragments interpreted as 
microbial mat rip-up clasts (Fig. le) and pur¬ 
ported examples of filamentous microfossils. 
These wrinkle-mat-type textures and morphol¬ 
ogies are certainly very suggestive of microbial 
processing and arguably better preserved than 
anything hitherto reported from Western Austra¬ 
lia. Recent studies documenting the facies and 
depth-dependent distribution of this carbona¬ 
ceous material using detailed petrography and 
elemental analysis have strengthened the case 
for biogenicity and argued for the presence of 
anoxygenic photosynthesizers —3.4 Gyr (Tice 
and Lowe 2004). 

Biomarker Compounds 

In rocks that do not preserve cellular microbial 
remains, ► biomarker compounds found in solu¬ 
ble hydrocarbon fractions have been used as 
markers of specific biological pathways (Brocks 
and Summons 2003). Such compounds are 
derived from lipids in cell membranes and repre¬ 
sent an important source of information about the 
diversity and evolution of life. For example, a 
suite of lipid biomarkers extracted from —2.7 
Gyr organic-rich shales from Western Australia 
included hopane and sterane compounds that 
were interpreted, respectively, as the membrane 
remnants of cyanobacteria, a group of organisms 
characterized by oxygen-producing ► photosyn¬ 
thesis, and of eukaryotes organisms that have a 
membrane-bound nucleus and a complex cyto- 
skeleton (Brocks et al. 2003). These findings in 
rocks of-2.7 Ga greatly extended the age of first 
appearance of cyanobacteria previously esti¬ 
mated at —2.15 Gyr old from fossil evidence 
and eukaryotes previously estimated at between 


1.78 and 1.68 Gyr. Moreover, these findings also 
seemed to suggest an early accumulation of 
atmospheric oxygen. Such biomarker studies, 
however, have long been surrounded by concerns 
of contamination from nonindigenous hydrocar¬ 
bons, especially since the carbon isotope ratios of 
the extracted biomarkers were significantly 
enriched relative to the bulk sedimentary organic 
matter. A recent nanoSIMS study has shown that 
the carbon isotope values of pyrobitumen 
(thermally altered petroleum) and ► kerogen 
contained within these rocks are strongly 
depleted in 13 C, confirming that the indigenous 
petroleum is 10-20 %o lighter than the extracted 
hydrocarbon biomarkers (Rasmussen et al. 
2008). These findings are inconsistent with an 
indigenous origin for the biomarkers that, more¬ 
over, have carbon isotopic values that are atypical 
of late Archean organic matter. Thus, it appears 
that the biomarkers derived from these 
2.7 Ga-rich ► shales are not indigenous to the 
rock and are not robust evidence for 
cyanobacteria and eukaryotes at 2.7 Ga 
(Rasmussen et al. 2008). This in situ nanoSIMS 
approach to measuring carbon isotopes on differ¬ 
ent carbon-bearing phases will be used to test the 
antiquity and endogenicity of other late Archean 
and younger reports of biomarkers. 

Carbon Isotopes 

Various microbial metabolisms have been argued 
for on the basis of carbon isotopic ratios mea¬ 
sured on organic matter contained within 
Archean rocks. These include anoxygenic photo¬ 
synthesis from C isotopes in the range of —20 %o 
to — 30 %o measured on kerogen (e.g., Tice and 
Lowe 2004) and methanogenesis from very low 
C ratios of — 56 %o measured on methane-bearing 
fluid inclusions (Ueno et al. 2006). These 5 13 C 
values are certainly consistent with life, but, 
unfortunately, carbon isotope fractionation pat¬ 
terns when taken alone are not a uniquely biolog¬ 
ical signal. This is because there are alternative 
nonbiological explanations for such light carbon 
isotopic values that need to be excluded, and 
these are the source of much debate in Archean 
rocks. For example, Fischer-Tropsch type (FTT) 
reactions between CO and metals (Sherwood 



Archean Traces of Life 


151 


Lollar et al. 2002) or the metamorphic reduction 
of siderite (van Zuilen et al. 2002) can generate 
carbon isotope fractionations that lie within the 
“biological domain.” Thus, in the early rock 
record, carbon isotopes need to be integrated 
with other isotope systems along with the geolog¬ 
ical context and any candidate morphological 
traces of life. 

One of the most ancient claims for life comes 
from isotopically light carbon found in ~3.8 Ga 
highly metamorphosed rocks from the island of 
► Akilia off the west coast of Greenland. The 
material analyzed was graphitic carbon found as 
inclusions within grains of apatite, with a 5 13 C 
signature of — 20 %o to —50 %o (Mojzsis 
et al. 1996). The vigorous debate that has 
surrounded these observations provides an illus¬ 
trative case study of the need to understand the 
complete geological history of a rock argued to 
contain chemical traces of life. Different workers 
have subsequently challenged the evidence for 
life in the Akilia rocks on the basis of the age of 
the outcrop, the apatite petrography, and the fact 
that the protolith is not sedimentary in origin. 
A parallel debate has played out regarding the 
original biogenic interpretation of isotopically 
light graphite in apatite crystals from another 
site in the Isua Greenstone Belt of Greenland 
(Mojzsis et al. 1996). Here, petrographic and 
geochemical studies have also rejected the origi¬ 
nal biogenic interpretation and proposed that the 
metamorphic decomposition of ferrous carbonate 
(siderite) is the more likely source of the depleted 
carbonaceous material (van Zuilen et al. 2002). 
There does remain, however, one locality in the 
Isua region where the association of graphite with 
metasedimentary rocks may still be suggestive of 
life (Rosing and Frei 2004), and this occurrence 
awaits further verification. 

Sulfur Isotopes 

The earliest sulfur isotope evidence suggestive of 
life comes from microscopic sulfides contained 
within barite crystals in the ~3.49 Gyr Dresser 
Formation of North Pole, Western Australia 
(Shen et al. 2001). Fractionations of up to 
21.1 %o between the sulfides and coexisting sul¬ 
fates together with the co-occurrence of organic 


carbon were used to argue that sulfate-reducing 
bacteria had evolved by ~3.49 Ga. More recent 
investigations of material from the North Pole 
have measured mass-independently fractionated 
sulfur isotopic anomalies (MIF) in these sulfides 
that differs from their host barite (Philippot 
et al. 2007). These authors interpret this com¬ 
bined negative 5 34 S and positive MIF signature 
of the sulfides as the product of microorganisms 
that disproportionate elemental sulfur and not 
sulfate-reducing bacteria. In contrast, Ueno 
et al. (2008) and Shen et al. (2009) found that 
these same microscopic sulfides possessed A 33 S 
values. They used these data together with A 33 S 
and A 36 S relationships to argue that their sulfides 
formed dominantly by microbial sulfate reduc¬ 
tion. These conflicting conclusions may in part be 
due to methodological differences between the 
studies. An alternative approach has been taken 
by Wacey et al. (2010) who investigated pm- 
sized, diagenetic pyrite grains from a 3.4 Gyr, 
regionally extensive shallow marine sandstone 
unit. They reported high-resolution multiple 
S isotope analysis ( 32 S, 33 S, 34 S) by secondary 
ion mass spectrometry and both nanoSIMS and 
traditional large-radius ion microprobe to reveal 
6 34 S values between —12 %o and +6%o and A 33 S 
values between —1.65 %o and +1.43 %o, from 
pyrite grains within a single thin section. 
A large spread of 5 34 S values over only 5-10 
pm, together with the spatial association of pyrite 
with C and N, indicates biological processing of 
sulfur. The presence of both +A 33 S and -A 33 S 
signals overprinted by significant mass- 
dependent 5 34 S fractionation in this pyrite popu¬ 
lation indicates that both microbial sulfate reduc¬ 
tion of aqueous sulfate (—A 33 S) and microbial 
disproportionation of elemental sulfur (+A 33 S) 
were co-occurring in an open-marine, 
sedimentary-hosted ecosystem in the early 
Archean. A parallel sulfur isotope story is starting 
to emerge from rocks of the ► Barberton Green¬ 
stone Belt of South Africa. Shales and black 
cherts from the ~3.3 Ga Mendon Formation 
yield 5 34 S values with 12 %o variation that was 
argued to be greater than that expected from 
purely magmatic or hydrothermal H 2 S and due 
to bacterial sulfate reduction (Ohmoto 



152 


Archean Traces of Life 


et al. 1993). But as yet, no corresponding MIF 
signature suggestive of sulfur-disproportionating 
bacteria has been reported from the Barberton 
rocks. 

In late Archean rocks, sulfur isotope evidence 
in conjunction with carbon isotopes and rare earth 
element studies give more definitive evidence for 
the emergence of sulfur metabolisms. Investiga¬ 
tions of the 2.7-2.6 Ga Belingwe Greenstone Belt 
of Zimbabwe have found pyrites in sulfidic shales 
with a wide range of 5 34 S values from —21.1 %o 
to +16.7 %o. This range together with the pyrite 
morphology and isotopic heterogeneity provides 
good evidence for sulfate-reducing and possible 
sulfur-oxidizing bacteria at this time (Grassineau 
et al. 2001). Carbon isotopic investigation 
accompanied by rare earth element analysis of 
associated stromatolitic and non-stromatolitic 
sediments across an onshore-offshore gradient 
has also been used to argue for the presence of a 
diverse microbial ecosystem including 
anoxygenic photosynthesizer, ► methanogens, 
and ► methanotrophs at this time (Grassineau 
et al. 2001). This type of integrated approach is 
the best way of deciphering Archean traces 
of life. 


Future Directions 

The controversies that currently surround the ear¬ 
liest claims for life on earth help astrobiologists 
to develop criteria for testing new and existing 
claims for extraterrestrial life. Some new tech¬ 
niques and approaches to seeking and verifying 
Archean traces of life are now highlighted. 
Firstly, emerging nanoscale techniques that 
allow high-resolution elemental and isotopic 
analysis using nanoSIMS and synchrotron-based 
techniques give the opportunity to investigate 
putative microbial fabrics at a scale never previ¬ 
ously obtainable and will help assess the 
biogenicity of stromatolites and microfossils in 
particular (e.g., Wacey 2009 and references 
therein). Secondly, renewed interest is being 
paid to a wider range of rock types in the search 
for Archean traces of life including microborings 
in not just volcanic glass but also silicate minerals 


and carbonates and also fine-grained siliciclastics 
to locate organic-walled microfossils and stro¬ 
matolitic structures in a range of lithologies in 
addition to classical carbonates. In conclusion, 
our current understanding of Archean ecosystems 
is like an unfinished and jumbled-up jigsaw - as 
new techniques, preservational windows, and 
rock types are found, new pieces in this jigsaw 
of early life and environments will come together 
refining our global picture. 

See Also 

► Abiotic 

► Akilia 

► Apex Chert 

► Archean Drilling Projects 

► Archean Environmental Conditions 

► Archean Eon 

► Archean Tectonics 

► Barberton Greenstone Belt 

► Biogenicity 

► Biomarkers 

► Biomarkers, Morphological 

► Carbon Isotopes as a Geochemical Tracer 

► Chemolithoautotroph 

► Complexity 

► Cyanobacteria 

► Earth’s Atmosphere, History of the Origins 

► Endogenicity 

► Endolithic 

► Fischer-Tropsch Effects on Isotopic 
Fractionation 

► GC/MS 

► Geochronology 

► Greenstone Belts 

► Isotope Biosignatures 

► Isotopic Ratio 

► Isua Supracrustal Belt 

► Kerogen 

► Metasediments 

► Microbial Mats 

► Microfossils 

► Nitrogen Isotopes 

► North Pole Dome (Pilbara, Western Australia) 

► Oxygen Isotopes 

► Photosynthesis 



Archean Traces of Life 


153 


► Pilbara Craton 

► Pillow Lava 

► Pseudofossil 

► Raman Spectroscopy 

► SIM 

► Steranes, Rock Record 

► Stromatolites 

► Sulfur Isotopes 

► Synchrotron Radiation 

► Syngenicity 

► Tumbiana Formation (Pilbara, Western 
Australia) 


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Geological Society of America, Boulder, 
pp 167-188, Geological Society of America special 
paper 329 


Areology 

Ralf Jaumann 

German Aerospace Center (DLR), Institute of 
Planetary Research, Berlin, Germany 

Synonyms 

Geology of Mars 


Definition 

Areology (Greek, Ares “Mars” and logos 
“speech, science”) is the science of the planet 
► Mars, excluding its atmosphere. It comprises 
the study of the structure, composition, physical 
properties, dynamics, origin, and evolution of 
Mars as well as the processes that formed and 
shaped Mars. The term areology is not frequently 
used because scientifically and methodologically 
it is synonymous to the term “Geology of Mars.” 
Thus it is common to use the latter term instead of 
“areology.” 




Argonium 


155 


See Also 

► Chronostratigraphy 

► Geological Time Scale, History of 

► Mars 

► Mars Stratigraphy 

► Selenology 


Argentina Space Agency 

► CONAE, Argentina 


174.21. Its three-letter symbol is Arg and 
one-letter symbol is R. It has a guanidinium 
group (H 2 NC(=NH)NH 2 ) in its side chain. The 
side chain is basic with a p K& of 12.48. When 
protonated, the positive charge of the 
guanidinium ion is delocalized on the three nitro¬ 
gen atoms. The isoelectric point (p/) of 
arginine is 10.76, which is the highest among 
the protein amino acids. Adult humans are able 
to biosynthesize arginine, but infants cannot. 
Thus, it is an essential amino acid only for 
infants. To date, arginine has not been found in 
extraterrestrial bodies like carbonaceous 
chondrites. 


Argillaceous Earth 

► Clay 


Arginine 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogaya-ku, Yokohama, Japan 

Definition 

Arginine, shown in Fig. 1, is one of the 20 ► pro¬ 
tein ► amino acids. Its molecular weight is 


See Also 

► Amino Acid 

► Protein 


Argonium 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 

Synonyms 

ArH + 


Arginine, 

Fig. 1 Structural formula 
of arginine 



Definition 

Argonium is the argon hydride cation, ArH + . 
Argon has three naturally occurring isotopes, 
with the cosmically most abundant being 36 Ar, 
followed by 38 Ar, and then 40 Ar. On Earth, in 
contrast, 40 Ar is by far the most abundant isotope, 
derived primarily from the radioactive decay of 
40 K. The K-Ar decay is important for geochro¬ 
nology. Argonium is the first noble gas molecule 
to have been found in space, with both the 36 Ar 








156 


ArH 


and the 38 Ar isotopologs observed by astrono¬ 
mers. Extensive laboratory studies of the rota¬ 
tional spectra and the electric dipole moment 
have been carried out for both 36 ArH + and 
38 AH + ; AH + is quite stable, with a dissociation 
energy of almost 4 eV. 

History 

Astronomically, argonium was first reported in 
the Crab Nebula, the remnant of the supernova 
observed by Chinese astronomers/astrologers in 
1,054 CE (Barlow et al. 2013). The observed 36 Ar 
was presumably produced by ► explosive nucle¬ 
osynthesis during the supernova event. Both 
36 ArH + and 38 AH + were more recently reported 
toward the Galactic Center molecular cloud 
SgrB2 (Schilke et al. 2014). Because ArH + reacts 
rapidly with molecular hydrogen, H 2 , but not at 
cold interstellar temperatures with atomic 
hydrogen, H, Schilke et al. suggest that ArH + 
may well be a useful tracer of the neutral atomic 
hydrogen in galaxies. 


See Also 

► Geochronology 

► Isotopolog 

► Molecular Cloud 

References and Further Reading 

Barlow MJ, Swinyard BM, Owen PJ, Cernicharo J, 
Gomez HL, Ivison RJ, Krause O, Lim TL, 
Matsuura M, Miller S, Olofsson G, Polehampton ET 
(2013) Detection of a noble gas molecular ion, 36 ArH + , 
in the crab nebula. Science 342:1343-1345 

Schilke P, Neufeld DA, Muller HSP, Comito C, Bergin 
EA, Lis DC, Gerin M, Black JH, Wolhre M, 
Indriolo N, Pearson JC, Menten KM, Winkel B, 
Sanchez-Monge A, Moller T, Godard B, Falgarone 
E (2014) Ubiquitous argonium (ArH + ) in the diffuse 
interstellar medium - a molecular tracer of almost pure 
atomic gas. Astron Astrophys 566:A29 


ArH + 

► Argonium 


Ariel 

Therese Encrenaz 

LESIA, Observatoire de Paris - Section de 
Meudon, Meudon, France 


Definition 

Ariel is one of the five big satellites of ► Uranus 
and the closest to the planet. It was discovered by 
William Lassen in 1851. Its diameter is 1,160 km 
and its distance to Uranus is 191,000 km or 7.5 
planetary radii. Its density is 1.66 g/cm 3 . 
Ariel has been explored by the Voyager 
2 spacecraft which flew by the Uranian system 
in January 1986. Ariel is assumed to consist 
of about 30 % silicates and 70 % ices. It has a 
bright surface that shows a network of 
canyons and faults, such that, after 
Miranda, Ariel is the most geologically active 
among Uranus’ satellites. The longest can¬ 
yon (622 km) is Kachina Chasmata. The activity 
may result from tidal heating due to the 
proximity of Uranus at the time of the satellite’s 
formation. 


See Also 

► Giant Planets 

► Uranus 

► Voyager, Spacecraft 





Arrhenius Svante 


157 


Aromatic Hydrocarbon 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Definition 

An aromatic hydrocarbon is a cyclic hydrocarbon 
where the series of saturated and unsaturated carbon- 
carbon bonds satisfies Hiickel’s mles, i.e., where the 
number of electrons in double and triple bonds in the 
ring is 4n + 2, where n = 0 or any positive integer. 
The name derives from the fact that the first such 
molecules discovered tended to have an aromatic 
odor. They are typically somewhat more stable than 
their hydrogen-saturated analogues. Aromatic 
hydrocarbons may be monocyclic or polycyclic. 

See Also 

► Benzene 

► PAH 


Arrhenius Plot 

Jeffrey Bada 

Scripps Institution of Oceanography, La Jolla, 
CA, USA 

Definition 

In 1889, the Swedish chemist Svante Arrhenius 
showed that the rate of a chemical reaction as a 


function of temperature could be described by the 
equation 

In £ = In A - EjRT 

where k is the reaction rate, R is the universal gas 
constant, E a is the ► activation energy (the energy 
required in order for the reactants to react), T is the 
absolute temperature (in degrees K ), and A is the 
so-called pre-exponential factor (associated with 
collision and transition state theory). 

A plot of In k versus 1 IT often yields a straight 
line, the slope of which is equal to the activation 
energy of the reaction divided by the universal 
gas constant ( EJR ) and the y-intercept of which 
is equal to In A. 

See Also 

► Activation Energy 


Arrhenius Svante 

Gerda Homeck 

DLR German Aerospace Center, Institute of 
Aerospace Medicine, Radiation Biology, 

Kohl, Germany 

History 

Svante August Arrhenius (1859-1927), Swedish 
scientist, received the Nobel Prize in Chemistry 
in 1903 “in recognition of the extraordinary ser¬ 
vices he has rendered to the advancement of 
chemistry by his electrolytic theory of dissocia¬ 
tion.” Among other achievements, Arrhenius is 
famous for the Arrhenius equation, which gives 
the dependence of the rate constant k of a chem¬ 
ical reaction on the temperature T (in K) and the 
activation energy of the reaction. For astrobiolo- 
gists, Arrhenius is famous for his thoughts that 






158 


Artificial Cells 


microscopic forms of life, for example, ► spores, 
can be propagated in space, driven by the radia¬ 
tion pressure from the Sun and thereby seeding 
life from one planet to another or even between 
planets of different stellar systems. Arrhenius 
based his considerations on the fact that the 
space between the planets of our Solar System is 
teeming with micron-sized cosmic dust particles, 
which at a critical size below 1.5 pm would be 
blown away from the Sun with high speed pushed 
by radiation pressure of the Sun. Herewith Arrhe¬ 
nius provided a scientific rationale for the theory 
of ► Panspermia, now called Radiopanspermia. 

See Also 

► Arrhenius Plot 

► Lithopanspermia 

► Panspermia 

► Spore 

References and Further Reading 

Arrhenius S (1903) Die Verbreitung des Lebens im 
Weltenraum. Umschau 7:481^185 
Arrhenius S (1908) Worlds in the making: the evolution of 
the universe. Harper & Row, New York 


Artificial Cells 

► Cell Models 

► Protocell 


Artificial Chemistries 

Pietro Speroni di Fenizio 

CISUC, Department of Informatics Engineering, 
University of Coimbra, Coimbra, Portugal 

Keywords 

Artificial chemistries; Artificial life; Evolution; 
Reaction network 


Synonyms 

Reaction network 


Definition 

Artificial chemistry (AC) is a field of research 
that studies systems that are similar to, and 
commonly a generalization of, chemical net¬ 
works. Those studies are usually done through 
computer simulations which are also called arti¬ 
ficial chemistries. An AC can be defined as triplet 
{M, R, A}, with M being the set of possible 
molecules (sometimes infinite), R the set of pos¬ 
sible reactions, and A the algorithm (Dittrich 
et al. 2001). 


Overview 

Artificial chemistry grew as a field from the early 
1990s. Different aims converged in producing 
this field. 

One of the aims of artificial chemistry was to 
investigate evolution and the appearance of life. 
Some of the main questions that have been inves¬ 
tigated deal with biology, proto-biology, and evo¬ 
lution and take a bottom-up approach to 
► artificial life: 

• Can we generate an artificial chemistry that 
can generate an artificial life? 

• What kind of chemistry can sustain life? 

• How does the Darwinian evolutionary process 
depend upon the chemistry on which it is 
based? 

Of course, as we extrapolate out of chemistry 
the basic network of relations that can produce 
life, this would eventually help to recognize life 
in different contexts. 

Another, more general, aim was to study 
reaction networks. Reaction networks appear in 
multiple fields, but our ability to study them 
has generally been limited by a difficulty in 





Artificial Chemistries 


159 


solving differential equations where the 
number of different interacting elements 
(< diversity , i.e., number of equations) were 
too high, and the quantity of each participating 
element in the reaction network (population size) 
was too low (which could lead to an 
element disappearing and the set of reactions 
changing). Some artificial chemistries 
investigated exactly this problem. As such the 
aim of artificial chemistries has often been a 
qualitative study, looking for what sets of mole¬ 
cules would be present in the reactor, more than 
how many elements would be present for each 
type of element in the system (Fontana and 
Buss 1996). 

Due to the computational difficulty in simu¬ 
lating a chemical system that is both unbounded 
in the complexity of the molecules involved and 
that permits a faithful representation of space, the 
field tends to be divided into two main subfields: 
Complex Artificial Chemistries and Spatial Arti¬ 
ficial Chemistries. 

Complex Artificial Chemistries are the 
most simple type of system and assume a 
well-mixed reactor. Each molecule is either 
present or absent, with no information about 
the position. Pairs of molecules are then ran¬ 
domly selected and reacted. Such a simple 
algorithm frees the computational resources 
permitting the presence of complex 
molecules, with different behaviors. It is not 
uncommon for artificial chemistries to study 
the behavior of little program strings with com¬ 
putational capabilities (traditionally lambda 
terms). 

Spatial Artificial Chemistries traditionally 
study systems made up of many simple elements, 
floating in a 2D or in a 3D spatial environment. 
The basic elements (in some systems called 
atoms) can often link together creating long 
chains (usually called molecules). In the first 
pioneering works of Spatial Artificial Chemis¬ 
tries, the positions of the molecules were impre¬ 
cise, as each molecule was generally assigned to a 
position on a lattice. Recent computational pro¬ 
gress permitted a more faithful representation of 
the movement using differential equations 
(Fellermann 2009). 


Basic Methodology 

The methodology is slightly different for Spatial 
Artificial Chemistries and for Complex Artificial 
Chemistries. 

Complex Artificial Chemistries, as mentioned 
before, are essentially reaction networks with a 
high diversity and a low population size. Such an 
AC can be defined as a triplet {molecules, reac¬ 
tions, algorithm}. Reactions are usually binary 
(i.e., two molecules reacting and generating a 
third). Yet not all pair of molecules can react. 
When two molecules cannot react, they are said 
to be elastic. The basic algorithm is generally 
very simple: 

1. Define a Soup S as a multiset of m molecules 
out of M. 

2. Two molecules are randomly selected. 

3. If the two molecules can react, a reaction takes 
place: 

1. The result of the reaction is inserted in 
the Soup. 

2. A random molecule is extracted from the 
Soup and eliminated. 

4. Go to 2. 

In many Artificial Chemistries, the reactions 
are catalytic, so when two molecules react, they 
are not taken away from the Soup while their 
product is added to the Soup (3a). Instead, the 
molecules catalytically induce the formation of 
the new molecule out of a substrate of basic 
material (too vast and ubiquitous to be explicitly 
modeled), while the disappearance (3b) would 
model the outflux due to molecules being washed 
away or breaking apart (Dittrich et al. 2001). This 
traditional structure has been strongly criticized 
(e.g., for not considering conservation of mass), 
and many alternatives have been offered but gen¬ 
erally with only partial differences in the 
observed behavior. Traditionally the standard 
way to investigate such a system is to run it 
until no new molecule would be generated, at 
which point the resulting multiset is studied. 
Lately, a more advanced method has been to 
calculate all the possible sets where the system 
could stop (called organizations) and study the 



160 


Artificial Chemistries 


structure of the lattice of organizations and use 
this to map the movement of the artificial chem¬ 
istry as time progresses (Kaleta 2009). 

Spatial Artificial Chemistries start in general 
with a set of atoms, to which a position in space 
is randomly assigned. At each time step all the 
atoms are randomly moved, and when two atoms 
end up near each other, they have the possibility of 
colliding. Unless the system is superimposed on a 
lattice, the movement of the molecules would fol¬ 
low a Brownian motion style of movement or a 
dissipative particle dynamic style, where the 
forces interacting on a molecule are taken into 
account in greater detail (Fellermann 2009). 

Key Research Findings 

The first result in AC is that there are sets of 
molecules, called organizations , which are qual¬ 
itatively stable, in the sense that each molecule 
present in the set can be generated by the reac¬ 
tions inside the set and that all reactions inside the 
cell can only generate molecules that are already 
inside the cell. Such organizations form an alge¬ 
braic lattice, and in the absence of external inputs, 
each experiment eventually leads to the system 
reaching one of those sets. As artificial chemis¬ 
tries can be represented using ordinary differen¬ 
tial equations (ODE), it has been shown that fixed 
points in the ODE of the system exist only inside 
organizations. In other words, if we take a fixed 
point of the system, find the molecules that are 
present with a quantity higher than 0, and then 
this set of molecules forms an organization. 
Those results permit a preliminary study of an 
artificial chemistry by finding (through algebraic 
studies) the lattice of organizations and produce a 
map of the system on which it is possible to track 
the changes in the system (Dittrich and Speroni di 
Fenizio 2007). 

Spatial Artificial Chemistries have been suc¬ 
cessfully used to model the lipid bilayer of cell 
membranes and to investigate the spontaneous 
emergence of artificial life protocells. More 
recently, experiments have been carried out gen¬ 
erating protocells that are able to reproduce 
(Rasmussen et al. 2007). 


Applications 

While the long-term aim of artificial chemistry, to 
investigate the appearance of life, has not been 
reached, a number of partial findings were recog¬ 
nized as being useful in different fields. As Com¬ 
plex Artificial Chemistry can investigate reaction 
network with a high diversity, they are often the 
right tool to study ► biological networks. In par¬ 
ticular, studies have been done on gene regula¬ 
tory networks and the internal metabolism of a 
cell. In this regard, AC has started merging with 
the other tools inside systems biology and bioin¬ 
formatics. Other studies have tried to consider 
social systems, language, and economical sys¬ 
tems (Dittrich et al. 2001). 

Future Directions 

Spatial Artificial Chemistries and Complex Arti¬ 
ficial Chemistries are going in separate ways, 
mostly answering different questions about 
nature. Spatial Artificial Chemistries try to pro¬ 
duce a minimal cell, but have not yet succeeded 
in generating a spontaneous emergence of a full 
Darwinian evolutionary system. So we can 
expect more research to go in this direction. 
Results in Complex Artificial Chemistries have 
been more connected with systems biology, and 
artificial chemistries have been used to explicitly 
study system biology models, and recent studies 
show that it is possible to use AC to build pro¬ 
grammable systems made up of many interacting 
components. In the future, we can expect those 
two trends to merge, as scientists investigate 
chemistries that can evolve and that can be 
programmed to evolve. 

See also 

► Artificial Life 

► Autopoiesis 

► Biological Networks 

► Chemical Reaction Network 

► Darwin’s Conception of the Origins of Life 

► Evolution, Biological 



Artificial Life 


161 


References and Further Reading 

Dittrich P, Speroni di Fenizio P (2007) Chemical organi¬ 
sation theory. Bull Math Biol 69(4): 1199-1231 
Dittrich P et al (2001) Artificial chemistries - a review. 
Artif Life 7:225-275 

Fellermann H (2009) Spatially resolved artificial chemis¬ 
try. In: Adamatzky A, Komosinski M (eds) Artificial 
life models in software, 2nd edn. Springer, p 343 
Fontana W (1992) Algorithmic chemistry. In: Proceedings 
of artificial life II conference 5:159-210 
Fontana W, Buss LW (1996) The barrier of objects: from 
dynamical systems to bounded organizations. In: 
Karlqvist A, Casti J (eds) Boundaries and barriers. 
Addison-Wesley, Redwood City, pp 56-116 
Kaleta C (2009) From artificial chemistries to systems biol¬ 
ogy. In: Adamatzky A, Komosinski M (eds) Artificial life 
models in software, vol 2. Springer, London, pp 319-342 
Rasmussen S et al (2007) Life cycle of a minimal 
protocell - a dissipative particle dynamics study. 
Artif Life 13(4):319-345 


Artificial Evolution 

► Evolution, In Vitro 


Artificial Life 

Hugues Bersini 

IRIDIA, Universite Libre de Bruxelles, Brussels, 
Belgium 

Keywords 

Bioinformatics; Genetic algorithms; Networks; 
Self-replication; Software simulations; Von 
Neumann 


Synonyms 

Life, artificial; Theoretical biology 


Definition 

Artificial ► life uses software simulation and, to a 
lesser degree, robotics in order to abstract and 


elucidate the fundamental mechanisms common 
to living organisms. It focuses on the rule-based 
mechanisms making life possible, supposedly 
neutral with respect to their underlying material 
embodiment, and to replicate them in a 
non-biochemical substrate. In artificial life, the 
importance of the substrate is purposefully under¬ 
stated for the benefit of the function. Minimal life 
begins at the intersection of a series of processes 
that need to be isolated, differentiated, and dupli¬ 
cated as such in computers. Only software devel¬ 
opment and running make it possible to 
understand the way these processes are intimately 
interconnected in order for life to appear at the 
crossroads. 


Overview 

Artificial life obviously relates to astrobiology; 
this other recent interdisciplinary field of scien¬ 
tific research equally centered on life and the 
study of its origins, not only on the obvious envi¬ 
ronment of Earth but also throughout the uni¬ 
verse. Astrobiology cannot restrict itself to a 
mere materialistic view of life, in order to detect 
it elsewhere, as the material substrate could be 
something totally different. This substrate could 
be as much singular on a distant planet as it could 
be in the RAM memory somewhere in a univer¬ 
sity computer laboratory. The presence of life 
might be suspected through its functions, much 
before scientists are able to dissect it. Artificial 
life does not attempt to provide an extra thou¬ 
sandth attempt at the definition of life, any more 
than do most biologists. As a matter of fact, the 
concept of “life,” as opposed to “gravity” or 
“electromagnetism” or “quantum reduction of a 
wave packet,” has already been in widespread 
existence prior to any scientific reading or reifi¬ 
cation. The rejection of an authoritative definition 
of “life” is often compensated for by a list of 
functional properties that never finds unanimity 
among its authors. Some demand more proper¬ 
ties, and others require fewer of those properties 
that are often expressed in terms of a vague 
expression such as “self-maintenance,” “self¬ 
organization,” “metabolism,” “autonomy,” 





162 


Artificial Life 


“► self-replication,” and “open-ended evolu¬ 
tion.” A first determining role of artificial life 
consists in the writing and implementing of soft¬ 
ware versions of these properties and of the way 
they do connect, so as to render them unambigu¬ 
ous, making them algorithmically precise enough 
that, at the end, the only reason for disagreement 
on the definition of life would lie in the length or 
the composition of this list and on none of its 
items. 

The biologist obviously remains the most 
important partner; but what may he expect from 
this “artificial life”? These computer platforms 
could be useful in several ways, presented in the 
following in terms of their increasing importance 
or by force of impact. First of all, they can open 
the door to a new style of teaching and advocating 
of the major biological ideas, that is, computer 
software as pedagogical help, as, for example, 
Richard Dawkins (1986) who, bearing the Dar¬ 
winian good news, did so with the help of a 
computer simulation where sophisticated crea¬ 
tures known as “biomorphs” evolve on a com¬ 
puter screen by means of a genetic algorithm. 
These same platforms and simulations can, inso¬ 
far as they are sufficiently flexible, quantifiable, 
and universal, be used more precisely by the 
biologist, who will find in them a simplified 
means of simulating and validating a given bio¬ 
logical system under study. Cellular automata, 
Boolean networks, ► genetic algorithms, and 
algorithmic chemistry are excellent examples of 
software to download, parameterize, and use to 
produce the natural phenomena required. Their 
predictive power varies from very qualitative 
(their results apparently reproduce very general 
trends of the real world) to very quantitative (the 
numbers produced by the computer may be pre¬ 
cise enough to be compared with those measured 
in the real world). Although being at first very 
qualitative, a precise and clear coding is already 
the guarantee of an advanced understanding 
accepted by all. Algorithmic writing is an essen¬ 
tial stage in formalizing the elements of the 
model and making them objective. The more the 
model allows us to integrate what we know about 
the reality being reproduced, that is, the detailed 
structures of objects and relationships between 


them, the more the predictions will move from 
qualitative to precise and the easier the model 
will be to validate according to the Karl Popper 
ideal falsifying process. 

Finally, through systematic software experi¬ 
ments, these platforms can lead to the discovery 
of new natural laws, whose impact will be greater 
if the simulated abstractions will be present in 
many biological realms. In the 1950s, when 
Alan Turing (1952) discovered that a simple dif¬ 
fusion phenomenon propagating itself at different 
speeds, depending on whether it is subject to a 
negative or positive influence, produces zebra or 
alternating motifs, it had a considerable effect on 
a whole section of biology studying the genesis of 
forms (animal skins, shells of sea creatures 
(Meinhardt 1998)). When some scientists discov¬ 
ered that the number of attractors in a Boolean 
network or a neural network exhibits a linear 
dependency on the number of units in these net¬ 
works (Kauffman 1993, 1995), these results are 
equally well applied to the number of cells 
expressed as dynamic attractors in a genetic net¬ 
work or the quantity of information capable of 
being memorized in a neural network. Entire 
chapters of biology dedicated to networks 
(neural, genetic, protein, immune, hormonal) 
had to be rewritten in the light of these discover¬ 
ies. When some scientists recently observed a 
nonuniform connectivity in many networks, 
whether social, technological, or biological, 
showing a small number of key nodes with a 
large number of connections and a greater num¬ 
ber of nodes with far fewer, and when, in addi¬ 
tion, they explained the way in which these 
networks are built in time (Barabasi 2002) by 
preferential attachment, again biology was 
clearly affected. Artificial life is of course at its 
apogee when it reveals new biological facts, 
destabilizing the presuppositions of biologists or 
generating new knowledge, rather than simply 
illustrating or refining the old. 

In the next section, I shall attempt to set out the 
history of life as the disciples of artificial life 
understand it, by placing the different landmark 
steps on a temporal and causal axis, showing 
which one is indispensable to the appearance 
of the next and how it connects to the next. 



Artificial Life 


163 


This history will certainly be very incomplete and 
full of numerous unknowns, but most people 
involved in artificial life will be in agreement. 
They will mainly disagree on the number of 
these functions and on the causal sequence of 
their appearance, acknowledging, however, that 
the appearance of any would have been condi¬ 
tioned by the presence and the functioning of the 
previous ones. The task of artificial life is to set 
up experimental software platforms where these 
different lessons, whether taken in isolation or 
together, are tested, simulated, and, more system¬ 
atically, analyzed. I shall sketch some of these 
existing software platforms whose running 
delivers interesting take-home messages to 
open-minded biologists. 

The History of Life as Seen by Artificial Life 
Proponents 

Appearance of Chemical Reaction Cycles and 
Autocatalytic Networks 

In order for a system to emerge and maintain 
itself inside a soup of molecules that are poten¬ 
tially reactive and contain very varied constitu¬ 
ents (which could correspond to the initial 
conditions required for life to appear, i.e., in the 
primordial soup), this reactive system must form 
an internally cycled network or a closed organi¬ 
zation, in which every molecule is consumed and 
reproduced by the network. Above all, in order 
for life to begin, all of the constituent components 
must have been able to stabilize themselves in 
time. These closed networks of chemical reac¬ 
tions are thus perfect examples of systems, 
which, although heterogeneous, are capable of 
maintaining themselves indefinitely, despite the 
shocks and impacts that attempt to destabilize 
them. This comes about through a subtle self¬ 
regeneration mechanism, where the molecules 
end up producing those molecules that have pro¬ 
duced them. It may be obtained on a basic level in 
a perfectly reversible chemical reaction but can 
be obtained more subtly in the presence of a lot of 
intermediary molecules and catalysts. By this 
reaction-based roundabout in which they all par¬ 
ticipate, all molecules contribute to maintaining 
themselves at a constant concentration, 


compensating and reestablishing any disruption 
in concentration undergone by anyone of them. 
The bigger the network, the more stable it should 
be and the more molecules it will maintain in a 
concentration zone that will vary very little, 
despite external disruptions. 

A network of this kind will be materially closed 
but energetically open if none of the molecules 
appears in or disappears from the network as a 
result of material fluxes, whereas energy, originat¬ 
ing in external sources, is necessary for the reac¬ 
tions to start and take place. The presence of such 
an energy flux, maintaining the network far from 
the thermodynamic equilibrium, is needed, since, 
without it, no reactive flow would be possible 
circulating through the entire network. 
A molecular end of the cycle must be reenergized 
in order to start again the whole circular reaction 
process. This cycle thus acts as a chemical 
machine, energetically driven from the outside. 
As soon as one of the molecules is being produced 
in the network without, in its turn, producing one 
of the molecules making up the network, it absorbs 
and thus destroys the network. In the presence of 
molecules of this kind, produced but nonproduc¬ 
tive (a kind of waste), the only way of maintaining 
the network becomes to feed it materially and to 
make it open to material influx. The network acts 
on the flow of material and energy as an interme¬ 
diate ongoing stabilization zone, made up of mol¬ 
ecules that may be useful to other vital functions 
(such as the composition of enclosing membranes 
or catalyzing self-replication), to be described in 
the following sections. It transforms, as much as it 
“keeps on,” all the chemical agents that it recmits. 
Biologists generally agree that a reactive network 
must exist prior to the appearance of life, at least to 
catalyze and make possible the other life processes 
such as genetic reading and coding; it is open to 
external influences in terms of matter and energy 
but necessarily contains a series of active cycles. 
They are most often designated as “► metabo¬ 
lism” or “proto-metabolism,” the most popular 
and active advocates of this “metabolism-first” 
hypothetical scenario of the origin of life being 
(De Duve 2002; Ganti 2003; Maynard Smith and 
Szathmary 1999; Kauffman 1993; Shapiro 2007; 
Dyson 1999). 





164 


Artificial Life 


Artificial Life, 

Fig. 1 Representation of a 
network of chemical 
reactions of polymerization 
(a + b —> ab) and 
depolymerization 
(ab —> a + b) taking place in 
a simulated chemical 
reactor. Molecules are 
represented by circles and 
reactions by square. Each 
reaction can be catalyzed, 
like the arrows pointing to 
the squares show, by a 
molecule of the network 
(giving rise to an 
autocatalytic network). 
Some molecules can appear 
(like the molecule “aab”) or 
simply disappear from the 
network. Reaction cycles 
can appear, like the one 
surrounded in the figure 
(aa —* baaaa —► baaaaaab 
—>• baaa —► aa) 



Lenaerts and Bersini (2009) give priority to 
the study of chemical reaction networks, viewing 
them as key protagonists in the appearance of life. 
These chemical reaction networks, where the 
nodes are the molecules participating in the reac¬ 
tions and the connections are the reactions 
linking the reacting molecules to the molecules 
produced, are generally characterized by fixed 
point dynamics, the chemical balances during 
which the producers and the products mutually 
support each other. The attractors in which these 
networks fix themselves are as dynamic (the con¬ 
centrations slowly stabilize) as they are structural 
(the molecules participating in the network are 
chosen and “trapped” by the network as a whole). 
These networks are perfect examples of systems 
that combine dynamics (the chemical kinetics in 
this case) and metadynamics (the network topo¬ 
logical change), as new molecules may appear as 
the results of reactions while some of the mole¬ 
cules in the network may disappear if their 


concentration vanishes in time. Both the structure 
of the network and the concentration of its con¬ 
stituents tend to stabilize over time. Kauffman 
(1993, 1995) and Fontana (1992) were the fore¬ 
runners in the study of the genesis and properties 
of these networks. Figure 1 illustrates the work of 
these two artificial life pioneers, dedicated to the 
study of prebiotic chemistry, limiting the reac¬ 
tions studied to polymerization, such as aa + bb 
—> aabb, or, inversely, depolymerization or 
hydrolysis, such as abaa —> ab + aa. 

Kauffman showed that provided the probabil¬ 
ity that a reaction takes place is affected by the 
presence of a catalyst, which is itself produced by 
the network (in such a case the whole network is 
said to be autocatalytic), a phenomenon of perco¬ 
lation or phase transition, characteristic of this 
type of simulation, is produced. For probabilities 
that are too low, the network does not pop up 
because the reactions are too improbable, but as 
soon as a threshold value is reached for this same 









Artificial Life 


165 



*>/•-• +^* x . 


2 ) 


VI. •*'* • 




^> / * N »+ J * 0R ^v* * 


3) 


Artificial Life, Fig. 2 The OO chemical simulator devel- right, the outcome of the simulator is an evolving reaction 
oped by Lenaerts and Bersini (2009). On the left, the network, which can be studied in its own right (the pres- 
molecules are represented as canonical graphs. On the ence of cycles, the type of topology) 


probability, the network “percolates,” giving rise 
to multiple molecules produced by multiple reac¬ 
tions. Kauffman grants a privileged status to this 
threshold value and to the giant “explosive” net¬ 
work resulting from it (in his scenario of the 
origin of life), without really arguing the reason 
why such a status should exist, but passing the 
immense interest and enthusiasm that the phe¬ 
nomena of phase transitions arouse among phys¬ 
icists onto the world of biology. Fontana for his 
part is concerned with the inevitable appearance 
of reaction cycles (such as that illustrated in 
Fig. 1). All the molecules produced by these 
cycles in the network in turn produce molecules 
of the network. He is among those many biolo¬ 
gists who see these closed networks or organiza¬ 
tions as forming a key stage in the appearance of 
life, due both to their stability and to the fact that 
they form structural and dynamic attractors for 
the system. They cause a stabilization and inter¬ 
nal regulation zone together with an energetic 
motor in a chemical soup, which is continually 
being crossed by a flow of matter and energy. 
Fontana goes on to show how these networks 


are also capable of self-regeneration and self¬ 
replication. 

Lenaerts and Bersini (2009) have programmed 
the genesis of these chemical reaction networks 
by adopting the object-oriented (OO) program¬ 
ming paradigm. The OO simulator aims to repro¬ 
duce a chemical reactor and the reaction network 
that emerges from it (like that shown in Fig. 2). 
This coevolutionary (dynamics + metadynamics) 
model incorporates the logical structure of con¬ 
stitutional chemistry and its kinetics on the one 
hand and the topological evolution of the chem¬ 
ical reaction network on the other hand. The 
network topology influences the kinetics and the 
other way round, since only molecules with a 
sufficient concentration are allowed to participate 
in new reactions (to avoid a combinatorial explo¬ 
sion of molecules and reactions). The model is 
expressed in a syntax that remains as close as 
possible to real chemistry. Starting with some 
initial molecular objects and some initial reaction 
objects, the simulator follows the appearance of 
new molecules and the reactions in which they 
participate, as well as the development of their 


















166 


Artificial Life 


concentration over a period of time. The mole¬ 
cules are coded as canonical graphs. They are 
made up of atoms and bonds that open, close, or 
break during the reactions. The result of the sim¬ 
ulation consists in various reaction networks, 
unfolding in time and whose properties can be 
further studied (for instance, the presence and the 
properties of reaction cycles or the nature of the 
network-particular topology such as scale-free or 
random). 

One of these reaction schemes, in addition to 
just cycling, can also be ► autocatalytic, when a 
product of the reaction cycle has twice the con¬ 
centration of one of the reactant: a + b —> a + a. 
This is, for instance, the case of the so-called 
formose reaction (that Ganti and Szatmary have 
discussed at large in Ganti 2003), during which a 
two-carbon molecule, reacting twice with 
a monomer composed of one carbon, leads to a 
four-carbon molecule, which then splits in order 
to duplicate the original molecule. This is the 
chemical variant of genetic self-replication, 
since in both cases an original molecule is dupli¬ 
cated. As will be discussed later, Ganti has been 
the first to connect and synchronize these two 
replication processes, chemical and genetic, in 
order for the cell to simultaneously duplicate its 
boundary, its metabolism, and its informational 
support. In the presence of autocatalysis, the reac¬ 
tion kinetics amounts to an exponential increase 
and, more interestingly, when various autocata¬ 
lytic cycles enter in antagonistic interaction, turns 
out to be responsible for symmetry breaking (one 
of the cycle, initially favored, wins and takes it 
all). The early origin of life should not be studied 
without taking account of the self-organization of 
chemical networks, the emergence and antago¬ 
nism of autocatalytic cycles, and how energy 
flows drive the whole process. Such chemical 
networks are, for instance, appealing to the effort 
to understand the onset of biological 
homochirality as the destabilization of the race¬ 
mic state resulting from the competition between 
enantiomers and from amplification processes 
concerning both autocatalytic competitors (one 
left oriented and the other right; see Plasson 
et al. 2007). The chemical reaction network 
under study (shown in Fig. 3) is made up of the 


L 

D 

L* 

D* 

L* + L 

D* + L 
L* + D 
D* + D 


Chemical reactions 


ap 


ap 


L 

D* 

L 

D 

LL 

DL 

LD 

DD 


LL 

DL 

LD 

DD 

LD 

DD 

LL 

DL 


h 


H L 


lh 


ye 


ye 


L+ L 
L+ D 

L+ D 

D+ D 

DD 

LD 

DL 

LL 


Reaction network 
e e 



Artificial Life, Fig. 3 The prebiotic chemical reactor 
system responsible for a homochiral steady state studied 
by Plasson et al. (2007). The complete set of reactions is 
indicated, containing activation (the necessary energy 
source), polymerization and hydrolysis (which together 
shape the cycles), and epimerization (which induces the 
competition between the enantiomers) 


same type of polymerization and depolymeriza¬ 
tion reactions as the one studied by Fontana. In 
the additional presence of epimerization reac¬ 
tions allowing the transformation of a right- 
hand monomer into a left-hand one and vice 
versa, the concentration of one family of mono¬ 
mers (for instance, the left one) vanishes in favor 
of the other. The flux of energy is transferred and 
efficiently distributed through the system, lead¬ 
ing to cycle competitions and to the stabilization 
of asymmetric states. 























Artificial Life 


167 


Production by This Network of a Membrane 
Promoting Individualization and Catalyzing 
Constitutive Reactions 

The appearance of a reaction network of this kind 
undeniably creates the stability necessary for 
exploiting its constituents in many reactive sys¬ 
tems such as the ones dedicated to the construc¬ 
tion of ► membranes or the replication of 
molecules carrying the ► genetic code. This net¬ 
work also acts as a primary filter as it can accept 
new molecules within it but can equally well 
reject other molecules seeking to be incorporated 
within it. They will be rejected, as they do not 
participate in any of the reactions making up the 
network. Can we see a primary form of individ¬ 
ualization in this network? No, because by defi¬ 
nition, it can only be unique as no spatial frontier 
allows it to be distinguished from another net¬ 
work. Although it is roughly possible to conceive 
of an interpenetration of several chemical net¬ 
works, establishing a clear separation between 
these networks would remain a problem. 

It would seem fundamental that a living organ¬ 
ism of any kind can be differentiated from 
another. We know that the reproduction of a 
second organism from a first is a central mecha¬ 
nism of life and can only operate if the “clone” 
elaborates something to spatially distinguish 
itself from its “original.” The best way of suc¬ 
cessfully completing this individualization and to 
be able to distinguish between these networks is 
to revert to a spatial divide, which can only be 
produced by some form of container capable of 
circumscribing these networks in a given space. 
Biochemists are well acquainted with an ideal 
type of molecule, the raw material for these mem¬ 
branes in the form of lipid/amphiphilic molecules 
or fatty acids, the two extremities of which 
behave in an antagonistic fashion - the first 
hydrophilic, attracted to water, and the second 
hydrophobic, repulsed by it. Quite naturally, 
these molecules tend to assemble in a double 
layer (placing the two opposing extremities oppo¬ 
site to each other), formed by the molecules lin¬ 
ing up and finally adopting the form of a sphere to 
protect the hydrophobic extremities from water. 
Like soap bubbles, these lipid spheres are semi- 
permeable and imprison the many chemical 


components trapped during its formation. They 
do, however, actively channel in and out the most 
appropriate chemicals for maintaining 
themselves. 

In assimilating living organisms to autopoietic 
systems, Varela et al. (1974) were the first to 
insist that this membrane should be endogenously 
produced by the elements and the reactions mak¬ 
ing up the network (e.g., lipids would come from 
the reactions of the network itself) and would in 
return promote the emergence and self¬ 
maintenance of the network. The membrane can 
help with the appearance of the reactive and 
growing network by the frontiers that it sets up, 
by the concentration of certain molecules trapped 
in it, or by acting as a catalyst to some of the 
reactions due to its geometry or its makeup. Basi¬ 
cally, autopoiesis requires a cogeneration of the 
membrane and of the reactive network that it 
“walls up.” The network presents a double 
closure - one chemical, linked to the cycling 
chain of its reactions, and another physical, due 
to the frontiers produced by the membrane. In the 
cellular automata model of Varela (Varela 
et al. 1974; McMullin and Varela 1994) illus¬ 
trated in Fig. 4, there are three types of particles 



a a 


a □ 
a 


□ □ a c □ a □ a 

a a e a a a 

ooa c b □ 9 ex 

o a a a c 09 a 


Artificial Life, Fig. 4 Simulation by means of cellular 
automata of the autopoietic model originally proposed by 
Varela. The minimal cell can easily be seen, together with 
the catalysts and the substrates that it encapsulates 









168 


Artificial Life 


capable of moving around a two-dimensional 
surface: “substrates,” “catalysts,” and “links.” 
The working and updating rules of these cellular 
automata go as follows: 

• If two substrates are near a catalyst, they dis¬ 
appear to create one single link where one of 
the two was located. 

• If two links are near each other, they link up 
and attach themselves to each other. Once 
attached, these links become immobile. 

• Each link is only allowed to attach itself to two 
other links at the most. This allows the links to 
form chains and to be able to make up a closed 
membrane. 

• The substrates can diffuse through the 
links and their attachments, while the 
catalysts and the other links cannot. We can 
therefore understand how the process of the 
cogeneration comes about. The membranes 
shut in the catalysts and the links, 
which in turn support the membrane by 
being essential to its formation and 
regeneration. 

• The reactions creating the links are reversible, 
as the links can recreate the two original sub¬ 
strates (and thus cause the membrane to dete¬ 
riorate), but at a lower speed. When this 
happens, the attachment between the links 
also disappears. 

Continuous updating and execution of these 
rules produces minimal versions of reactive sys¬ 
tems, physically closed and confined by means of 
a membrane, which is itself produced by the 
reactive system. For Varela and the others fol¬ 
lowing him, this turns out to be an essential stage 
in the road to life. Running the software, many 
difficulties are encountered such as the simple 
attainment of a closed cell on account of the 
many more possibilities for the membranes to 
unfold in a straight way. Only software simula¬ 
tions can interconnect the physical compartment 
played by the membrane with the generating 
metabolism and further show how far from obvi¬ 
ous it is for these two systems to mutually sustain 
each other. 


The whole, interactive “metabolism and mem¬ 
brane” prefigures a minimal elementary ► cell, 
which already seems capable both of maintaining 
itself and detaching itself from its environment 
and from cells similar to it. It is at this stage on the 
way to establishing a better and more exact char¬ 
acterization of life that the definition given by 
Luigi Luisi (2002) takes on its full meaning 
(restating the idea of autopoiesis in more biolog¬ 
ical terms). “Life is a system which can be 
self-maintaining by using external energy and 
nutritional sources to the production of its inter¬ 
nal constituents. This system is spatially 
circumscribed by a semipermeable membrane of 
its composition.” In the footsteps of Varela, con¬ 
sidering life impossible without a way for 
individualization and compartmentalization, the 
constitution of the membrane by simple self¬ 
organization or self-assembly processes of bipo¬ 
lar molecules (hydrophilic and hydrophobic) has 
become a very popular field of artificial life. It is 
indeed rather simple to reproduce this phenome¬ 
non in software (as illustrated in Fig. 5). You 
need water molecules that just randomly move, 
in blue in the figure. You need two kinds of 
submolecules (call then A and B), which when 
they meet - through the only authorized additive 



Artificial Life, Fig. 5 Simulation of a minimal cell based 
on A-B (A is hydrophobic and B hydrophilic) and water 
molecules. All molecules move in reaction to repulsive 
forces of different intensities and thermal agitations. The 
pink dots are the A; the gray dots are the B that do connect 
to give A-B (represented in red and black) by a simple 
chemical reaction. The blue dots are the water molecules 



Artificial Life 


169 


chemical reaction - form an A-B molecule (A is 
hydrophobic and B hydrophilic) whose two poles 
are connected by a small string. You need also to 
adjust the degree of repulsion between A and 
water and between B and water, the strength of 
the string of the A-B molecule, and the random 
component (akin to the thermal noise) to add on 
each of the intermolecular forces. Nevertheless, 
the final outcome turns out to be rather robust. 
The bilayer of B-A/A-B molecules will very nat¬ 
urally and spontaneously form just as for real 
cells. 

Again, as for Varela’s minimal cell, the clo¬ 
sure turns out to be quite delicate to obtain. One 
very simple way to obtain it is to locate the source 
of A submolecules (the pink dots in the figure) in 
a singular point, so that the closed membrane will 
simply surround that source, the circular shape 
being the local minimal of the mechanical energy 
connecting all A-B together. Like in Varela’s 
model, and somewhat paradoxically, the source 
needs to be circumscribed by the membrane for 
that same membrane to close on itself. However, 
in contrast with this autopoietic model, once in 
place, the membrane cannot deteriorate, and thus, 
no further internal chemistry is required to endog¬ 
enously produce what would be needed to fix 
it. Ultimately, this membrane should exhibit 
some selective channeling in and channeling out 
(akin, for some authors (Luisi 2002), to a very 
primitive form of cognition) providing its internal 
metabolism with the right nutrients and the right 
evacuating way out so as to facilitate the cell’s 
self-maintenance. These two software models 
raise interesting questions for the biologists like: 
how are the molecular parts of the membrane 
generated (endogenously or exogenously) and is 
this cogeneration of the membrane and the inter¬ 
nal metabolism the signature of minimal life? 

Self-Replication of This Elementary Cell 

Self-replication, or the ability of a system to 
produce a copy of itself on its own, is one of the 
essential characteristics that has most intrigued 
and impassioned disciples of artificial life, begin¬ 
ning with John Von Neumann. Biology, and in 
particular this faculty of self-replication, fasci¬ 
nated Von Neumann. For if we want to compare 


a cell to a computer and a genome to a code, we 
need to explain how the computer itself was able 
to be created out of this code. Let us follow the 
reasoning of this genius step by step, as it is the 
perfect illustration of an “artificial life” type of 
approach: no material realization but just pure 
functions or rules. Through a sequence of purely 
functional questions and showing an almost com¬ 
plete ignorance of actual biology, his reasoning 
led to a logical solution, the content of which 
retraces astonishingly closely those lessons we 
have since learned about the way biology func¬ 
tions. Von Neumann begins from the principle 
that a universal constructor C must exist, which, 
based on the plan of some kind of machine P M 
(P the plan, M the machine), must be capable of 
constructing the machine M p . This idea may be 
simply translated by C(P M ) = M p . The question 
of self-replication that is then raised is, “Is this 
universal constructor capable of constructing 
itself?” In order to do so, it must, following the 
example of other construction products, have a 
plan of what it wants to construct; in this specific 
case, it is the constructor’s plan P c . The problem 
is then expressed as follows: can C(P c ) give C 
(P c ) in order for there to be a perfect replication 
of the original? Von Neumann therefore realized 
that the question at issue is that of the fate of the 
construction plan, because if the constructor con¬ 
structs itself, it has to add the plan itself to the 
product of the construction. Von Neumann pro¬ 
posed then allotting two tasks to the universal 
constructor: constructing the machine according 
to the given plan and thus adding the original plan 
to this construction. The constructor’s new for¬ 
mula then becomes C(P M ) = M p (P m ). If the con¬ 
structor applies itself to its own plan, this time the 
replication will be perfect: C p (P c ) = C p (P c ). 

The fascinating aspect of Von Neumann’s 
solution is that it anticipated the two essential 
functions that, as we have since discovered, are 
the main attributions of the protein tools consti¬ 
tuting the cell: constructing and maintaining this 
cell and also duplicating the code in order for this 
construction to be able to prolong itself for fur¬ 
ther generations. Starting with the ► DNA, the 
whole ► protein machinery first of all builds the 
cell and then, by an additional procedure, 



170 


Artificial Life 


duplicates this same DNA. Von Neumann did not 
stop at duplication, because, at the same time, he 
imagined how this same machinery could evolve 
and become gradually more complex as a result 
of random mutations taking place while the plan 
recopies itself. Von Neumann gave also a cellular 
automata solution of the problem in which each 
cell of the automata possessed 5 neighbors and 
29 states, and around 200,000 cells were neces¬ 
sary for the phenomenon of self-replication to 
take place. Many years later, Chris Langton 
(Langton 1984, 1989), the organizer of the first 
conference on artificial life in 1989, proposed an 
extremely simplified version of this (8 states, but 
219 rules remain necessary), although it still fol¬ 
lows the pattern mapped out by Von Neumann. 
This automaton, shown in Fig. 6, incessantly 
reproduces a little motif shaped as a loop. 

For many biologists, as opposed to Varela, 
Luisi, Ganti, and Maynard-Smith, life is not sim¬ 
ply indissociable from but also essentially reduc¬ 
ible to this capacity for self-replication. 
Nevertheless, they still need to explain how life 
can actually reproduce without an entire preexis¬ 
tent metabolic chemical machinery. Departing 
from the elementary cell introduced in the pre¬ 
ceding section and in the interest of an unbroken 
narrative, let us imagine a simpler scenario lead¬ 
ing to self-replication. The closed circuit of 
chemical reactions could be destabilized by 
some kind of disturbance, causing a growth in 
concentration of some of its constituents, 


■j 


d 


a 


* B QOO( 

nooooo; 

HOpDOOODlSlSU 


d 


di 


P 


Artificial Life, Fig. 6 Langton’s self-replicating cellular 
automata 


including those involved in the formation of 
membranes. This would also be the case provided 
all the reactions of the metabolism turn out to be 
autocatalytic, entailing the exponential growth in 
the concentration of all its molecular elements 
(including again the membrane constituents). 
The membrane and the elements that it captures 
begin to grow (as illustrated in Fig. 7) until they 
reach the fatal point where the balance is upset. 
This is followed by the production of a new cell 
produced by and from the old one. When the new 
one comes, it quickly grows fast enough to catch 
up with the “generator” and “nursing” cell, as a 
chemical network is capable of some degree of 
self-regeneration due to its intrinsic stability; 
each molecule looks around for another that it 
can couple up to. This reconstitutes the natural 
chain reaction of the whole. The new membrane 
and the new chemical network reconstitute on 
their own by helping each other. Again, obtaining 
such duplication is far from obvious since, any 
cell being intrinsically stable, only a thermal but 
quite unnatural agitation would do the job. 

Rather than this elementary form of chemical 
self-replication coupled to the physical self¬ 
replication induced by the growth and division 
of the membrane, life has opted for a more 
sophisticated physicochemical version of it, 
more promising for the evolution to come: self¬ 
replication by the interposing of an “information 
template.” Each element of the template can only 
couple itself with one complementary element. 
The new elements will as a whole naturally 
reconstitute the template they were attracted to, 
causing then the replication of the entire tem¬ 
plate. In biology, it is the extraordinarily 
emblematic double helix of DNA that acts as a 
template, shouldering the major role in the his¬ 
tory of life - that of the first known replicator. Our 
elementary cell must now be internally equipped 
with this information template. Since the 1950s, 
Timor Ganti (2003) proposed the first minimum 
mathematical system, named “chemoton,” 
represented in the Fig. 8. This is the first abstract 
computational protocell that we know, 
constructed by Ganti as the original ancestor of 
living organisms. It possesses three autocatalytic 
chemically linked subsystems: a metabolic 



Artificial Life 


171 



Artificial Life, Fig. 7 The elementary minimal cell of 
Fig. 5 in a process of self-replication induced by the 
growing and the division of the chemical metabolic 

network, a membrane, and an information tem¬ 
plate responsible for scheduling and regulating 
self-replication. All three grow exponentially 
until they are able to reproduce, and they depend 
on each other for their existence and stability. The 
metabolism feeds the membrane and the tem¬ 
plate, the membrane concentrates the metabo¬ 
lites, and the template mechanism dictates the 
reproduction of the whole. The triad ensemble is 
indeed capable of a whole synchronous self¬ 
replication and tries to computationally answer 
questions about the three subsystems and their 
interdependency, such as “how does the self¬ 
replication of the template automatically accom¬ 
pany the self-replication of the whole.” This com¬ 
plex software object, the “chemoton,” has also 
become the topic of many software developments 
and experimentations and is emblematic of arti¬ 
ficial life at its best. 


network together with the membrane enclosing it. A lot 
of random thermal noise is here indispensable to destabi¬ 
lize the initial cell 

Genetic Coding and Evolution by Mutation, 
Recombination, and Selection 

In the information template introduced in the last 
section, each letter constituting it contributes to 
the code of a functional component essential to 
the cell and designed on the basis of that code - a 
protein. As soon as he hears anyone talking about 
code, the software specialist has, quite legiti¬ 
mately, to put his head in through the window, 
because it is to him and him alone that we in fact 
owe the metaphor of the genetic code. Since 
► Darwin and thereafter throughout all evolu¬ 
tionary science, we have a good idea of what the 
last chapter of the history of life is. Doubtless 
what has stimulated most developments in “arti¬ 
ficial life” (primarily from the point of view of 
engineering) is the fact that the genetic code can 
evolve through ► mutation and sexual crossing 
between the old machines, evolving so as to 
















172 


Artificial Life 


produce new machines that are more and more 
efficient. Over the past 20 years, many of those 
developments into artificial life have been eager 


y 



Artificial Life, Fig. 8 The schematic representation of 
Ganti’s chemoton. One can easily see the three autocata- 
lytic subsystems: the metabolism, the membrane, and the 
information template, chemically coupled 


to show how beneficial this idea is for the 
research and the automated discovery of sophis¬ 
ticated solutions to complex problems. As illus¬ 
trated in Fig. 9, this research can take place 
through a succession of mutations and recombi¬ 
nations operating at the level of the code, with the 
best solutions proposed being preserved in the 
next generation in order to be used for a new 
cycle of these same operations. The brute force 
of the computer is used to its full effect. 

These are the same genetic algorithms that 
Dawkins used in his Darwinian crusade, when 
he developed his biomorphs. It should also be 
stressed that another element in Dawkins’ pro¬ 
gram is that, when it is finally evaluated, the 
phenotype is not directly obtained from the geno¬ 
type, as would be the case for classical optimiza¬ 
tion in a real or combinatory space. In his work, 
the biomorphs are the product of a recursive 
sophisticated program, which is carried out 
starting from a given ► genotype to give a 
► phenotype. A great “semantic distance” is 
maintained between these genotypes and pheno¬ 
types, which reflect the long process of cell con¬ 
struction from the genetic code and the need for a 
sophisticated metabolism building the machine 
out of the code. In brief, this constant program, 


Artificial Life, 

Fig. 9 Illustration of the 
genetic algorithms: the 
recurrent iterated sequence 
of selection, mutation, and 
recombination easily leads 
to an interesting solution of 
a complex optimization 
problem 


















Artificial Life 


173 


able to interpret the evolving genotype, is much 
more important for the complexity of the final 
outcome than the genotype itself. Similarly, a 
very prized derivative of these algorithms is 
genetic programming (Koza 1992), where the 
individuals now to be optimized are software 
codes. 

Conclusions 

Parallelism, functional emergence, and adapt¬ 
ability are the conditions necessary to allow 
these new biologically inspired artifacts to 
emerge, to “face the world.” We are jumping 
straight into the robotics branch of artificial life 
(Brooks 1991). The interfacing with the real 
world required by these robots needs a parallel 
information reception mechanism, because the 
environment subjects it to a constant bombard¬ 
ment of stimuli. They have to leam to organize 
and master this avalanche falling on their percep¬ 
tions. They have to learn to build their own con¬ 
cepts, fed and stimulated by this environment, 
which, in turn, allows them to master it. The 
conceptual high-level cognitive processes are 
bom out of motor-sensory interactions and serve 
to support them. Cognitive systems extend at new 
levels what the minimal cell in the primitive soup 
does, with a flow of matter and energy crossing 
straight through, maintaining itself by selectively 
integrating this influx to form a closed reactor 
network and the membrane enclosing it. 

My conclusions are addressed to the three 
partners: the biologist, the engineer, and the phi¬ 
losopher. To the first, the outcomes of artificial 
life consist in bringing out what the computer and 
biology share intimately: an elementary way of 
working at the ultimate lowest level, but, which 
by the brute force of parallelism and incessantly 
repeated iterations, can make unknown and 
sophisticated phenomena to emerge at higher 
levels. The qualitative aspect of these simulations 
can give them new roles in the vast scientific 
register: use it for education, illustrate biological 
principles that are already understood, open up 
possible experiences of thought, play and replay 
multiple biological scenarios very quickly, titil¬ 
late the imagination by on-screen representa¬ 
tions, call into question some of the 


ambiguously interpreted but commonly accepted 
facts, and, when detailed at most, be able to 
predict experimental measurements. 

The second partner, the engineer, is vigor¬ 
ously encouraged to use the computer for what 
it is best at doing - this infinite possibility of trial 
and error. There is a perfect synergy, where both 
participants complement each other ideally: the 
engineer must bow to the computer in terms of 
calculating power, but this is compensated for by 
his judgment. Genetic algorithms, ant colonies, 
neural networks, and reinforced learning have 
enriched the engineer’s toolbox. 

Finally, for the philosopher, for each attempt at 
a definition of life, artificial life makes a real 
attempt to achieve a computerized version in con¬ 
formity with this definition. For the skeptic, 
unhappy with this computerized “lining,” the 
question now becomes how to refine his definition, 
to complete it, or to renounce the possibility that 
there is no definition that cannot be computerized. 
The other possibility, doubtlessly more logical but 
more difficult for many philosophers to accept, 
would be that life poses no problem for a computer 
snapshot since it is computational at its roots. 


See Also 

► Autocatalysis 

► Bioinformatics 

► Biological Networks 

► Cellular Automata 

► Code 

► Complexity 

► Emergence of Life 

► Genetic Algorithms 

► Life 

► Membrane 

► Self-Replication 

References and Further Reading 

Barabasi L-A (2002) Linked. The new science of net¬ 
works. Perseus, Cambridge 

Bersini H (2004) Whatever emerges should be intrinsi¬ 
cally useful. In: Proceedings of artificial life, 
vol 9. MIT Press, Cambridge, pp 226-231 



174 


Artificial Meteorite 


Billoud B (2010) Origins of life: computing and simula¬ 
tion approaches. In: Gargaud M, Lopez-Garcia P, 
Martin H (eds) Origin and evolution of life: an astro- 
biology perspective. Cambridge University Press 
(Chapter 5) 

Brooks R (1991) Elephants don’t play chess. In: Maes 
P (ed) Designing autonomous agents. MIT Press, Cam¬ 
bridge, MA 

Dawkins R (1986) The blind watchmaker. WW Norton, 
New York. ISBN 0-393-31570-3 
De Duve C (2002) Life evolving: molecules, mind, and 
meaning. Oxford University Press, Oxford 
Dyson F (1999) Origins of life, 2nd edn. Cambridge Uni¬ 
versity Press, Cambridge 

Fontana W (1992) Algorithmic chemistry. In: Langton 
CG, Farmer JD, Rasmussen S, Taylor C (eds) Artificial 
life II: a proceedings volume in the SFI studies in the 
sciences of complexity, vol 10. Addison-Wesley, 
Reading 

Ganti T (2003) The principles of life. Oxford University 
Press, Oxford 

Goldberg DE (1989) Genetic algorithms in search, opti¬ 
mization, and machine learning, 1st edn. Addison- 
Wesley Professional, Reading 
Kauffman S (1993) The origins of order: self-organization 
and selection in evolution. Oxford University Press, 
Oxford 

Kauffman S (1995) At home in the universe. The search 
for the laws of self-organisation and complexity. 
Oxford University Press, New York 
Koza J (1992) Genetic programming. MIT Press, 
Cambridge 

Langton CG (1984) Self-reproduction in cellular autom¬ 
ata. Phys D 10:135-144 

Langton CG (ed) (1989) Artificial life I. Addison-Wesley, 
Reading 

Lenaerts T, Bersini H (2009) A synthon approach to arti¬ 
ficial chemistry. Artif Life 15(1):89—103 
Lovelock J (2000) Gaia: a new look at life on earth. 

Oxford University Press, Oxford 
Luisi PL (2002) Some open questions about the origin of 
life. In: Fundamentals of life. Elsevier, Paris, 
pp 287-301. ISBN 2-84299-303-9 
Maynard Smith J, Szathmary E (1999) The origins of life: 
from the birth of life to the origin of language. Oxford 
University Press, Oxford 

McMullin B, Varela FR (1994) Rediscovering computa¬ 
tional autopoiesis. In: Husband P, Harvey I (eds) Pro¬ 
ceedings of the fourth European conference on 
artificial life. MIT Press, Cambridge, p 38 
Meinhardt H (1998) The algorithmic beauty of sea shells, 
2nd edn. Springer, Heidelberg 
Nagel T (1974) What is it like to be a bat? Philos Rev 
83:435^50; Repr. Mortal questions. Cambridge Uni¬ 
versity Press, New York, pp 165-180 
Plasson R, Kondepudi DK, Bersini H, Commeyras A, 
Asakura K (2007) Emergence of homochirality in 
far-from-equilibrium systems: mechanisms and role 
in prebiotic chemistry. Chirality 19:589-600 


Shapiro R (2007) A simpler origin for life. Sci Am 
296:46-53 

Turing AM (1952) The chemical basis of morphogenesis. 
Philos Trans R Soc Lond B 237:37-72; Also in 
Saunders PT (ed) (1992) The collected works of 
A. M. Turing: morphogenesis. North-Holland, 
Amsterdam 

Varela FR, Maturana HR, Uribe R (1974) Autopoiesis: the 
organisation of living systems, its characterization and 
a model. Biosystems 5:187-196 


Artificial Meteorite 

► STONE 


ASA 

Michel Viso 

CNES/DSP/SME, Veterinaire/DVM, 
Astro/Exobiology, Paris Cedex 1, France 

Synonyms 

Aeronautics and Space Agency of FFG; Agentur 
fiir Luft- und Raumfahrt der FFG; Austrian Space 
Agency, Austria 


Definition 

The FFG’s Aeronautics and Space Agency 
(ASA) is the gateway to the international aero¬ 
space industry for Austria’s industry and science 
sectors and aims to strengthen their international 
standing in these key technologies. The agency 
supports the participation of Austrian researchers 
in international and bilateral aerospace collabo¬ 
rations and fosters the creation and development 
of international networks. It implements Austrian 
aeronautical space policy and represents 
Austria’s interests in international aeronautical 
and space organizations. 





ASI 


175 


The FFG’s main focus is on managing the 
contributions of the Republic of Austria to the 
programs of the ► European Space Agency 
(ESA), and FFG is responsible for the 
management of the Austrian Space Applications 
Programme (ASAP), a bottom-up program 
targeted to space science, technology, 
space technology transfer, direct applications 
of space technology, and international 
cooperation. 

Bilateral cooperative projects were under¬ 
taken in particular with the former Soviet 
Union, such as the development of Austrian 
instruments for space probes and missions. 
These projects include, for example, the two 
Venus probes, Venera 13 and 14 (1981-1982), 
the Vega 1 and 2 (1984-1986) missions to 
Halley’s Comet, and the PHOBOS Mars 
probes (1988-1989). The highlight of bilateral 
cooperation with the former Soviet Union 
was the AUSTROMIR-91 mission - the flight 
of the first Austrian cosmonaut, Franz Viehbock, 
to the MIR space station. Other bilateral projects 
were, and still are, run in partnership with Nor¬ 
way, Sweden, France, Switzerland, and 
Germany. 

Among other activities, FFG is organizing 
annually since 1975, the well-known 
Alpbach Summer School that has a long 
tradition in providing in-depth teaching on 
aspects of space science and space technology 
with the aim of advancing the training and 
working experience of European graduates, post¬ 
graduate students, young scientists, and 
engineers. 

Number of employees of the Aeronautics and 
Space Agency of FFG is ten in 2010. 

History 

The Space Research Institute of the Austrian 
Academy of Sciences was founded in 1970, and 
the Austrian Space Agency in 1972 (which had 
been merged into FFG in 2004). Austria has been 
participating in ESA programs since 1975 and 
became a full member in 1987. 


Aseptic Process 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 

Definition 

Any operation which is carried out under condi¬ 
tions that minimize the potential for contamina¬ 
tion by ► microorganisms. 


ASI 

Michel Viso 

CNES/DSP/SME, Veterinaire/DVM, 
Astro/Exobiology, Paris Cedex 1, France 

Synonyms 

Agenzia Spaziale Italiana; Italian Space Agency 

Definition 

The Italian Space Agency was established in 
1988 to coordinate all of Italy’s efforts and 
investments in the space sector that had begun 
in the 1960s. Today, ASI has a key role at the 
European level where Italy is the third contribut¬ 
ing country to the ► European Space Agency. 

Italy is directly involved in major European 
and international programs. It provides several 
elements for the International Space Station like 
the multipurpose logistic module (MPLM) used 
to transfer cargo with the US space shuttle, Nodes 
2 and 3, and is participating within ESA in the 
European Automated Transfer Vehicle activities. 
ASI selected five astronauts flying either through 
bilateral cooperation or through ESA. Franco 
Malerba was the first Italian in space in 1992 
onboard the STS 46 flight. Italy is involved also 
in many missions dedicated to planetology, 





176 


Asparagine 


astronomy, and exploration. It is playing a major 
role in the Cassini-Huygens mission, the 
► ExoMars ESA mission, and many others. 
Italy is taking also a major share (65 %) in the 
medium launcher program (Vega rocket) of ESA. 

Beyond the headquarters in Rome, ASI has 
three bases and one center. “Luigi Broglio” 
Space Centre of Malindi, Kenya, was used to 
launch US Scout rockets with Italian satellites 
from oceanic platforms (the marine segment) up 
to 1988. Nowadays this base (the ground seg¬ 
ment) is dedicated to receive data from satellites 
and launchers. 

A stratospheric balloon launch base is located 
on a former airport in Trapani (since 1975). This 
base is, in particular, actively involved in trans- 
Mediterranean flights of research balloons. 

In Matera, in collaboration with several insti¬ 
tutions, ASI opened in 1983 a Space Geodesy 
Center dedicated to this discipline. Now this 
base is diverting its activities welcoming some 
technical activities required for robotic 
exploration. 

Finally, an ASI Science Data Center (ASDC) 
was established in September 2000 for the man¬ 
agement and analysis of scientific data collected 
by scientific satellites. This center is located in 
the ESA facility (European Space Research 
Institute-ESRIN) in Frascati, which is dedicated 
to the Earth observation. 


Asparagine 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Definition 

Asparagine, shown in Fig. 1, is one of the 
20 ► protein ► amino acids. Its three-letter sym¬ 
bol is Asn and one-letter symbol is N. It has a 
molecular weight of 132.12. It has an amide 



group (-CONH 2 ) in its side chain, and it is easily 
hydrolyzed to give ► aspartic acid, another pro¬ 
tein amino acid (Asp), and ammonia. In the 
hydrolysis of proteins, both aspartic acid and 
asparagine are determined as aspartic acid 
(noted Asx as the origin cannot be determined 
unambiguously). It is classified as a neutral 
amino acid with an isoelectric point (p/) of 5.41. 

See Also 

► Amino Acid 

► Aspartic Acid 

► Protein 


Aspartic Acid 

Kensei Kobayashi 

Yokohama National University, Tokiwadai, 
Hodogayaku, Yokohama, Japan 

Definition 

Aspartic acid, shown in Fig. 1, is one of the 
20 protein ► amino acids. Its three-letter symbol 
is Asp and one letter symbol is D. It is a 
monoaminodicarboxylic acid, and it is classified 
as an acidic amino acid. Aspartic acid has the 
lowest isoelectric point (p/) 2.77 of the protein 
amino acids. It is among the five amino acids that 








Association Constant 


177 


O 

OH NH 2 

Aspartic Acid, Fig. 1 Structural formula of aspartic acid 

were detected in Miller’s electric discharge 
experiment in 1953 and is found in extracts 
from carbonaceous chondrites. Since it has two 
carboxyl groups (oc- and (3-carboxyl group), it can 
make both oc- and [3-peptide bonds with other 
amino acids. In biosynthesis of ► proteins, only 
oc-peptide bonds are formed. As the ► racemiza- 
tion of aspartic acid is relatively rapid, the D/L 
ratio of aspartic acid can be used for dating bio¬ 
logical materials such as bone. 

See Also 

► Amino Acid 

► Miller, Stanley 

► Protein 

► Racemization 


Assay 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 

Definition 

In ► planetary protection, an assay is the suite of 
actions performed during the integration of a 
spacecraft or an instrument to collect and mea¬ 
sure the biological contamination using a speci¬ 
fied procedure, in order to estimate the number or 
types of ► microorganisms associated with an 
item of interest (exposed surface, material, envi¬ 
ronment, etc.). 


Assimilative Metabolism 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 


Definition 

Assimilative ► metabolism is the process by 
which an inorganic compound (NO 3 ", S0 4 2- , 
C0 2 ) is reduced for use as a cell nutrient source. 
Assimilative metabolism is conceptually differ¬ 
ent from the ► reduction reactions that take place 
when the same inorganic compounds are used as 
electron acceptors to obtain energy by ► anaero¬ 
bic respiration (► dissimilative metabolism). 
There are important differences between both 
types of ► metabolism. In the assimilative metab¬ 
olism, only enough of the compound is reduced to 
satisfy the needs for cell growth, and the products 
are normally converted into cell material, while 
in the dissimilative metabolism, a large amount 
of ► electron acceptor must be reduced to guar¬ 
anty the generation of sufficient energy and the 
product is excreted into the environment. 


See Also 

► Anaerobic Respiration 

► Dissimilative Metabolism 

► Electron Acceptor 

► Metabolism, Prebiotic 

► Reduction 

► Sulfate Reducers 


Association Constant 

► Affinity Constant 










178 


Asteroid 


Asteroid 

Alan W. Harris 

DLR, Institute of Planetary Research, Berlin, 
Germany 

Keywords 

Dynamical and physical properties; Taxonomy; 
Mineralogy; Impact hazard; Mitigation 

Synonyms 

Minor planet; Planetoid; Small Solar System 
body 

Definition 

An asteroid is an irregularly shaped rocky body 
orbiting the Sun that does not qualify as a planet 
or a dwarf planet under the International Astro¬ 
nomical Union’s (IAU) definitions of those terms 
introduced in 2006. In contrast to planets and 
dwarf planets, asteroids do not have sufficient 
mass for their self-gravity to overcome rigid 
body forces and assume a hydrostatic equilibrium 
(nearly round) shape. In contrast to comets, aster¬ 
oids are inert bodies that do not display a coma of 
gas and dust (although a few objects originally 
classed as asteroids have subsequently been 
found to display cometary activity). Very small 
objects with a size of less than about 10 m are 
normally referred to as meteoroids. 

Overview 

The first asteroid, 1 Ceres, was discovered in 
1801 by the Italian astronomer Giuseppe Piazzi, 
quickly followed in succeeding years by the dis¬ 
covery of 2 Pallas, 3 Juno, and 4 Vesta. Ironi¬ 
cally, Ceres is now classed as a dwarf planet 
under IAU Resolution B5 of 2006, and Pallas 
and Vesta are candidates for transfer to this new 


category of dwarf planets. Since about 1850 
the discovery rate has increased dramatically, 
especially in recent years, leading to the 
current tally (June 2013) of over 360,000 num¬ 
bered asteroids. An asteroid is assigned a perma¬ 
nent designation, i.e., a sequential number, once 
its orbit has become accurately established 
through a sufficient number of astrometric 
observations. 

Asteroids and comets are considered to be 
remnant bodies from the epoch of planet forma¬ 
tion. Planet embryos, roughly lunar-sized bodies, 
formed in the protoplanetary disk about 4.5 bil¬ 
lion years ago via the accretion of dust grains and 
collisions with smaller bodies (kilometer-sized 
planetesimals). A number of planet embryos 
succeeded in developing into the planets we 
observe today; the growth of other planet 
embryos and planetesimals was terminated by 
catastrophic collisions or a lack of material in 
their orbital zones to accrete. Most asteroids are 
thought to be the fragments of bodies that formed 
in the inner Solar System and were subsequently 
broken up in collisions. Comets and related icy 
bodies are thought to have accreted in the cold, 
outer regions of the protoplanetary disk where 
volatile materials, such as water and carbon diox¬ 
ide, were abundant as ices. 

Most numbered asteroids are in the main aster¬ 
oid belt between the orbits of Mars and Jupiter. 
The existence of the main belt is thought to be due 
to the collisional fragmentation of remnant planet 
embryos and planetesimals that were prevented 
from accreting into planets by the gravitational 
perturbations of the nearby massive planet 
Jupiter. 

Main-belt asteroids consist largely of silicates 
and metals and come in all shapes and sizes up to 
about 1,000 km in diameter. Table 1 lists physical 
data for the first ten asteroids discovered. Large 
asteroids with diameters of several hundred km 
tend to be roughly ellipsoidal, but smaller objects 
generally have very irregular shapes. Asteroid 
surfaces appear to consist of loose dust mixed 
with gravel and boulders (regolith), whereby 
there is evidence that the regolith of km-sized 
bodies is coarser and less dusty than that of 
large main-belt asteroids. 




Asteroid 


179 


Asteroid, Table 1 The first ten numbered asteroids 


Number 
and name 

Discovery: year, 
site, discoverer 

Diameter (km) 

Taxonomic class 
(see below) [4] 

Bulk density 
(g cm -3 ) [1] 

Rotation 
period (h) [5] 

1 Ceres 

1801, Palermo, 

G. Piazzi 

949 ± 11 [1] 

G, C 

2.12 db 0.04 

9.074 

2 Pallas 

1802, Bremen, 

H. W. Olbers 

533 db 6 [1] 

B 

2.71 db 0.11 

7.813 

3 Juno 

1804, Lilienthal, 

K. Harding 

234 db 11 [2] 

S 

- 

7.210 

4 Vesta 

1807, Bremen, 

H. W. Olbers 

529 =b 10 [1] 

V 

3.44 db 0.12 

5.342 

5 Astraea 

1845, Driesen, 

K. L. Hencke 

119 =b 7 [2] 

s 

- 

16.80 

6 Hebe 

1847, Driesen, 

K. L. Hencke 

185 db 3 [2] 

s 

- 

7.274 

7 Iris 

1847, London, 

J. R. Hind 

200 db 10 [2] 

s 

- 

7.139 

8 Flora 

1847, London, 

J. R. Hind 

136 db 3 [2] 

s 

- 

12.80 

9 Metis 

1848, Markree, 

A. Graham 

172 db 13[3] 

s 

- 

5.079 

10 Hygiea 

1849, Naples, A. de 
Gasparis 

407 db 7 [2] 

c 

2.76 db 1.2 

27.62 


References: [1] Britt et al. (2002); [2] Tedesco et al. (2002); [3] Miiller and Barnes (2007); [4] Bus and Binzel (2002); 
[5] Harris et al. (2008) 


Asteroid Dynamical Groupings 

Asteroids are classified dynamically according to 
their orbital elements (semimajor axis, period, 
inclination, eccentricity, etc.). The most signifi¬ 
cant grouping of asteroids is the main belt, 
between about 2.0 and 3.5 astronomical units 
(AU, the mean Sun-Earth distance) from the 
Sun. The main belt is populated by millions of 
asteroids, some 360,000 of which have been 
assigned sequential numbers to date. 

A number of asteroid families exist in the main 
belt. Family members have very similar dynam¬ 
ical characteristics and may be fragments from 
relatively recent (relative to the history of the 
Solar System) collisions. For example, there are 
large families associated with the main-belt aster¬ 
oids 4 Vesta, 8 Flora, and 10 Hygiea (Table 1). In 
these cases the families presumably arose as the 
result of cratering events that gave rise to ejecta 
from the surfaces of the large asteroids. In other 
cases precursor asteroids were apparently 
completely broken up. In both scenarios the result 
is a family of fragments with similar orbits (and 
dust particles that probably contribute to the 


cloud of dust associated with the ecliptic plane 
and give rise to the zodiacal light). In most cases 
the family members have very similar 
compositions. 

Other major dynamical groups are described 
below and listed in Table 2. 

Jupiter Trojans are asteroids that are trapped in 
dynamically stable zones 60° ahead of and 
behind Jupiter in its orbit. The stable zones are 
associated with the L4 and L5 Lagrangian points 
of Jupiter’s orbit. There are some 5,900 known 
Jupiter Trojans orbiting between about 5.0 and 
5.4 AU from the Sun. 

Trans-Neptunian Objects (TNOs) are very dis¬ 
tant, presumably icy, bodies with semimajor axes 
larger than 30 AU. Most TNOs are classed as 
asteroids according to the formal definition of 
an asteroid given above, but in terms of their 
physical characteristics, they may have more in 
common with comets. The first TNO was discov¬ 
ered in August 1992; some 1,500 have been dis¬ 
covered since. 

The Centaurs have orbits between that of Jupi¬ 
ter and the TNOs. Centaurs are possibly objects 




















180 


Asteroid 


Asteroid, Table 2 Selected asteroid dynamical groups 


Dynamical category 

Semimajor axis 
[AU] 

Approx, 
no. known a 

Notes 

Trans-Neptunian objects 
(TNOs) b 

>30 

1,500 


Centaurs' 3 

5.2-30 

130 

Possibly TNOs whose orbits have been 
perturbed by Neptune 

Jupiter Trojans 

5.05-5.4 

5,900 

Associated with the Lagrangian points of 
Jupiter’s orbit 

Main belt 

2.0-3.5 

6.1 x 10 5 

3.6 x 10 5 numbered asteroids 

Amors c 

>1 

3,741 

1.017 < perihelion <1.3 AU 

Apollo s c 

>1 

5,373 

Perihelion < 1.017 AU 

Atens c 

<1 

774 

Aphelion > 0.983 AU 

Inner-Earth objects 0 

<1 

12 

Aphelion < 0.983 AU 


a The listed approximate numbers of known objects are valid as of June 2013; these numbers increase rapidly with time as 
new objects are discovered. For more details and updates, see the Minor Planet Center web site http://www.cfa.harvard. 
edu/iau/mpc.html 

b TNOs and Centaurs are distant icy bodies that may have much in common with comet nuclei 

c The orbital characteristics of the different classes of NEAs are defined with respect to the Earth’s perihelion (0.983 AU) 
and aphelion (1.017 AU) distances 


that originated as TNOs but due to perturbations 
by Neptune are now in orbits that bring them 
closer to the Sun. The number of known Centaurs 
is currently around 130. A few Centaurs have 
been observed to display comae and are classed 
as both asteroids and comets. TNOs and Centaurs 
are of particular scientific interest because they 
have been subject to less thermal alteration and 
processing than main-belt asteroids and may con¬ 
tain well-preserved primordial material from the 
epoch of formation of the Solar System. 

Near-Earth asteroids (NEAs) are asteroids that 
are thought to originate in the main belt but which 
now have highly evolved orbits with perihelion 
distances of less than 1.3 AU. NEAs are further 
categorized dynamically as Amors, Apollos, 
Atens, or Inner-Earth objects (IEOs) according 
to the semimajor axes, aphelion and perihelion 
distances of their orbits (Table 2). The orbits of 
NEAs may evolve to intersect that of the Earth. 
Interest in the population of NEAs is focused 
mainly on the associated impact hazard (see 
below), but close approaches of NEAs to the 
Earth facilitate detailed telescope observations, 
including radar investigations, which provide 
insight into the characteristics of asteroids in 
general. Furthermore, two rendezvous missions, 
NEAR-Shoemaker (Cheng 2002) and Hayabusa 


(Fujiwara et al. 2006), have provided a wealth of 
data on two very different NEAs in recent years 
(Figs. 1 and 2). 

The Taxonomic Classification and Mineralogy 
of Asteroids 

Sunlight incident on the surface of an asteroid 
suffers absorption in particular wavelength 
bands depending on the minerals present; 
reflected light therefore carries a spectral signa¬ 
ture of the mineralogical composition of the 
asteroid’s surface. Attempts have been made to 
classify asteroids according to details of the 
absorption features in their optical reflection 
spectra observed with astronomical telescopes. 
A number of classification schemes have been 
devised based on letters of the alphabet (e.g., 
Bus and Binzel 2002; Tholen and Barucci 
1989). For example, a very common spectral or 
taxonomic type is S, originally intended to sig¬ 
nify a stony or “silicaceous” object. Another 
common type is C, originally signifying carbon 
rich or “carbonaceous.” Other letters, which are 
in common use, are M for metallic and V for 
Vesta-like. As the inventory of asteroid spectral 
data grew, and more distinct spectral types were 
discovered, the taxonomic alphabet had to 
expand to incorporate more letters. Thanks to 
















Asteroid 


181 



Asteroid, Fig. 1 Near-Earth asteroid 433 Eros was the 
target of the NASA NEAR-Shoemaker spacecraft in 
2000-2001. Eros is 34 km in length and of taxonomic 
type S. The large number of impact craters indicates an 
age of 1-2 Gyr (Credit: JHUAPL, NASA) 



Asteroid, Fig. 2 Near-Earth asteroid 25143 Itokawa was 
the target of the Japanese Hayabusa spacecraft in 
2005-2006. Itokawa is 535 m in length and of type 
S. Itokawa, which lacks craters, is much younger than 
Eros and may be an aggregate of components weakly 
bound by gravity or “rubble pile” (Courtesy of JAXA) 


the improved sensitivity of modem astronomical 
instrumentation, it has become possible to iden¬ 
tify subtle differences in spectral features within 
the classical taxonomic types, leading in some 
cases to the addition of small letters after the 
class letter to signify subclasses, e.g., Cb, Sq, etc. 

Key Research Findings 

Water and Organic Material in Asteroids 

The mineralogical associations listed in Table 3 
include hydrated (water-bearing) silicates and 
organics. There is considerable evidence that 
hydrated minerals are also present on a number 
of M-type asteroids (Rivkin et al. 2000). Further¬ 
more, water ice and organic material have been 
detected on the surface of the main-belt C-type 
asteroid 24 Themis (Rivkin and Emery 2010; 
Campins et al. 2010). Some asteroids evidently 
carry significant amounts of water and organic 
materials, a fact that may be relevant to questions 
concerning the origin of water and life on Earth. 
It is widely believed that bodies similar to aster¬ 
oids and comets contributed to the early Earth’s 
inventory of water and organics, but there is 
currently no consensus as to when or how. 

A point of current debate is whether Earth’s 
water was provided primarily by asteroidal mate¬ 
rial from the outer main belt at the time of for¬ 
mation of the Earth or whether comets and 
asteroids contributed a “veneer” of water-bearing 
material at a later stage after the Earth had formed 
and cooled. Measurements indicate that the 
hydrogen isotopic ratio D/H in the few comets 
for which such measurements have been made is 
an order of magnitude higher than that of 
protosolar material, but this significantly exceeds 
the factor of 6 enrichment of the Earth’s oceans 
(Lellouch et al. 2001; Drake and Righter 2002). 
On the other hand, the D/H ratio of carbonaceous 
chondritic asteroidal material is compatible with 
that of the Earth’s oceans. Therefore, at face 
value, the D/H evidence appears to argue against 
a dominant post-formation water contribution 
from comets. 

Investigations of the composition of meteor¬ 
ites, which are thought to originate in asteroids, 





182 


Asteroid 


Asteroid, Table 3 Important asteroid taxonomic (spectral) classes 


Class 

Probable mineralogy 

Associated geometric 
albedo a (p v ) range 

Approx. % of all 
classified asteroids 13 

D, P 

Carbon, organic-rich silicates 

0.03-0.06 

2 

C, B 

Carbon, organics, hydrated silicates 

0.03-0.1 

30 

M 

Fe, Ni, enstatite 

0.1-0.2 

2 

S 

Olivine, pyroxene, metals 

0.1-0.3 

40 

Q 

Olivine, pyroxene, metals 

0.2-0.5 

1 

V 

Pyroxene, feldspar 

0.2-0.5 

3 

E 

Enstatite, other Fe-poor silicates 

0.3-0.6 

1 

X 

Unknown (signifies otherwise unclassifiable 
featureless spectrum) 

0.03-0.6 

15 


a The geometric albedo p v is the ratio of a body’s (V-band) brightness at zero-phase angle to the brightness of a perfectly 
diffusing (Lambertian) disk with the same apparent size as the body 

b Estimated from the data of Bus and Binzel (2002) and Tholen and Barucci (1989). Note that discovery and observation 
bias against objects with dark surfaces implies that the distribution of taxonomic classes in the known population may 
not be representative of the entire asteroid population 

indicate that carbonaceous chondritic asteroidal 
material contains up to 10 % by mass of water 
(Drake and Righter 2002; Morbidelli et al. 2000). 

Therefore asteroidal material, in the form of 
planet embryos from the outer main belt incorpo¬ 
rated into the forming Earth (Morbidelli 
et al. 2000), may have contributed much of the 
Earth’s water. On the basis of current knowledge, 
e.g., comparisons of isotope ratios and noble gas 
ratios, it appears unlikely that either comets or 
asteroids bombarding the Earth after the forma¬ 
tion phase could have contributed significant 
water (Drake and Righter 2002). 

In the case of organic material, a post¬ 
formation source is required because it seems 
significant quantities of organics could not have 
survived on the Earth until formation was com¬ 
plete and the Earth had cooled. The most plausi¬ 
ble source of organic material is therefore the flux 
of asteroids and comets that deposited material 
on the Earth after the formation phase. Some 
100 amino acids have been detected in meteorites 
and it is widely believed that many comets and 
asteroids carry amino acids and other organic 
molecules. 

The Densities and Structure of Asteroids 

Reliable estimates of density are difficult to 
obtain, since techniques for obtaining accurate 
masses and sizes of asteroids are complex and 
subject to large uncertainties. There are various 


methods of determining asteroids masses (see 
Britt et al. 2002 for a review), which all require 
measurement of the asteroid’s gravity field by 
means of, for example, a spacecraft, observations 
of the perturbations of the orbits of other asteroids 
or Mars (applicable to large asteroids only), or 
observations of a satellite or companion asteroid 
by means of precision optical or radar observa¬ 
tions. Asteroid sizes can be determined from, for 
example, spacecraft, thermal-infrared measure¬ 
ments (see Harris and Lagerros 2002 for a review 
and the section on asteroid physical properties 
below), radar observations (see Ostro 
et al. 2002, also Fig. 3), polarimetry, 
(e.g. Delbo’ et al. 2007), and occultation obser¬ 
vations (e.g. Dunham et al. 1990). 

Density estimates for just a few hundred aster¬ 
oids are available to date (Carry 2012). An impor¬ 
tant finding is that asteroid bulk densities tend to 
be significantly lower in general than expected 
from measurements of meteorites and terrestrial 
analogues of asteroid material (2-8 g cm -3 ). In 
fact the bulk densities of some asteroids appear to 
be similar to that of water (1 g cm -3 ), implying 
that these bodies must be highly porous. Such 
results have increased speculation that some 
asteroids, e.g., 25143 Itokawa, may be aggregates 
of components of various sizes weakly bound by 
gravity, or “rubble piles.” An asteroid that has 
been shattered by collisions with other objects 
may survive under the collective weak 
















Asteroid 


183 



Asteroid, Fig. 3 Radar images of binary near-Earth 
asteroid 1999 KW 4 (left-hand row of three frames) 
received at the Goldstone 70-m antenna in May 2001. 
Each image has a resolution of 19 m/pixel and is a time 
exposure spanning several hours, showing the motion of 
the secondary relative to the primary. Due to the complex¬ 
ities of radar imaging, these three images do not show true 

gravitational attraction of the resulting fragments 
as a cohesionless, consolidated rubble pile; this 
idea is supported by the images of Itokawa 
returned by the Hayabusa spacecraft (Fig. 2), 
revealing a highly irregular object apparently 
consisting of separate component blocks of vari¬ 
ous shapes and sizes. 

The rubble-pile idea leads to a natural expla¬ 
nation for the existence of the many binary aster¬ 
oid systems or asteroids with natural satellites 
(moons) that have been discovered (see Fig. 3 
for an example). The spin rates of asteroids can 
be modified by dynamical phenomena, such as 
the close approach to a planet, or the reflection 
and/or absorption and thermal reradiation of sun¬ 
light. If a loosely bound rubble pile is spun up 
sufficiently, it can shed mass that may form a 
companion body or moon gravitationally bound 
to it. Recent computer simulations have demon¬ 
strated the credibility of binary asteroid produc¬ 
tion via the spin-up and rotational breakup of a 
rubble pile (Walsh et al. 2008). 

Near-Earth Asteroids and the Impact Hazard 

As a result of subtle thermal effects and the very 
strong gravitational field of Jupiter, small main- 
belt asteroids can drift into certain orbital zones 
from which they may be ejected under the influ¬ 
ence of Jupiter into the inner Solar System. As a 
result there exists a population of near-Earth 
asteroids, with orbits that can cross that of the 
Earth. Comets can also collide with the Earth but 
the risk of a comet impact is thought to be much 
lower than that of an NEA impact (although 


relative sizes or shapes of the components. The right-hand 
frame shows a computer model of the system in which the 
two components are seen to scale. The diameters of the 
primary and secondary bodies are 1.5 km and 0.5 km, 
respectively (Images courtesy of L. A. M. Benner, 
NASA/JPL) 

given the potentially high relative velocities the 
effects in the case of a comet impact could be 
much more devastating). 

The phenomenon of collisions in the history of 
our Solar System is very fundamental, having 
played the major role in forming the planets we 
observe today. Asteroids and comets may have 
contributed to the delivery of water and organic 
materials to the early Earth necessary for the 
development of life, but later impacts probably 
played a role in mass extinctions and they cur¬ 
rently pose a small but significant threat to the 
future of our civilization. Collisions of objects 
with the Earth have taken place frequently over 
geological history, and it is an irrefutable scien¬ 
tific fact that major collisions with the Earth will 
continue to occur at irregular, unpredictable 
intervals in the future. 

Collisions of asteroids and comets with the 
Earth can have dramatic effects on the biosphere. 
A well-known example is the so-called 
Cretaceous-Tertiary (K-T) event 65 million 
years ago, which is thought to have been caused 
by the impact of an object with a diameter of 
10-15 km, bringing about the extinction of not 
only the dinosaurs, but also more than 70 % of all 
species living at the time. The idea that the K-T 
mass extinctions observed in the paleontological 
record were caused by the impact of a near-Earth 
asteroid was proposed by Alvarez et al. (1980), 
and given a great deal of credibility by the dis¬ 
covery of a 65 million year old circular impact 
structure nearly 200 km in diameter centered near 
the town of Chicxulub on the Yucatan Peninsula, 




184 


Asteroid 


Mexico (Pope et al. 1991). The impactor must 
have had a diameter of at least 10 km and may 
have hit the Earth with a velocity of some 
15-25 km s" 1 . The results of such an event 
would have included the deposition of billions 
of tons of dust and aerosols into the stratosphere 
that would have spread around the world, dim¬ 
ming sunlight and cooling the surface for many 
months. The ensuing climatic effects could have 
created a very stressful environment for life on 
the Earth’s surface for many years. 

While past impacts have probably altered the 
evolutionary course of life on Earth, and paved 
the way for the dominance of mankind, we would 
now rather not remain at the mercy of this natural 
process. Can we protect our civilization from the 
next major impact? Various initiatives are being 
taken by space agencies, including ESA and 
NASA, and research groups around the world to 
identify potential future impactors, investigate 
their physical characteristics, and develop strate¬ 
gies to mitigate against impacts. 

A number of observatories are operated spe¬ 
cifically to discover near-Earth objects and estab¬ 
lish their orbits. The main currently active 
asteroid search programs, such as the Catalina 
Sky Surveys, Lincoln Near-Earth Asteroid 
Research (LINEAR), and Spacewatch (see 
Yeomans and Baalke 2009), are funded primarily 
by NASA and the US Air Force. Many observers, 
including amateur astronomers, around the world 
contribute to the tracking of asteroids and submit 
their astrometric data to the Minor Planet Center 
in Cambridge, Massachusetts, which acts as a 
clearing house for asteroid position data and 
maintains databases of orbits. 

As of June 2013 the number of known near- 
Earth objects is approaching 10,000, of which 
some 860 have diameters of 1 km or more; the 
total number of the latter, including as yet 
undiscovered objects, is thought to be about 
1,000 (see below). A special term, “potentially 
hazardous asteroids” (PHAs), is reserved for 
those with diameters above 120 m and orbits 
that bring them within 0.05 AU of the Earth’s 
orbit. PHAs are large enough to survive passage 
through the Earth’s atmosphere and cause exten¬ 
sive damage on impact. 


The estimated impact frequency of NEAs on 
the Earth depends on size. The impact frequency 
increases with decreasing size due to the size 
distribution of the asteroid population: there are 
many more small objects than large ones. The 
impact risk to the Earth from NEAs based on a 
recent assessment (Harris 2009) is summarized in 
Table 4. 

Asteroid Physical Properties Relevant to the 
Impact Hazard 

Accurate assessment of the impact hazard 
depends on knowledge of the size distribution 
and orbits of the NEA population. Which physi¬ 
cal parameters are most relevant for mitigation 
considerations? Preventing a collision with a 
NEA on course for the Earth would require either 
total destruction of the object, to the extent that 
the resulting debris poses no hazard to the Earth 
or, perhaps more realistically, deflecting it 
slightly from its catastrophic course. In either 
case accurate knowledge of the object’s mass 
would be of prime importance. In order to 
mount an effective mission to destroy the object, 
knowledge of its density, internal structure, and 
strength would also be required. Deflection of the 
object from its course would require the applica¬ 
tion of an impulse or continuous or periodic 
thrust, the magnitude and positioning of which 
may depend on the mass and its distribution 
throughout the (irregularly shaped) body, the sur¬ 
face characteristics, and the spin vector, 
depending on the strategy deployed. Mitigation 
planning takes on a higher level of complexity if 
the Earth-threatening object is a rubble pile or 
binary system. 

Since the observed brightness of an asteroid is 
proportional to its surface albedo and cross- 
sectional area, a very rough size estimate can be 
obtained from the observed brightness and 
knowledge of the asteroid’s orbit. However, the 
albedo can have any value between 3 % and 60 % 
(Table 3), so the assumption of a typical albedo 
of, say, 15 %, can lead to errors in diameter and 
mass of a factor of 2 and 8, respectively. While 
current estimates of the overall impact hazard are 
necessarily based on the assumption of a typical 
or mean albedo for NEAs, more accurate 



Asteroid 


185 


Asteroid, Table 4 Estimated frequency and effects of asteroid impacts on the Earth 


Impactor size (m) 
larger than 

Mean impact 
interval (year) 

Energy released 
(megatons TNT) 

Crater 

diameter 

(km) 

Possible effects/ 
comparable event 

30 

300 

2 

- 

Fireball, shock wave, 
minor damage 

50 

2,000 

10 

<1 

Tunguska-type explosion 
or small crater 

100 

10,000 

80 

2 

Largest H-bomb detonation 

200 

40,000 

600 

4 

Destruction on national 
scale 

500 

200,000 

10,000 

10 

Destruction on continental 
scale 

1,000 

600,000 

80,000 

20 

Many millions dead, global 
effects 

5,000 

20 million 

10 million 

100 

Billions dead, global 
climate change 

10,000 

100 million 

80 million 

200 

Extinction of human 
civilization 


The energy release estimates assume a density of 3,500 kg m -3 (stony body) and an impact velocity of 20 km s -1 . The 
given impact intervals are statistical: for example, the probability of a 100-m or larger object impacting in the next 
100 years is 1 %, which is the same as the probability of such an object not impacting in 46,000 years 


methods of size determination are clearly neces¬ 
sary for accurate hazard estimation and mitiga¬ 
tion purposes. 

Telescope observations in the thermal infrared 
combined with knowledge of an asteroid’s opti¬ 
cal brightness offer a means of obtaining more 
accurate information on size and albedo (Harris 
and Lagerros 2002). Darker, low albedo, aster¬ 
oids are less reflective in the visible spectral 
region and absorb more solar radiation; they are 
therefore warmer and brighter in the thermal- 
infrared spectral range. The opposite is true for 
high albedo asteroids. The two different physical 
relationships governing visible and thermal- 
infrared brightness enable simultaneous solutions 
for size and albedo to be obtained. While the 
number of asteroids observed in the thermal 
infrared is still only a very minor fraction of the 
total known, this technique has provided the vast 
majority of size and albedo determinations to 
date. For example, surveys of the sizes and albe¬ 
dos of hundreds of NEAs have been carried out 
by the NASA WISE (Wide-held Infrared Survey 
Explorer) and Spitzer infrared space telescopes. 
WISE was launched to Earth orbit in December 
2009 carrying a 40-cm-diameter telescope and 
infrared detectors. WISE surveyed the sky for 


nearly 12 months and observed a total of at least 
584 NEAs, of which more than 130 were new 
discoveries. 

An important result from thermal-infrared 
observations is the apparent size dependence of 
the albedos of some types of NEA in the 
0.1-10 km size range, such that the mean albedo 
appears to increase with decreasing size (Delbo’ 
et al. 2003; Harris 2006). As explained above, the 
mean albedo of NEAs is important for current 
estimates of their size distribution. If the mean 
albedo is higher, the diameter derived from a 
particular observed brightness is smaller and the 
overall impact hazard from NEAs is reduced 
(Stuart and Binzel 2004). The impactor sizes in 
Table 4 are based on a mean geometric albedo of 
14 %, slightly larger than the value of 11 % 
adopted in earlier studies, which leads to some¬ 
what longer mean impact intervals for each size 
category. 

Future Directions 

The rate of discovery of NEAs has increased 
dramatically in recent years and is now seriously 
outstripping the rate at which the population can 

















186 


Asteroid 


be physically characterized. The NEA population 
is still largely unexplored. Telescope observa¬ 
tions will continue to provide valuable informa¬ 
tion about the NEA population as a whole, but 
rendezvous missions are vital for probing the 
detailed characteristics of individual objects. To 
date only two NEAs have been visited by space¬ 
craft (Figs. 1 and 2), but many more rendezvous 
missions to NEAs of different taxonomic types 
will be necessary before we can start to under¬ 
stand the diverse compositions, structure, and 
origins of NEAs and their relation to meteorites. 

Mitigation of Hazardous Asteroids 

At present there is no general agreement on the 
most effective strategy to adopt in the case of a 
predicted impact. In the case of an object with a 
diameter below 100 m, the best course of action 
may be to simply evacuate the region around the 
predicted impact point (see Table 4), assuming 
there would be sufficient advance warning (only a 
small fraction of the asteroids in this size cate¬ 
gory have been discovered to date). For objects 
larger than 100 m, a number of mitigation strate¬ 
gies may be considered, depending on 
circumstances. 

The NASA report to Congress (2007) on the 
surveying and deflection of near-Earth objects 
concluded that nuclear devices offer the most 
effective means of applying a deflecting force to 
an asteroid. While they may offer the only feasi¬ 
ble solution in desperate circumstances, e.g., in 
the case of very little advanced warning, it is 
widely felt that the obvious political problems 
associated with launching nuclear devices and 
testing them in space seriously compromise the 
practicability of this technique. The NASA report 
concluded that the most effective nonnuclear 
option is the kinetic impactor, which involves 
applying an impulsive force to the asteroid by 
means of a large mass in the form of a spacecraft 
accurately guided to the target at a high relative 
velocity. This technique was the subject of stud¬ 
ies commissioned by ESA in 2006 of a dual¬ 
spacecraft mission called Don Quijote (ESA 
NEO Space mission Preparation 2006). The 
change of momentum of the target asteroid 
depends on the porosity and the amount of ejecta 



Asteroid, Fig. 4 Artist’s impression of a kinetic- 
impactor spacecraft deployed to modify the orbit of a 
near-Earth asteroid. The second spacecraft at the bottom 
of the picture is orbiting the asteroid or “hovering” near it 
to observe the effects of the impact and monitor the altered 
trajectory of the asteroid. The scenario depicted derives 
from the Don Quijote mission, studies of which were 
commissioned by ESA in 2006. The European-led 
NEOShield project is currently carrying out detailed 
investigations of this and other promising deflection tech¬ 
niques (Credit: ESA-AOES Medialab) 

produced in the impact (Fig. 4), predictions of 
which would require some prior knowledge of the 
asteroid’s physical properties. To facilitate effec¬ 
tive mission planning, the kinetic-impactor 
approach would require an initial reconnaissance 
mission to gather relevant physical data. 

Alternative approaches include the “gravity 
tractor” and “space tug.” The gravity tractor 
relies on the force of gravity between the target 
asteroid and a spacecraft hovering under power in 
close proximity to gradually modify the aster¬ 
oid’s orbit. A significant advantage of the gravity 
tractor is that no contact with the target is 
required. The principle of the space tug is similar, 
but in this case, the spacecraft is physically 
attached to the asteroid’s surface and prior 
knowledge of surface characteristics would be 
necessary for effective mission planning. 




Asteroid 


187 


0.15 


^ 0.10 

C/D 

C 

CD 

■o 0.05 
x 


0.00 



Excess emission from HD69830 


0.20 


Crystal I i 
olivine 
.Amorphous 
^olivine \ 


Crystalline 
olivine (forsterite) 


Crystalline 

olivine 


Crystalline 

ivine 


Crystalline 

proxene Crystalline' 


10 15 20 25 30 35 

Wavelength (pm) 


Scaled emission from Hale-Bopp 



Asteroid, Fig. 5 Comparison of features in the spectra of 
the excess thermal emission from the star HD 69830 and 
the comet Hale Bopp. The similarity of the spectra 
strongly suggests that the dust in the debris disk around 
HD 69830 has a very similar composition to dust in the 
Solar System. Despite the similarities to the spectrum of 

The gravity tractor and space tug are “slow-push” 
approaches that require sustained, reliable pro¬ 
pulsion and sophisticated autonomous control 
systems to achieve the required amount of deflec¬ 
tion, but may be promising techniques in cases in 
which there is sufficient advance warning (e.g., 
decades), the target is relatively small, and/or a 
very slight, precise deflection is required to pre¬ 
vent an impact on the Earth. 

A unique research program funded by the 
European Commission and involving 13 partner 
organizations in 6 countries, including Russia 


Hale Bopp, detailed analysis of the spectral signature of 
the dust around HD69830 indicates that it probably orig¬ 
inates from the breakup of asteroids (Lisse et al. 2007). 
The figure is taken from Beichman et al. (2005) and is 
reproduced by permission of the AAS 

and the USA, was established in 2012 to investi¬ 
gate deflection techniques in detail. The project, 
called NEOShield (www.neoshield.net), aims to 
provide solutions to scientific and technical 
issues that will enable the feasibility of promising 
mitigation options to be demonstrated in the 
future via test missions. Research into the 
mitigation-relevant physical properties of 
NEOs, including laboratory experiments and 
associated modeling, is aimed at supporting tech¬ 
nological development work leading to the 
detailed design of demonstration missions. 





188 


Asteroid 


Asteroids in Extrasolar Planetary Systems 

The presence of asteroids and comets outside our 
Solar System cannot be confirmed by direct 
observation, but there is considerable evidence 
that such objects play a role in the formation 
and development of extrasolar planetary systems. 
Infrared observations have shown that many stars 
exhibit thermal emission in excess of that 
predicted for their stellar types. The excess ther¬ 
mal emission can be modeled in terms of sur¬ 
rounding dust disks heated by the star that may 
be the debris of asteroids and comets destroyed 
by collisions or close approaches to planets or the 
central star. 

Data obtained with the Spitzer Space Tele¬ 
scope in the mid-infrared spectral region suggest 
that some extrasolar systems have multiple debris 
disks: warm disks analogous to the main asteroid 
belt and cooler outer disks possibly containing 
bodies analogous to the distant TNOs in the Solar 
System (Morales et al. 2009). Attempts have been 
made to match the infrared spectra of extrasolar 
debris disks with spectra obtained from observa¬ 
tions of comets and asteroids. In the case of the 
star HD 69830, which exhibits unusually intense 
emission from dust (Fig. 5), the best match 
appears to be materials found in P- or D-type 
asteroids (Lisse et al. 2007), which are very 
numerous in the outer main belt. The production 
of dust would follow the collisional break up of 
asteroids, as invoked to explain the existence of 
asteroid families and zodiacal dust in the Solar 
System (see section on Asteroidal Dynamical 
Groupings above). 

The discovery of extrasolar planets and debris 
disks strongly suggests that planet formation is a 
common phenomenon in the Galaxy. Knowledge 
gained from investigations into the processes of 
planet formation and development in our Solar 
System will continue to stimulate and guide 
future research into similar processes taking 
place elsewhere in the Galaxy. 

See Also 

► Carbonaceous Chondrite 

► Centaurs (Asteroids) 


► Chondrite 

► Dwarf Planet 

► Near-Earth Objects 

► Planet 

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vey and deflection. Analysis of alternatives, http:// 
www.nasa.gov/pdf/17133 lmain_NEO_report_march07. 
pdf. Accessed 26 Jan 2010 

Ostro S, Hudson RS, Benner LAM, Giorgini JD, Magri C, 
Margot J-L, Nolan MC (2002) Asteroid radar astron¬ 
omy. In: Bottke WF, Cellino A, Paolicchi P, Binzel RP 
(eds) Asteroids III. Univ Arizona Press, Tucson, 
pp 151-168 

Pope KO, Ocampo AC, Duller CE (1991) Mexican site for 
the K/T impact crater? Nature 351:105 

Rivkin AS, Emery JP (2010) Detection of ice and 
organics on an asteroidal surface. Nature 
464:1322-1323 

Rivkin AS, Howell ES, Lebofsky LA, Clark BE, Britt DT 
(2000) The nature of M-class asteroids from 3-pm 
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size distribution, and impact hazard for near-Earth 
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Tedesco EF, Noah PV, Noah M, Price SD (2002) The 
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2010 


Asteroid (433) Eros 

► Eros Asteroid 


Asteroid 25143 

► Itokawa Asteroid 


Asteroid Belt, Main 

Alan W. Harris 

DLR, Institute of Planetary Research, Berlin, 
Germany 

Synonym 

Main asteroid belt 


Definition 

The ► asteroid belt is a region of the ► Solar 
System between the orbits of ► Mars and ► Jupi¬ 
ter that contains the orbits of most of the known 
asteroids (over 600,000 to date). The reason for 
the existence of the asteroid belt is thought to be 
gravitational perturbations of the orbits of 
► planetesimals and planetary embryos 
(planetary building blocks) in the region by the 
massive ► planet Jupiter that have prevented 
these objects from combining to form a planet. 
Collisions between objects in the asteroid belt 






190 


Asteroseismology 


cause them to be ground down into an ever- 
increasing number of smaller bodies. 


See Also 

► Asteroid 

► Jupiter 

► Mars 

► Planet 

► Planetesimals 

► Solar System, Inner 


Asteroseismology 

Patrick Eggenberger 

Geneva Observatory, University of Geneva, 
Geneva, Switzerland 

Synonyms 

Stellar seismology 

Definition 

Asteroseismology is the study of stellar oscilla¬ 
tions aiming at determining the internal structure 
and global properties of stars. The oscillation 
patterns observed on the stellar surface result 
from waves that propagate into the interior of 
the star. The observation of these oscillations, 
done either by monitoring the variation of the 
star’s brightness or of its radial velocity, offers 
therefore a unique means to probe the otherwise 
unobservable internal layers of stars and to help 
us in our understanding of the complex physical 
processes at work in stellar interiors. 


See Also 


Asthenosphere 

Daniele L. Pinti 

GEOTOP Research Center for Geochemistry and 
Geodynamics, Universite du Quebec a Montreal, 
Montreal, QC, Canada 


Definition 

The asthenosphere is the viscous mechanically 
weak-ductile region of the upper ► mantle of 
the Earth. It lies below the ► lithosphere, at 
depths between 100 and 200 km, and it is 
involved in the plate tectonic movements and 
isostatic adjustments. The heat is transmitted by 
convection and the thickness and viscosity of 
this layer controls the stress applied at the base 
of the lithosphere. This, in turn, influences 
the global tectonic style of the Earth and of 
any other terrestrial planet. The viscosity and 
the convective regime of the asthenosphere 
has also a control on the degassing history of a 
terrestrial planet and the evolution of its 
atmosphere. 


See Also 

► Lithosphere, Planetary 

► Magma 

► Mantle 

► Plate Tectonics 


Astrobiology 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 


Synonyms 


► Stellar Pulsation 


Bioastronomy; Exobiology 






Astrometric Orbit 


191 


Definition 

This encyclopedia defines astrobiology as the 
study of the origin, evolution, and distribution 
of life in the universe (see Preface). Such 
studies, or some part of them, have also been 
referred to as exobiology or bioastronomy 
(the term employed by the International 
Astronomical Union), and at the present time, 
these terms can be considered synonymous. 
Although it has been stated that astrobiology 
is a science without a subject (since life 
outside the Earth remains undiscovered), in 
fact there is a vast and growing volume of 
research in fields included in the present 
encyclopedia. 

Overview 

Thus, although the physical and chemical pro¬ 
cesses that led to the origin of life on Earth are 
still far from understood, they clearly involve, 
inter alia, the nucleosynthesis of chemical ele¬ 
ments including carbon that are essential for life; 
the formation and evolution of the Sun and 
► planets, including the delivery of water and 
organic material to the ► Earth; prebiotic chemi¬ 
cal processes; and the nature and evolution of the 
early Earth’s atmosphere, crust, and interior. Fur¬ 
thermore, the study of the evolution of life and 
ultimately the development of ► intelligence on 
our planet requires research, e.g., in biochemistry, 
biophysics, microbiology (including life in envi¬ 
ronments that seem extreme by human standards), 
and ► genetics. 

There is also the question of whether life exists 
elsewhere in the solar system or at other locations 
in the universe. These issues are addressed in the 
Encyclopedia of Astrobiology through 
entries characterizing various bodies in the solar 
system (particularly the existence of water, the 
universal solvent of terrestrial life), current knowl¬ 
edge concerning planets around other stars 
(extrasolar or exoplanets), how life might be iden¬ 
tified beyond the Earth (biosignatures or ► bio¬ 
markers), and space missions to investigate these 
topics. 


Moreover, many questions relevant to astrobi¬ 
ology have in fact been asked by humanity 
throughout recorded history and certainly before 
that. In consequence, the Encyclopedia includes a 
section on History of Science, which includes 
theories on the origin and evolution of life and 
on the possible multiplicity of habitable worlds 
from classical Greek and Roman times, from the 
Islamic world, from ancient Asia, from 
pre-Columbian America, and from the modern 
world. 

Lastly, what is the future of life, at least on 
Earth? Entries concerning ► artificial life 
are included which address some of these 
questions. 


See Also 

► Enceladus 

► Europa 

► Evolution, Biological 

► Mars 

► Planetary Theories and Cosmology, Islamic 
Theories 

► Prebiotic Chemistry 

► Solar System, Inner 

► Solar System, Outer 

► Titan 

► Water in the Solar System 

► Water in the Universe 


Astrometric Orbit 

David W. Latham 1 and Nader Haghighipour 2 
1 Harvard-Smithsonian Center for Astrophysics, 
Cambridge, MA, USA 

institute for Astronomy, University of Hawaii- 
Manoa, Honolulu, Hawaii, HI, USA 

Definition 

When two bodies are in ► Keplerian orbits 
around a common center of mass, the apparent 




192 


Astrometric Planets 


motion projected onto the plane of the sky defines 
an astrometric orbit. In some cases, such as the 
famous example of Sirius A and its white dwarf 
companion Sirius B, both objects can be spatially 
resolved, and their absolute positions and 
motions can be determined. This allows the 
ratio of the two masses to be determined, which 
can be combined with the total mass, if the dis¬ 
tance is known, to derive individual masses. 
More often, only a single photocenter can be 
resolved, and only motions relative to nearby 
stars can be determined. In this case an orbital 
solution requires additional information about the 
relative brightness of the components. In the case 
of a planetary companion, the contribution of the 
planet to the total light can almost always be 
neglected, and the mass of the planet can be 
estimated from the observed wobble of the parent 
star if the mass of the star and its distance can be 
estimated. In common with a spectroscopic orbit 
determined from radial velocities along the line 
of sight, an astrometric orbit also yields the 

► period, ► eccentricity, and time of 

► periastron passage. Astrometry has the 
advantage over radial velocity of measuring 
motions in two dimensions on the plane of the 
sky instead of just one motion along the line of 
sight, and this allows the orbital inclination to be 
determined. Thus, astrometric orbits can elimi¬ 
nate the ambiguity of the unknown orbital incli¬ 
nation and can yield actual masses under certain 
circumstances, for example, when applied to 
minimum masses determined by spectroscopic 
orbits. 


See Also 

► Astrometric Planets 

► Eccentricity 

► Exoplanets, Discovery 

► Inclination (Astronomy) 

► Keplerian Orbits 

► Periastron 

► Period 


Astrometric Planets 

G. Fritz Benedict 1 and Nader Haghighipour 2 
McDonald Observatory, The University of 
Texas, Austin, TX, USA 
institute for Astronomy, University of Hawaii- 
Manoa, Honolulu, Hawaii, HI, USA 

Keywords 

Astrometry; Coplanar orbits; Orbital inclination; 
Perturbation; Planetary mass; HST FGS 

Definition 

Astrometry is a discipline of astronomy that is 
concerned with the measurements of stellar posi¬ 
tions. As applied to exoplanets, a series of astro- 
metric measurements over time is analyzed to 
obtain an estimate of the size of the reflex motion 
of the host star caused by the gravitational pull of 
its unseen planet. The planet and its host star orbit 
a common center of mass. Given an estimate of 
the mass of the host star, normally from the mass- 
luminosity relation, one can determine the mass 
of the planet. Astrometry also provides the orbital 
inclination of exoplanets. The knowledge of the 
orbital inclination of a planet will enable us to 
determine the true value of its mass (see “► Incli¬ 
nation (Astronomy)”) and can also be used to 
constrain models of planet formation. 

History 

The history of astrometric planets is littered with 
past failures. A notable example was the reported 
discovery of a planetary system associated with 
Barnard’s Star by van de Kamp (1969) which was 
subsequently disproven through reanalysis of the 
data by Ianna (1995) and re-observation of the 
same system by Benedict et al. (1999). Astrome¬ 
try has yet to discover an independently verified 




Astrometric Planets 


193 


exoplanet; although as a technique to further 
characterize the companions to stars discovered 
by precision Doppler measurements (radial 
velocities), it has enjoyed some recent successes. 
Future successes (both discovery and characteri¬ 
zation) are expected from the astrometric satellite 
Gaia. 

Overview 

We describe some of the astrometric planet 
results obtained using one of the Fine Guidance 
Sensors (FGS) aboard the Hubble Space Tele¬ 
scope (. HST ). The techniques employed are illus¬ 
trative of both past astrometric approaches and 
future astrometric investigations. Exoplanetary 
astrometry relates the time-varying position of a 
target to positions of stars defining a reference 
frame. To obtain the orbital elements of the per¬ 
turbation due to the companion, one must first 
characterize motions extrinsic to the system: par¬ 
allax and proper motion (defined below). Anyone 
attempting to measure a perturbation will find 
(to either their delight or horror) that the Earth 
orbits the ► barycenter of the Solar System. The 
corresponding apparent motion of the host star 
evidences itself as an ellipse, which for nearby 
stars can exceed 100 milli-arcsec (mas) in size. 
Added to that parallactic motion is the apparent 
motion of the host star across the line of sight due 
to the transverse component of the star’s space 
velocity relative to our Sun. This proper motion 
often exceeds 50 mas/year. We use the determi¬ 
nation of the mass of the planetary companion 
HD 38529 c (Benedict et al. 2010) as an example 
of the methodology. The star HD 38529 (= HIP 
27253 = HR 1988 = PLX 1320) hosts two 
known companions b and c, discovered by high- 
precision ► radial velocity (RV) monitoring (see 
Wright et al. 2009). Previously published mini¬ 
mum masses of HD 38529b and c were 0.85 and 
13.1 Jupiter masses, respectively. The latter lies 
just above the official definition of the transition 
between planets and brown dwarfs. A predicted 
minimum perturbation of the semimajor 


axis = 0.8 mas for the outermost companion, 
HD 38529 c, motivated us to obtain astrometric 
observations with mas precision using HST FGS, 
to determine the orbital inclination and thus the 
true mass of this planet. These astrometric data 
span 3.25 years of the complete 5.85-year period. 

Basic Methodology 

Our approach depends on the discovery and 
orbital characterization results from radial veloc¬ 
ity studies. Specifically, the period, eccentricity, 
time of periastron passage, and position angle of 
periastron (P, e,T,co) of the perturbing body are 
initially known. As can be seen from the 
Table below, most of our target systems have 
periods far in excess of 2 years. The data from 
the astrometry and radial velocity are combined 
through the constraint (Pourbaix and Jorissen 
2000), a sin i/n abs =P K( 1 - e 2 ) 1 ' 2 / 
(2n x 4.7405), where quantities derived only 
from astrometry (parallax, 7i abs ; apparent 
semimajor axis of the elliptical perturbation, a; 
and inclination, /) appear on the left, and quanti¬ 
ties derivable from both the period P and eccen¬ 
tricity e , or from radial velocity only (the RV 
amplitude of the primary K ), appear on the 
right. In most cases such as the one here, given 
the fractional orbital coverage of the HD 38529 c 
perturbation afforded by the astrometry, all the 
quantities on the right-hand side are dominated 
by the radial velocities (Table 1). 

Before analysis, all astrometric measurements 
from the FGS are corrected for optical field angle 
distortion. Like the part of an iceberg below the 
water, this correction, while typically “out of 
sight” (McArthur et al. 2003), is an essential 
part of our process. Actual FGS distortions with 
amplitudes in excess of 1 arcsec are reduced to 
1 mas or less over the FGS field of regard. 

We are able to relate the position of the bright 
host star to the far fainter reference frame stars 
through the use of a neutral density filter. The 
astrometric reference frame for HD 38529 con¬ 
sists of four stars. Any prior knowledge 



194 


Astrometric Planets 


Astrometric Planets, Table 1 HST FGS astrometric results. Fe/H measures the abundance of iron relative to hydrogen 
on a logarithmic scale normalized to the Sun. Sp.T. is the spectral type of the host star 


Companion 

M*(M 0 ) 

[Fe/H] 

Sp.T. 

d(pc) 

ecc 

M(M Jup ) 

a (mas) 

inc(°) 

p(d) 

GJ 876 b 

0.32 

-0.12 2 

M4 V 

4.7 

0.1 

1.9 db 0.5 

0.25 

84 db 6 

61 

55 Cnc d 

1.21 

+0.32 

G8 V 

12.5 

0.33 

4.9 db 1.1 

1.9 

53 db 7 

4,517 

s Eri b 

0.83 

-0.03 

K2 V 

3.2 

0.7 

1.6 db 0.2 

1.9 

30 ± 4 

2,502 

HD 33636 B 

1.02 

-0.13 

GOV 

i28.1 

0.48 

142 ± 11 

14.2 

4.0 d= 0.1 

2,117 

HD 136118 b 

1.24 

-0.01 

F9 V 

52.3 

0.35 

42 db 15 

1.5 

163.1 db 3 

1,191 

HD 38529 c 

1.48 

+0.27 

G4IV 

40.0 

0.36 

17.6 ± 1.4 

1.1 

48.3 d= 3.7 

2,136 

u And c 

1.31 

+0.15 

F8 V 

13.5 

0.25 

14 db 4 

0.62 

8 ± 1 

240.94 

u And d 

1.31 

+0.15 

F8 V 

13.5 

0.32 

10 db 2 

1.4 

24 db 1 

1281.51 

HD 128311 C 

0.84 

0.02 

K0 V 

16.5 

0.16 

3.8 db 0.7 

0.46 

56 ± 14 

921.5d 


concerning these four stars eventually enters our 
modeling as observations with errors, which 
helps improve the values of the parallax and 
proper motion for the prime target, HD 38529. 
Distances to the reference stars are estimated 
from (BVIJHK) photometry and stellar classifi¬ 
cation spectroscopy. Of particular value are inde¬ 
pendently measured proper motions from the 
UCAC3 catalog (Zacharias et al. 2010). All 
these periodic and nonperiodic motions must be 
removed as accurately and precisely as possible 
to obtain the orbital inclination, /, and perturba¬ 
tion size, a, caused by HD 38529 c. 

Key Research Findings 

Results from HST astrometry are presented in the 
Table above. HD 38529 c is clearly more massive 
than 13 Jupiter masses, the threshold above 
which deuterium fuses to helium. This threshold 
has been adopted by the International Astronom¬ 
ical Union as the official transition between 
planets and brown dwarfs. 

Other results: McArthur et al. (2010) deter¬ 
mined the inclinations of components c and d in 
the o Andromeda system, indicating 
non-coplanarity. Whether this architecture is a 
result of the migration of component b (with 
Msini = 0.69 Mjup) now in a P = 4.6-day 
orbit, or the past passage of the M star compan¬ 
ion, u Andromeda B, is as yet unknown (Bames 
et al. 2011). A recent attempt to determine the 
degree of coplanarity for HD 128311 was 


unsuccessful, but did yield a planetary mass for 
component c (McArthur et al. 2014). 

Applications 

These techniques are presently being applied to 
determine masses for 14 Her b, HD 47536 b, and 
HD 168443 c. There now exist sufficient FGS 
astrometric measurements to attempt to deter¬ 
mine orbital inclinations for b and c, HD 
202206 b and c, p Ara b and c, and y Cep A and 
b. The latter two host stars may be too bright for 
Gaia. If the degree of orbital coplanarity can be 
established for those systems, astronomers will 
have valuable data to probe the architectural 
uniqueness (or not) of our own Solar System, 
complementing analogous results from the recent 
Kepler transit discoveries and the study of 
► radial velocity planets. 

Future Directions 

Major progress will result from two improve¬ 
ments to past practice as exemplified by HST 
FGS astrometry. First, future missions will 
employ global (as opposed to local) reference 
frames, removing the correction to absolute par¬ 
allax required when using a local reference 
frame. Second, the astrometric precision will 
improve by two orders of magnitude, from milli¬ 
second of arc to micro-arcseconds (pas). Future 
success is expected from Gaia , an astrometric 























Astrometry 


195 


satellite launched on December 2013 by the 
► European Space Agency (ESA). The expected 
10 pas mission accuracy (Lindegren et al. 2008) 
should permit the determination of thousands of 
exoplanet masses and the degree of orbital copla¬ 
narity for nearly 100 systems (Casertano 
et al. 2008). These results should be in hand by 
2020. However, the unambiguous astrometric 
identification of an Earth-mass exoplanet, 
orbiting a nearby Sunlike star at a star-planet 
separation allowing surface liquid water, remains 
a difficult goal, one requiring 1 pas per observa¬ 
tion precision. 


See Also 

► Aeronautics and Space Agency of FFG 

► Barycenter 

► Doppler Shift 

► European Space Agency 

► Exoplanets, Discovery 

► Gaia Mission 

► Radial-Velocity Planets 

► Spectral Type 

References and Further Reading 

Barnes R et al (2011) Origin and dynamics of the mutually 
inclined orbits of u andromedae c and d. Astrophys 
J 726:71 

Benedict GF et al (1999) Interferometric astrometry of 
proxima centauri and bamard’s star using HUBBLE 
SPACE TELESCOPE fine guidance sensor 3: detec¬ 
tion limits for substellar companions. Astron 
J 118:1086 

Benedict GF et al (2010) The mass of HD 38529c from 
hubble space telescope astrometry and high-precision 
radial velocities. Astron J 139:1844 

Casertano S et al (2008) Double-blind test program for 
astrometric planet detection with Gaia. Astron 
Astrophys 482:699 

Heintz WD (1978) Double stars. Reidel, Dordrecht 

Ianna PA (1995) Barnard’s star: twenty years of McCor¬ 
mick observations. Astrophys Space Sci 223:161 

Lindegren L et al (2008) The Gaia mission: science, orga¬ 
nization and present status. In: Jin WJ, Platais I, 
Perryman MAC (eds) A giant step: from milli- to 
micro-arcsecond astrometry. Proceedings of the IAU 
Symposim 248. Cambridge University Press, Cam¬ 
bridge, pp 217-223 


McArthur B et al (2003) In: Arribas S, Koekemoer A, 
Whitmore B (eds) The 2002 HST calibration work¬ 
shop. STScI, Baltimore, p 373 
McArthur B et al (2010) New observational constraints on 
the v andromedae system with data from the hubble 
space telescope and hobby-eberly telescope. 
Astrophys J 717:776 

McArthur B et al (2014) Astrometry, radial velocity, and 
photometry: The HD 128311 System Remixed with 
Data from HST, HET, and APT, Astrophys J 795:41 
Pourbaix D, Jorissen A (2000) Re-processing the 
hipparcos transit data and intermediate astrometric 
data of spectroscopic binaries. I. Ba, CH and Tc-poor 
S stars. A&AS 145:161 

Standish EM Jr (1990) The observational basis for JPL’s 
DE 200, the planetary ephemerides of the astronomical 
almanac. Astron Astrophys 233:252 
van de Kamp P (1969) Alternate dynamical analysis of 
Barnard’s star. Astron J 74:757 
Wright JT et al (2009) Ten new and updated multiplanet 
systems and a survey of exoplanetary systems. 
Astrophys J 693:1084 

Zacharias N et al (2010) The third US naval observatory 
CCD astrograph catalog (UCAC3). Astron J 139:2184 


Astrometry 

Francis Mignard 

CNRS, Observatoire de la Cote d’Azur, 
University of Nice Sophia-Antipolis, Nice, 
France 


Keywords 

Coordinate systems; Fundamental astronomy; 
Gaia; Hipparcos; Reference frame 

Synonyms 

Positional astronomy 


Definition 

Astrometry is that part of astronomy dealing with 
the determination of the position, distance, and 
motion of celestial bodies and by extension their 
size and shape. This is by far the oldest branch of 




196 


Astrometry 


astronomy, and until the mid-1800s the word did 
not even exist. It was only coined at that time to 
make the distinction from the new field of 
astrophysics. 

Overview 

Taken as a broad subject, astrometry covers the 
definition and realization of the astronomical 
► coordinate systems and the construction and 
maintenance of positional star catalogues, but 
also the techniques for the computation of astro¬ 
nomical events, like eclipses, passages of inner 
planets across the Sun’s disk, orbits of ► binary 
stars, stellar ► occultation by the Moon, or the 
minor planets. Classical astrometry is undergoing 
a true revolution with the access to radio interfer¬ 
ometry and above all the possibility to carry out 
accurate measurements from space, thanks to the 
Hipparcos mission (1989-1996) and in the near 
future the Gaia mission. The main benefit of 
doing astrometry in space is the measurement of 
absolute ► parallaxes of stars, that is to say their 
distances, just from the geometric method with¬ 
out any assumptions on the physics of the sources 
or on the absorption of the light during its journey 
to the telescope. 

Given the fundamental nature of its investiga¬ 
tions, it is fair to state that astrometric data, lead¬ 
ing to the realization of an accessible ► reference 
frame or giving the distances and the masses of 
the stars, provide the foundation of stellar physics 
and of the cosmic distance ladder. Stellar dis¬ 
tances are the key to determining stellar luminos¬ 
ities and then for calibrating further methods to 
determine distances up to the most remote 
galaxies. 

Based on the tools employed and on the objec¬ 
tives, astrometry can be further divided up into 
three broad categories: 

• Small-angle astrometry, measuring the 
position or the motion of stars in a very small 
field (less than 1°) with respect to local refer¬ 
ences. This was typical of astronomical pho¬ 
tography until the advent of charged coupled 
device (► CCDs) and is still used for solar 


system astrometry or to determine the relative 
motion within a binary system. Its accuracy 
can reach 1 mas (0.001 arc sec) in relative 
positions. 

• Wide-angle astrometry was the basis for the 
construction of the fundamental catalogues 
and their extension to fainter magnitudes. 
The classical instruments were the meridian 
circles and the astrolabes. Stars over the whole 
celestial sphere were tied together, thanks to 
the rotation of the Earth or by overlapping 
frames in photographic or ► CCD astrometry. 
The accuracy, including zonal errors, is of the 
order of 20 mas for the bright stars (visual 

► magnitude V <8) and 50-70 mas at around 
V = 15. 

• Space astrometry is the only way to do abso¬ 
lute measurements over the whole sky with a 
single instrument able to connect widely sep¬ 
arated directions (>60°) and perform repeated 
observations over several years. This method 
leads to an absolute catalogue of positions 
and ► proper motions, independent of any 
preexisting reference frame. It is aligned to 
the radio frame constructed on extragalactic 
sources by using sources observed by 
both techniques. Accuracy was 1 mas with 

► Hipparcos (^120,000 sources) and 
should be close to 0.025 mas at V = 15 with 

► Gaia and several hundred million 
sources. Radio ► interferometry performs 
also absolute astrometry of quasars on the 
whole celestial sphere. The associated 
catalogue is currently the basis of the astro¬ 
nomical reference frame (ICRF: International 
Celestial Reference Frame) with an accuracy 
of about 0.1 mas over a few hundreds of 
sources. 

See Also 

► Coordinate Systems 

► Gaia Mission 

► Hipparcos 

► Magnitude 

► Parallax 

► Proper Motion 



Asymmetric Reaction, Absolute 


197 


References and Further Reading 

Green RM (1985) Spherical astronomy. Cambridge Uni¬ 
versity Press, Cambridge 

Kovalevsky J (2002) Modem astrometry, 2nd edn, Astron¬ 
omy and astrophysics library. Springer, Berlin 

Kovalevsky J, Seidelman PK (2004) Fundamentals of 
astrometry. Cambridge University Press, Cambridge 

Murray CA (1983) Vectorial astrometry. Adam Hilger, 
Bristol 

Walter H, So vers OJ (2000) Astrometry of fundamental 
catalogues, Astronomy and astrophysics library. 
Springer, Berlin 


Astronomical Unit 

► AU 


Asymmetric Reaction, Absolute 

Kazumichi Nakagawa 

Graduate School of Human Development and 
Environment, Kobe University, Nada, 

Kobe, Japan 

Keywords 

Asymmetric decomposition; Asymmetric synthe¬ 
sis; Circularly polarized light; Origin of 
homochirality; Induction of chirality 

Definition 

An absolute asymmetric chemical reaction is one 
induced by asymmetric physical conditions such as 
circularly polarized light (CPL) instead of by 
chemical reagents or catalysts. They can be divided 
into two categories: one is asymmetric synthesis 
and the other is asymmetric decomposition. 

Overview 

Asymmetric synthesis is driven by the introduc¬ 
tion of chirality into an achiral system, a process 


known as asymmetric induction. One example of 
absolute asymmetric synthesis is the introduction 
of optical activity into helicenes (twisted 
polyaromatic hydrocarbons with six rings) stud¬ 
ied by Kagan et al. (1974) in 1971, in which the 
optical yield was lower than 1 %. Enantiomeric 
enrichment of racemic compound such as 
amino acids by irradiation with circularly polar¬ 
ized light (CPL) is one of the well-known exam¬ 
ples of asymmetric decomposition. The first 
experimental evidence of CPL-induced asym¬ 
metric decomposition was reported by Kuhn 
and Knopf (1930). 

Various light sources such as lasers and syn¬ 
chrotron radiation are now available as powerful 
tools to study asymmetric reactions. Several stud¬ 
ies have examined the role of asymmetric reac¬ 
tions on the origin of ► homochirality in 
biological molecules: Flores et al. (1977), 
Nishino et al. (2001), and Meierhenrich 
et al. (2005). 

Polarized radiation from pulsars and interstel¬ 
lar masers has been known for several decades. 
Natural sources of circularly polarized light were 
found in space and reported by Bailey 
et al. (1998). Mie scattering and synchrotron 
radiation are thought to be the natural sources of 
circularly polarized light. 

Other mechanisms of absolute asymmetric 
reactions have been discussed by Bonner 
et al. (1974), Bonner (2000), and Goldanskii 
and Kuzmin (1989). 


See Also 

► Chirality 

► Homochirality 

► Polarized Electron 

► Polarized Light and Homochirality 

References and Further Reading 

Bailey J, Chrysostomou A, Hough JH, Gledhill TM, 
MacCall A, Clark S, Menard F, Tamura M (1998) 
Circular polarization in star-formation regions: impli¬ 
cations for biomolecular homochirality. Science 
281:672-674 





198 


Asymptotic Giant Branch Star 


Bonner WA (2000) Parity violation and the evolution of 
biomolecular homochirality. Chirality 12:114-126 
Bonner WA, Kavasmaneck PR, Martin FS (1974) Asym¬ 
metric adsorption of alanine by quartz. Science 
186:143-144 

Flores JJ, Bonner WA, Massey GA (1977) Asymmetric 
photolysis of (RS)-leucine with circularly polarized 
ultraviolet light. J Am Chem Soc 99:3622-3624 
Goldanskii VI, Kuzmin VV (1989) Spontaneous breaking 
of mirror symmetry in nature and the origin of life. Sov 
Phys Usp 32:1-29, Asp Fiz Nauk 157:3-50 
Kagan HB, Balavoine G, Moradpour A (1974) Can circu¬ 
larly polarized light be used to obtain chiral com¬ 
pounds of high optical purity? J Mol Evol 4:41^18 
Kuhn W, Knopf E (1930) Darstellung optisch aktiver 
Stoffe mit Hilfe von Licht. Z Phys Chem Abteil 
B 7:292-310 

Meierhenrich UJ, Nahon L, Alcaraz C, Bredehoft JH, 
Hoffmann SV, Barbier B, Brack A (2005) Asymmetric 
vacuum UV photolysis of the amino acid leucine in the 
solid state. Angew Chem Int Ed 44:5630-5634 
Nishino H, Nakamura A, Inoue Y (2001) Synchronous 
enantiomeric enrichment of both reactant and product 
by absolute asymmetric synthesis using circularly 
polarized light. Part 1. Theoretical and experimental 
verification of the asymmetric photoisomerization of 
methyl norbornadiene-2-carboxylate to methyl 
quadricyclane-l-carboxylate. J Chem Soc Perkin 
Trans 2:1693-1700 


Asymptotic Giant Branch Star 

Nikos Prantzos 

Institut d’Astrophysique de Paris, Paris, France 


Synonyms 

AGB 


Definition 

An asymptotic giant branch (AGB) star is a low- 
or intermediate-mass star (of mass M < 8 M©) at 
a late evolutionary phase in its life, during which 
it appears as a red giant in the ► Hertzsprung- 
Russell diagram. After the star has exhausted the 
supply of He for fusion in its core, it draws energy 
from He fusion in a shell around the inert carbon- 
oxygen core, in the early AGB (E-AGB) phase. 
Later, the star enters the thermally pulsing 
(TP-AGB) phase, with intermittent burning 


(fusion) of the hydrogen and He shells. In the 
He shell, neutrons are released through (a,n) 
reactions and are captured on preexisting nuclei 
of the Fe peak to produce heavier elements 
(s-process). The thermal pulses occur in time- 
scales of 10 4 -10 5 years. They mix material from 
the burning shells to the convective envelope (the 
3d dredge up), and they also induce heavy mass 
loss from the star (more than 50 % of its mass), 
creating a ► planetary nebula. 


See Also 

► Hertzsprung-Russell Diagram 

► Planetary Nebula 

► S-process 

► Stellar Evolution 


Atacama Desert 

Richard Leveille 

Natural Resource Sciences, McGill University, 
St. Anne de Bellevue, Quebec, Canada 

Definition 

The Atacama is a hyperarid desert located in 
northern Chile. It is considered to be one of the 
driest places on Earth with average annual rain¬ 
fall of less than 1 mm in some locations. It is a 
useful analogue to the arid surface of Mars and 
for analog studies of hydrology, mineralogy, and 
microbiology. Features that may be analogous to 
Mars also include caves, salt deposits, water- 
derived mudflows, and gully-type deposits. 
Field tests of prototype instruments and rovers 
have also been conducted there. 


See Also 

► Desiccation 

► Extreme Environment 





Atmosphere Escape 


199 


► Extremophiles 

► Mars Analogue Sites 

► Terrestrial Analog 


Atacama Large Millimeter Array 

► ALMA 


Atacama Large Millimeter/ 
Submillimeter Array 

► ALMA 


Atmosphere Escape 

Ray Pierrehumbert 

Department of the Geophysical Sciences, 
University of Chicago, Chicago, IL, USA 

Definition 

Atmospheric escape refers to the loss of a planet’s 
atmosphere to space. Broadly speaking, escape 
may be energy limited or diffusion limited. For 
the energy-limited case, permanently removing a 
molecule from a planet’s atmosphere can be com¬ 
pared to sending a rocket from Earth to space: one 
must impart enough velocity to the object, and in 
the right direction, to allow the object to over¬ 
come the potential energy at the bottom of the 
gravitational well and still have enough kinetic 
energy left over to allow the object to continue 
moving away. The study of atmospheric escape 
in this case thus amounts to the study of the 
various ways in which the necessary energy can 
be imparted to molecules to reach the escape 
velocity, which is the minimum velocity an 
object needs in order to escape to infinity, pro¬ 
vided no drag forces intervene (Pierrehumbert 
2011 ). 


Overview 

The thermal escape velocity is obtained by equat¬ 
ing initial kinetic energy to the gravitational 
potential energy: 

1 /2 mv 2 = GM F m/r, v = y/lGM^fr = ^fl^r 

where m is the mass of the object (molecule in the 
present case), v its speed, r its initial distance 
from the center of the planet, M P the mass of the 
planet, G the universal gravitational constant, and 
g the acceleration of gravity at distance r from the 
planet’s center. In order to allow a molecule to 
escape, enough energy must be delivered to the 
molecule to accelerate it to the escape velocity. 
Since the kinetic energy of a molecule with mass 
m is Vi mv 2 , light molecules like H 2 will move 
faster and hence escape more easily than heavier 
molecules like N 2 , given an equal delivery of 
energy. Dissociation of a molecule like C0 2 or 
H 2 into lighter individual components also aids 
escape. Using the formula for escape velocity, we 
can define the escape energy of a molecule with 
mass m as mgr. For escape of N 2 from altitudes 
not too far from the Earth’s surface, this energy is 
2.9 x 10 -18 J; for H 2 the escape energy is only 
0.2 x 1CT 18 J. 

Atmospheric escape may be categorized as 
follows: 

• Thermal (Jeans) escape - molecular speeds 
generally obey the Maxwell-Boltzmann distri¬ 
bution. Fast-moving species in the high- 
energy tail of the distribution may attain 
enough energy to escape the atmosphere. The 
general thermal energy of the atmospheric gas 
ultimately comes from, e.g., absorbed stellar 
radiation or from heat leaking out of the inte¬ 
rior of the planet. 

• Nonthermal escape mechanisms. Here, a “col- 
lisional process” energizes gas species above 
the escape barrier. For example, “ion 
exchange” involves charged species, e.g., 
hydrogen cations (H + ), which are accelerated 
in the planet’s magnetic field to high energies. 
If the H + acquires an electron from a neigh¬ 
boring neutral species, it is converted into a 







200 


Atmosphere, Model ID 


neutral, high-energy atom (H*) which can 
escape the atmosphere. Nonthermal escape 
can also involve interaction of, e.g., atmo¬ 
spheric species with the stellar wind (e.g., 
“sputtering” refers to the collisional ejection 
of a neutral species from the atmosphere by 
incoming high-energy species). “Impact ero¬ 
sion” refers to atmospheric escape driven by 
high-energy impacting material. 

See also 

► Absorption Cross Section 

► Atmosphere, Structure 

► Scale Height 

References and Further Reading 

Pierrehumbert RT (2011) Principles of planetary climate. 
Cambridge University Press, Cambridge 


Atmosphere, Model 1D 

Lisa Kaltenegger 

Cornell University, Ithaca, NY, USA 

Synonyms 

Model atmospheres 

Definition 

The simplest atmosphere is gravitationally bound 
with no vertical motions, i.e., in hydrostatic equi¬ 
librium and spherically symmetric. For terrestrial 
planets, solar radiation and the radiative proper¬ 
ties of the atmospheric components provide a 
first-order description of the vertical thermal 
structure. An atmosphere controlled by stellar 
light can hardly be spherically symmetric; never¬ 
theless, it is very useful to think of a mean plan¬ 
etary atmosphere, i.e., averaged over, e.g., 
latitude and day-night. The properties of such a 


mean atmosphere depend only on the altitude 
above the planetary surface, so that the depen¬ 
dence is one-dimensional (a ID atmosphere). The 
vertical structure of the atmosphere is determined 
by the pressure, temperature, density, and chem¬ 
ical composition with height above the surface. 
The average atmospheric profile of the Earth 
reproduces the flux detected if the Earth were 
seen from far away as an exoplanet, thus provid¬ 
ing a disk-integrated view of our planet. The 
assumption of an average atmospheric profile is 
very useful to explore a variety of effects on 
exoplanet atmospheres. 

See Also 

► Atmosphere, Structure 

► Grey Gas Model 

► Non-Grey Gas Model: Real Gas Atmospheres 

► Scale Height 


References and Further Reading 

Chamberlain J (1987) Theory of planetary atmospheres. 
Academic, New York 


Atmosphere, Organic Synthesis 

Henderson James (Jim) Cleaves II 
Earth-Life Science Institute (ELSI), Tokyo 
Institute of Technology, Meguro-ku, Tokyo, 
Japan 

Institute for Advanced Study, Princeton, NJ, 
USA 

Blue Marble Space Institute of Science, 
Washington, DC, USA 

Center for Chemical Evolution, Georgia Institute 
of Technology, Atlanta, GA, USA 

Definition 

It is widely thought that the origin of life on a 
planet may depend on the availability of 





Atmosphere, Structure 


201 


abiotically synthesized organic compounds. Var¬ 
ious potential sources for these exist, including 
extraterrestrial delivery and submarine hydro- 
thermal synthesis. However, one of the first 
suggested means of producing these compounds 
was via synthesis in the gas phase in planetary 
atmospheres, as shown by the results of the now 
famous experiment published by Stanley Miller 
in 1953. It has now been amply demonstrated that 
the action of various forms of energy, including 
shock waves, electricity, and ionizing and UV 
radiation acting on various simulated planetary 
atmospheres can result in the synthesis of a vari¬ 
ety of organic compounds. In general, more 
reduced gas mixture atmospheres appear to give 
more favorable yields of organic compounds; 
however, even relatively oxidized gas mixtures 
still produce organics to some extent. 


See Also 

► Electric Discharge 

► Miller, Stanley 

► Proton Irradiation 

► UV Radiation 


Atmosphere, Primitive Envelope 

Sean N. Raymond 

Laboratoire d’Astrophysique de Bordeaux, 
CNRS, Universite de Bordeaux, France 

Synonyms 

Primary atmosphere; Primitive atmosphere 

Definition 

An atmosphere (or an atmospheric envelope) typ¬ 
ically refers to the gas that is gravitationally 
bound to a planet or another planetary object. In 
relation to planet formation, atmospheres 


composed of hydrogen and helium are thought 
to form as a result of gas accretion by a growing 
planet embedded in a ► protoplanetary disk. For 
low-mass planets or even Moon- to Mars-sized 
planetary embryos, a relatively small amount of 
gas may be gravitationally captured into a prim¬ 
itive atmosphere. The atmospheres of full-size 
terrestrial planets are then made up of a combi¬ 
nation of atmospheres from their constituent 
planetary embryos, as well as volatiles that may 
be degassed from the planetary interior or deliv¬ 
ered to the planet via impacts of small bodies 
during final stages of accretion (► late veneer). 
In that case a large range of atmospheric compo¬ 
sitions is possible, and the atmospheres can con¬ 
sist of water and other volatile materials. 


See Also 

► Earth’s Atmosphere, Origin and Evolution of 

► Late Veneer 

► Protoplanetary Disk 


Atmosphere, Structure 

John Lee Grenfell 

German Aerospace Center (DLR), Berlin, 
Germany 

Definition 

Atmospheric structure usually refers to changes 
in physical quantities such as temperature, den¬ 
sity etc. in the vertical. Atmospheres can be clas¬ 
sified into regions (troposphere, stratosphere, 
mesosphere etc.) depending upon the variation 
of temperature in the vertical. In lower regions 
where convection is important, the decrease in 
pressure with height leads to expansion hence 
adiabatic cooling. Warm air lies below cool air 
and vertical mixing is strong - this is the “tropo¬ 
sphere” region. At higher altitudes, temperature 
may increase with altitude due to absorption of 





202 


Atmosphere, Temperature Inversion 


some of the incoming UV energy, e.g., on Earth 
via ozone. At pressures lower than about 0.1 bar 
(on Earth, Jupiter, Uranus) radiative transfer 
starts to dominate over convection. Cool air lies 
below warm air and vertical mixing is weak - this 
is the “stratosphere” region. At higher still alti¬ 
tudes, temperature may revert back to a decrease 
with altitude e.g., on Earth above about 50 km 
where ozone concentrations are small - this is the 
mesosphere region. Above the mesosphere lies 
the thermosphere, where temperature starts to 
increase again in the vertical e.g., on Earth due 
to oxygen absorption of high energy radiation. 
Finally, above the thermosphere lies the 
exosphere - the uppermost atmosphere region 
before space. The bottom of the exosphere, the 
exobase, occurs where the atmospheric scale 
height equals the molecular mean free path. The 
top of the exosphere can be defined to occur 
where the stellar pressure equals the planetary 
gravitational pull on a hydrogen atom. 


Atmosphere, Temperature Inversion 

Lisa Kaltenegger 

Cornell University, Ithaca, NY, USA 

Keywords 

Atmosphere structure; Biomarkers; Habitability; 
Habitable zone; Temperature inversion 

Definition 

A temperature inversion refers to a reversal in the 
normal decrease of atmospheric temperature with 
altitude in the lower portion (► troposphere) of a 
planetary atmosphere (► atmosphere, Structure). 
Temperature inversions inhibit vertical motion, 
because the warmer, less dense air is at a higher 
altitude and tends to remain there. The net result 
of a temperature inversion is a long time constant 
for exchange between a stratosphere and a tropo¬ 
sphere. It exists due to the heating produced by 


absorption of sunlight by molecules or aerosols 
that are chemically produced. There exists a 
highly nonlinear positive feedback between 
chemistry, radiation, and dynamics, such that 
absorbers will remain longer, hence lead to a 
larger thermal inversion, resulting in the trapping 
of even more absorbers (Pierrehumbert 2011). 

Overview 

In the troposphere, convection dominates and the 
temperature decreases according to the so-called 
wet lapse rate, about 6.5 K/km for Earth (which 
includes the latent heat released by the conden¬ 
sation of water). Mixing is generally rapid in a 
troposphere, as the warm, lighter air at the bottom 
tends to rise and the colder air at the top tends to 
sink down. The thermal inversion in the strato¬ 
sphere on Earth is due to absorption of ultraviolet 
radiation by Ozone (0 3 ) but can be generated by 
other molecules on different planets. Above 
Earth’s stratosphere where 0 3 is no longer 
strongly produced, the temperature decreases 
with height due to cooling in the infrared, mainly 
by C0 2 . In the outermost atmosphere, Earth’s hot 
thermosphere is related to absorption of extreme 
ultraviolet radiation by 0 2 , N 2 , and O. 

In contrast to the Earth, Mars has a thin and 
Venus a thick atmosphere, which is reflected in 
their surface temperatures. The tropospheric tem¬ 
peratures of Mars and Venus follow their respec¬ 
tive lapse rates (atmospheric thermal gradient). 
There are no well defined stratospheric inver¬ 
sions, except during dust storms on Mars. The 
thermospheres of both planets are relatively cold 
compared to Earth’s, because the major atmo¬ 
spheric gas (C0 2 ) is a very effective radiator of 
thermal energy. In contrast, the primarily apolar 
constituents of Earth’s atmosphere (N 2 , 0 2 ) have 
virtually no bands in the infrared and are poor 
radiators. 

See Also 

► Adiabatic Processes 

► Albedo 




Atmospheric Habitability 


203 


► Apolar Molecule 

► Atmosphere, Model ID 

► Atmosphere, Structure 

► Clouds 

► Greenhouse Effect 

► Latent Heat 

► Scale Height 

References and Further Reading 

Pierrehumbert RT (2011) Principles of planetary climate. 
Cambridge University Press, Cambridge 


Atmosphere-Ocean General 
Circulation Model 

► AOGCM 


Atmospheric Dusts 

► Aerosols 


Atmospheric Habitability 

John Lee Grenfell 

German Aerospace Center (DLR), Berlin, 
Germany 

Keywords 

Habitable; Habitable zone; Life; Atmospheric 

Definition 

“Habitability” is classically defined as the (past 
or present) existence of surface conditions which 
support life. This in turn leads to the requirement 
for the presence of liquid water which is needed 
by all known life. “Atmosphere” refers to the 
envelope of gas trapped within a planet’s 


gravitational field and for a terrestrial planet 
extends from the surface up to the exosphere. 
This entry discusses the critical importance of 
atmospheres for habitability. 

Overview 

“Habitable” is derived from the Latin habitabilis 
meaning “to inhabit.” “Habitable” denotes envi¬ 
ronmental conditions which could support life 
(Steele et al. 2005) but does not necessarily 
imply that life is present. In simple terms one 
can imagine a house which is habitable but may 
be unlived in. In its simplest terms habitability is 
classically defined as the requirement for liquid 
water. However, “conditions which could sup¬ 
port life” can be rather more many and varied. 
Broadly speaking, one can define three central 
criteria, namely, the access to (i) energy, (ii) a 
suitable solvent (e.g., water), and (iii) molecular 
complexity (e.g., via carbon chain molecules). 
Other factors such as the availability of nutrients 
and protected conditions (e.g., shelter from UV, 
cosmic rays, climate excesses, strong impacts, 
etc.) also play a role. The distribution of habit¬ 
ability in the Universe depends, therefore, on how 
well we understand the limits and occurrences of 
these various criteria and on how sensitively life 
responds to them. In this entry we will focus on 
the central role for habitability played by plane¬ 
tary atmospheres in and beyond the Solar System. 

Atmospheres are essential for habitable con¬ 
ditions for several reasons. First, liquid water 
(needed for habitability) is thermodynamically 
unstable at low pressures. Second, (in addition 
to a magnetosphere) atmospheres protect the 
planetary surface, e.g., from harmful radiation 
and cosmic rays. Third, atmospheres transport 
heat from warm to cool regions which helps to 
maintain stable conditions favored by life. 
Fourth, atmospheres may interact with biological 
and geochemical processes via feedback cycles 
such as the “carbonate-silicate” cycle which sta¬ 
bilizes the (Earth’s) climate. Fifth, (on Earth) the 
atmosphere supplies C0 2 for autotrophic life and 
0 2 needed for aerobic respiration and hence 
directly supports higher life on our planet. 






204 


Atmospheric Habitability 


Finally, atmospheric spectral signatures on rocky 
exoplanets may provide indications of surface 
habitability and even biosignature signals. 

Key Research Findings 

Huang (1960) investigated the key requirements 
a star should meet to maintain life in its habitable 
zone (HZ). Dole (1964) introduced the “complex 
life habitable zone (HZ)”- the region where a 
planet could have surface temperatures between 
0 and 30°C (for >10 % of its surface with an 
oxygen (0 2 )-rich atmosphere and <1.5 Earth 
gravity). Early climate modeling by Hart (1978) 
suggested a narrow HZ from 0.95 to 1.01 astro¬ 
nomical units (AU) for a solar-type star. 
Kasting et al. (1988) subsequently suggested 
that including negative (i.e., opposing the origi¬ 
nal change) feedback mechanisms such as the 
carbonate-silicate cycle could significantly 
expand the HZ. Kasting et al. (1993) calculated 
the HZ boundaries for different main sequence 
stars. 

Modem Solar System 

The (classical) HZ in the Solar System lies some¬ 
where between Venus and Mars. There are two 
HZ inner boundaries which may be defined. 
Firstly, the “water loss limit” (-0.95 AU, Kasting 
et al. 1993) occurs where a planet would lose its 
mass of ocean within its current lifetime due to 
atmospheric escape. Secondly, the “runaway 
greenhouse limit” (-0.84 AU, Kasting 
et al. 1993) occurs where the planetary surface 
temperature exceeds the critical point of water. 
Atmospheric clouds if present could strongly 
influence the HZ boundaries. Kitzmann 
et al. (2010) investigated the radiative effects of 
clouds upon atmospheric temperature for Earth¬ 
like planets orbiting F, G, and K stars. Results 
suggest that cloud type and altitude could signif¬ 
icantly impact surface temperature. The HZ 
limits, as estimated from numerical model stud¬ 
ies, also depend on, e.g., planetary mass, density, 
and atmospheric mass and composition. 

Regarding the inner HZ, Abe et al. (201 1) var¬ 
ied ocean mass and calculated the effect on the 


inner HZ boundary. Applying an atmospheric 
column model, Kopparapu et al. (2013) suggest 
that using updated water absorption coefficients 
and applying the same approach as in Kasting et 
al. (1993) lead to the inner HZ moving out to 
0.99 AU. 

Regarding the outer HZ, here, C0 2 clouds 
could form in the atmosphere although their radi¬ 
ative properties are challenging to estimate since, 
e.g., their shapes and sizes are not well defined. 
The “maximum greenhouse effect” is defined to 
occur at the furthest distance of planet to star for 
which a planetary surface temperature of 273 K 
can be held for a planet having a cloud-free, C0 2 
atmosphere. 

Atmospheric Evolution 

The solar neighborhood includes some rather 
young stars (e.g., Woolley et al. 1970) which 
could have planets resembling the early Earth in 
age. The Earth’s atmosphere has changed signif¬ 
icantly over geological time. The above has moti¬ 
vated studying the early Earth in an exoplanetary 
context. For example, Grenfell et al. (2011) 
investigated different epochs of hypothetical 
Earth-like exoplanets. The Sun’s net luminosity 
was (20-30 %) weaker on the early Earth 
(-2.5-4.0 Gyrs ago) compared with the modern 
Earth. Although observations from ancient soils 
(paleosols) suggest the presence of liquid water 
on early Earth, numerous climate model studies 
(see, e.g., Kasting et al. 1988) imply a completely 
frozen planet - the so-called Snowball Earth. The 
contradiction between paleosol data and model 
predictions is named “the faint young Sun prob¬ 
lem.” Several possible solutions have been put 
forward, e.g., supplying additional greenhouse 
gases such as methane (CH 4 ) or nitrous oxide 
(N 2 0) (Grenfell et al. 2011) to the early Earth 
atmosphere. Goldblatt et al. (2009) suggested a 
stronger greenhouse effect on early Earth due to 
enhanced atmospheric N 2 (considering up to 
three times the modem value). Greenhouse 
warming on early Earth is also expected to be 
sensitive to surface pressure (P 0 ). Som 
et al. (2012) suggested that early Earth featured 
(P 0 < 2) bars, based on fossilized mud 
droplet data. 



Atmospheric Habitability 


205 


Early Venus and Mars 

How early Venus’ atmosphere evolved, whether/ 
for how long the surface was habitable, and how 
it finally diverged into its modern extreme state 
are critical questions to address. On Mars, 
observed surface flow features suggest that liquid 
water likely existed early in its history. Analo¬ 
gous to the early Earth, there are difficulties for 
numerical studies to reproduce sufficiently warm 
surface temperatures. The study by von Paris 
et al. (2013) suggested that including pressure 
broadening (which enhanced the atmospheric 
greenhouse effect) of N 2 can help address this 
issue. How the Martian atmosphere developed 
from possible habitable conditions to its 
modem-day state is challenging for interior, 
atmospheric, and impact models. Clearly, under¬ 
standing the developments of Venus and Mars 
will provide useful insights for understanding 
the HZ boundaries around different stars. 

Beyond the Solar System 

Recent works have expanded the parameter range 
with the aim of determining which are the key 
factors affecting the atmospheric habitability of 
Earth-like planets beyond the Solar System. Fac¬ 
tors investigated include, e.g., climate feedbacks, 
interactive atmospheric climate chemistry (e.g., 
Segura et al. 2003; Grenfell et al. 2007), radiative 
effects of clouds (Kitzmann et al. 2013), plane¬ 
tary orbit (e.g., Williams and Pollard 2003), stud¬ 
ies of climate evolution (e.g., Selsis et al. 2007), 
and (of particular interest) planetary mass (see 
“Super-Earths” below) and ocean mass (Abe 
et al. 201 1) (see “Waterworlds and Desertworlds” 
below). 

Super-Earths 

These objects (with mass M such that 
M Eart h<M<10 M Earth ) are already starting to be 
found in the HZ (see below). There exists a lively 
discussion as to their ability to maintain plate 
tectonics (e.g., Noack and Breuer 2013) which 
would favor habitability and affects atmospheric 
mass and composition via outgassing. The 
enhanced planetary mass of super-Earths favors 
slower thermal escape of the original (proto) 
H 2 -rich atmosphere. For example, Pierrehumbert 


and Gaidos (2011) suggested that collision- 
induced greenhouse warming of high pressure 
(-40 bar) H 2 protoatmospheres (which may be 
relevant for super-Earths) could also lead to a 
significant increase of the outward HZ 
boundary - maybe to as far as 10 AU for solar¬ 
like stars. 

Waterworlds and Desertworlds 

“Waterworld” here refers to a terrestrial exoplanet 
with complete ocean coverage, i.e., without 
exposed surface continents. “Desertworld” here 
refers to a terrestrial exoplanet whose surface 
lacks large-scale oceans and vegetation. On 
waterworlds, it is currently unclear whether stabi¬ 
lizing climate cycles, i.e., analogous to the 
carbonate-silicate cycle on Earth, could operate. 
More work on, e.g., seafloor carbonization and its 
dependence on, e.g., pressure, pH etc. are required 
(see, e.g., Wordsworth and Pierrehumbert 2013). 
Regarding desertworlds, additional work estimat¬ 
ing, e.g., the dependence of ocean mass (e.g., 
including the lower limit) on, e.g., plate tectonics 
and habitability would be useful. 

Earth-Like Planets Orbiting M Dwarf Stars 

These are favored targets for exoplanet search 
missions. Such objects are already starting to be 
found in the HZ. Scalo et al. (2007) provide a 
detailed review of habitability issues. The HZ is 
rather close to the star (typically -0.2 AU) so that 
Earth-like exoplanets could be tidally locked, 
slow rotators. The 3D modeling study of Joshi 
(2003) suggested that atmospheres of such 
worlds could effectively transport heat from the 
dayside to the nightside, hence maintaining hab¬ 
itable conditions. Joshi and Haberle (2012) 
suggested that including the spectral dependence 
of the snow-ice albedo for modeled planets 
orbiting red dwarf stars led to an increase in the 
outer HZ by up to 30 % due to a weaker snow-ice 
albedo feedback. Shields et al. (2013) investi¬ 
gated similar effects, finding that Earth-like 
planets in the HZ of M stars could withstand a 
reduction of up to -19 % in incoming insolation 
without “going snowball” - partly because of the 
weaker ice-albedo feedback. Kite et al. (2011) 
modeled potentially destabilizing (negative) 



206 


Atmospheric Habitability 


climate feedbacks involving weathering and 
pressure on tidally locked planets. Decreasing 
dayside pressure led to a warming (air is less 
efficiently transported to the nightside) which in 
turn led to a faster weathering rate, which further 
decreases the atmospheric pressure. Leconte 
et al. (2013) studied (near) tidally locked planets 
close to the inner HZ boundary and discussed two 
opposing 3D effects - firstly, water evaporated on 
the dayside (suggesting a runaway climate effect) 
but secondly, water froze out on the nightside 
(opposing the runaway effect). Yang 
et al. (2013) analyzed a cloud feedback mecha¬ 
nism in their 3D model study which increased the 
planetary albedo and hence expanded the inner 
HZ boundary toward the host star for Earth-like 
planets orbiting M dwarf stars. A recent highlight 
is, e.g., planetary studies of the GJ-667 system 
(e.g., Anglada-Escude et al. 2013). Finally, the 
recent Kepler results are starting to suggest that 
planets in the HZ could be quite common. 

Although Earth-like planets in the HZ of 
M dwarfs are in some ways favored objects, 
there are nevertheless some aspects which could 
oppose the habitability of rocky planets orbiting 
in the HZ of M dwarf stars. Lammer et al. (2007), 
for example, suggested efficient escape of even 
hundreds of bars of C0 2 or/and N 2 atmospheres 
due to nonthermal escape processes for planets in 
the close-in HZ of M dwarf stars especially dur¬ 
ing extended early, active stellar phases - this 
aspect needs further investigation. Also, possibly 
weak (or even absent) magnetospheres for Earth¬ 
like planets in the HZ of M dwarf stars could 
result in strong bombardment of the planetary 
atmosphere by stellar and galactic cosmic rays. 
Associated climate and photochemical effects 
have been discussed by, e.g., Grenfell 
et al. (2012, 2013) and Segura et al. (2010). 

Atmospheric Habitability of K and F Stars 

K stars are also favored targets for exoplanet 
search missions, being rather cool, but unlike 
the case of the M dwarfs, planets in their HZs 
are unlikely to be tidally locked. Segura 
et al. (2003) and Grenfell et al. (2007) modeled 
the climate and photochemistry of Earth-like 
planets in the HZ of K and F stars and showed 


the importance of coupling climate and photo¬ 
chemistry when calculating biosignature abun¬ 
dances. For example, they showed that key 
bioindicators such as 0 3 and important green¬ 
house gases such as CH 4 respond sensitively to 
the stellar input spectrum and the planet’s posi¬ 
tion in the HZ. The 3D study of Godolt (2012) 
discussed a climate feedback which could warm 
(cool) the atmospheres of Earth-like planets 
orbiting in the HZ of K stars (F stars) - they 
found that enhanced (suppressed) incoming 
longwave infrared radiation for the M dwarf star 
scenario favors stronger (weaker) planetary 
atmospheric heating, and the effect is strength¬ 
ened by enhanced (decreased) water vapor evap¬ 
oration and a stimulated (suppressed) 
hydrological cycle. Additional exoplanets 
orbiting K stars which could be habitable are 
recently emerging, e.g., HD85512b (Pepe 

et al. 2011). 

Habitability Beyond the Classical HZ 

The main motivation here is to estimate how 
common is habitability (in all its possible 
forms) in the Universe. Most studies to date 
have focused on the Earth (“what we know”). 
On the other hand, one should clearly keep an 
open mind on the new and exciting results to 
come. Beyond the classical definitions, one 
might include alternatives to the classical requi¬ 
sites of life, including energy coming, e.g., not 
only from main sequence stars or from white 
dwarf HZs which move continuously inward 
with time. Also, Neubauer et al. (201 1) calculated 
the (much-expanded) HZ based on non-water 
solvents. 


Applications 

Key applications of the above theoretical studies 
(e.g., in an exoplanet context) are, e.g., to gener¬ 
ate scientific debate by helping to understand the 
main physical responses (e.g., between atmo¬ 
spheric dynamics, climate and composition, and 
their effect on habitability), to produce scientific 
databases (e.g., theoretical atmospheric spectral 
catalogs) which help interpret current and 



Atmospheric Habitability 


207 


future-planned data, and to drive future instru¬ 
mentation design by predicting the range of 
observed signals expected and the associated 
signal-to-noise ratio. 

Future Directions 

Theoretical studies to assess our understanding of 
habitability are needed now, to prepare the way 
for next-generation missions such as the James 
Webb Space Telescope (JWST) and the Euro¬ 
pean Extremely Large Telescope (E-ELT) 
which could detect the first exoplanetary atmo¬ 
spheric biosignatures (although this task is very 
challenging). 

See Also 

► Habitable Zone 

► Paleosols 

► Plate Tectonics 

References and Further Reading 

Abe A, Abe-Ouchi A, Sleep NH, Zahnle KJ (2011) Habit¬ 
able zone limits for dry planets. Astrobiology 
11(5);443—460 

Anglada-Escude G, Tuomi M, Gerlach E, Barnes R, 
Heller R et al (2013) A&A 556:126 
Dole SH (1964) Habitable planets for man, 1st edn. 

Blaisdell, New York. ISBN 0-444-00092-5 
Godolt M (2012) 3D climate modeling of Earth-like extra¬ 
solar plants orbiting different types of central star, PhD 
thesis, Technische Universitat Berlin (TUB), Germany 
Goldblatt C, Matthews AJ, Claire MW, Lenton TM, Wat¬ 
son AJ, Zahnle KJ (2009) Nitrogen enhanced green¬ 
house warming on early Earth. Nat Geosci 2:891-896 
Grenfell JL, Stracke B, von Paris P, Patzer ABC, Titz R, 
Segura A, Rauer H (2007) The response of atmo¬ 
spheric chemistry on Earth-like planets around F, 
G and K stars to small variations in orbital distance. 
Planet Space Sci 55:661-671 
Grenfell JL, Gebauer S, von Paris P, Godolt M, Hedelt P, 
Patzer ABC, Stracke B, Rauer H (2011) Sensitivity of 
biomarkers to changes in chemical emissions in 
Earth’s proterozoic atmosphere. Icarus 211:81-88 
Grenfell JL, Griessmeier J-M, von Paris P, Patzer ABC, 
Lammer H, Stracke B, Gebauer S, Schreier F, Rauer 
H (2012) Response of atmospheric biomarkers to 
NOx-induced photochemistry generated by stellar 


cosmic rays for Earth-like planets in the habitable 
zone of M dwarf stars. Astrobiology 
12(12): 1109-1122 

Grenfell JL, Gebauer S, Godolt M, Palczynski K, Rauer 
H (2013) Potential biosignatures in Super-Earth- 
atmospheres, II. Photochemical responses. Astrobiol¬ 
ogy 13(5):415-438 

Hart MH (1978) The evolution of the atmosphere of the 
Earth. Icarus 33:23-39 

Huang SS (1960) Life outside the solar system. Sci Am 
202:55-63 

Joshi M (2003) Climate model studies of synchronously 
rotating planets. Astrobiology 3(2):415-427 

Joshi MM, Haberle RM (2012) Suppression of the water 
ice and snow albedo feedback on planets orbiting red 
dwarf stars and subsequent widening of the habitable 
zone. Astrobiology 12(l):3-8 

Kasting JF, Toon OB, Pollack JB (1988) How climate 
evolved on the terrestrial planets. Sci Am 256:90-97 

Kasting JF, Whitmire DP, Reynolds RT (1993) Habitable 
zones around main sequence stars. Icarus 101:108 

Kite E, Gaidos E, Manga M (2011) Climate instability on 
tidally locked exoplanets. Astrophys J 743(1): 1-12 

Kitzmann D, Patzer ABC, von Paris P, Godolt M, 
Stracke B, Gebauer S, Grenfell JL, Rauer H (2010) 
Clouds in the atmospheres of extrasolar planets. 
I. Climatic effects of multi-layered clouds for Earth¬ 
like planets and implications for habitable zones. 
Astron Astrophys 511:A66 

Kitzmann D, Patzer B, Rauer H (2013) Clouds in the 
atmospheres of extrasolar planets. IV. On the scatter¬ 
ing greenhouse effect of C0 2 ice particles: numerical 
radiative transfer studies. A&A 557:A6 

Kopparapu R, Ramirez R, Kasting JF, Eymet, Robinson T, 
Mahadevan S, Ryan C, Terrien RC, Domagal- 
Goldman S, Meadows V, Deshpande R (2013) Habit¬ 
able zones around main-sequence stars: new estimates. 
Astrophys J 770:82 

Lammer H, Lichtenegger HIM, Kulikov Y, Griessmeier 
JM, Terada N, et al (2007) Coronal mass ejection 
(CME) activity of low mass stars as an important factor 
for the habitability of terrestrial exoplanets, 7(1), 
167-184 

Leconte J, Forget F, Charney B et al (2013) 3D climate 
modeling of close-in land planets: circulation patterns, 
climate moist bistability and habitability. A&A 554: 
A69 

Neubauer D, Vrtala A, Leitner JJ, Femeis MG, 
Hitzenberger R (2011) Development of a model to 
compute the extension of life supporting zones for 
Earth-like exoplanets. Orig Life Evol Biosph 
41(6):545-552 

Noack L, Breuer D (2013) First- and second-order Frank- 
Kamenetskii approximation applied to temperature-, 
pressure- and stress-dependent rheology. Geophys 
JInt 195:27-46 

Pepe F, Lovis C, Segransan D, Benz W, Bouchy F, 
Dumusque X, Mayor M, Queloz D, Santons NC, 
Udry S (2011) The HARPS search for Earth-like 



208 


Atmospheric Particles 


planets in the habitable zone. I. Very low-mass planets 
around HD20794, HD85512, and HD192310. A&A 
534:A58 

Pierrehumbert R, Gaidos S (2011) Hydrogen greenhouse 
planets beyond the habitable zone. Astrophys J 734: 
L13 

Scalo J, Kaltenegger L, Segura A, Fridlund M, Ribas 
I et al (2007) A re-appraisal of the habitability of 
planets around M-dwarf stars. Astrobiology 7:30-65 

Segura A, Krelove K, Kasting JF, Sommerlatt D, 
Meadows V, Crisp D, Cohen M, Mlawer E (2003) 
Ozone concentrations and ultraviolet fluxes on Earth¬ 
like planets around other stars. Astrobiology 
3:689-708 

Segura A, Walkowicz LM, Meadows V, Kasting J, 
Hawley S (2010) The effect of a strong stellar flare 
on the atmospheric chemistry of an Earth-like planet 
orbiting an M-dwarf. Astrobiology 10(7):751-771. 
doi: 10.1089/ast.2009.0376 

Selsis F, Kasting JF, Levrard B, Paillet J, Ribas I, Delfosse 
X (2007) Habitable planets around the star Gliese 581? 
A&A 476:1373-1387 

Shields AL, Bitz CM, Meadows VS, Joshi MM, Robinson 
TD (2013) The effect of host star spectral energy 
distribution and ice-albedo feedback on the climate 
of extrasolar planets. Astrobiology 13(8):715-739 

Som SM, Catling DC, Harnmeijer JP, Polivka JP, Buick 
R (2012) Air density 2.7 billion years ago limited to 
less than twice modern levels by fossil raindrop 
imprints. Nature, doi: 10.1038/nature 10890 

Steele A, Beaty DW, Amend J, Anderson R, Beegle L, 
Benning L et al (2005) The astrobiology field labora¬ 
tory, MEPAG white paper, 75 pp Dec 2005 

von Paris P, Gebauer S, Godolt M, Grenfell JL, Hedelt P, 
Kitzmann D, Patzer ABC, Rauer H, Stracke B (2010) 
The extrasolar planet GL 58 Id: a potentially habitable 
planet? A&A 522:A23 

von Paris P, Grenfell JL, Rauer H, Stock J (2013) 
N 2 -associated warming on early Mars. Planet Space 
Sci 82:149-154 

Williams DM, Pollard D (2003) Extraordinary climates of 
earth-like planets: three-dimensional climate simula¬ 
tions at extreme obliquity. Int J Astrobiol 2:1-19 

Woolley R, Epps EA, Penston MJ, Pocock SB (1970) Roy 
Obs Ann 5:227 

Wordsworth R, Pierrehumbert RT (2013) Water loss from 
terrestrial planets with C0 2 -rich atmospheres. 
Astrophys J 778:154 

Yang J, Cowan NB, Abbot DS (2013) Stabilizing cloud 
feedback dramatically expands the habitable zone of 
tidally locked planets. Astrophys J Lett 771(2):L45 


Atmospheric Redox Change 

► Oxygenation of the Earth’s Atmosphere 


Atomic Fine Structure Cooling 

Steven B. Charnley 

Solar System Exploration Division, Code 691, 
Astrochemistry Laboratory, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 

Definition 

Atomic fine stmcture cooling is one of the processes 
by which ► interstellar medium material can lose 
thermal energy. Atomic and molecular hydrogen 
collisions excite the fine stmcture components of 
ground state terms in atoms and atomic ions - e.g., 
in neutral carbon and oxygen atoms and in C + - and 
these subsequently decay radiatively with the 
escaping photon leading to a net cooling of the gas. 

See Also 

► Interstellar Medium 

► Molecular Line Cooling 

► Photodissociation Region 


Atomic Nitrogen 

► Nitrogen 


ATP 

Shin Miyakawa 

Ribomic Inc., Minato-ku, Tokyo, Japan 


Atmospheric Particles Synonyms 


► Aerosols 


Adenosine triphosphate; pppA 








ATPase 


209 


Definition 

ATP is one of the four activated nucleotides 
incorporated into ► RNA by RNA polymerases. 
It is also extremely important in biochemistry as a 
high-energy molecule that releases the energy 
needed for many metabolic reactions by coupling 
hydrolysis into ADP and inorganic phosphate, or 
AMP and pyrophosphate, with various synthetic 
and mechanical processes. The formation of ATP 
in living organisms takes place through two main 
biochemical pathways, substrate-level phosphor¬ 
ylation (in which phosphate is transferred to ADP 
from activated phosphorylated intermediates) 
and membrane-associated processes (found in 
respiration and photosynthesis). Although prebi- 
otic phosphorylation may have led to ATP from 
adenosine, ATP is usually not considered to have 
been abundant in prebiotic environments, and 
polyphosphates have been proposed as alterna¬ 
tive primordial energy carriers. 

See Also 

► Adenine 

► Nucleotide 

► RNA 


ATP Phosphohydrolase 

► ATPase 


ATP Synthase 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 

Definition 

ATP synthase is an enzymatic complex responsi¬ 
ble for converting the energy of a transmembrane 


► electrochemical potential of an ion (H + or Na + ) 
into chemical energy of the system ATP-ADP. 
ATP synthases have a universal phylogenetic 
distribution, and hence, it is supposed that 
they were present in the universal common 
ancestor. 


See Also 

► ATP 

► Bioenergetics 

► Electrochemical Potential 

► Last Universal Common Ancestor 

► Transduction 


ATPase 

Jose Pascual Abad 

Facultad de Ciencias, Departamento de Biologia 
Molecular, Universidad Autonoma de Madrid, 
Cantoblanco, Madrid, Spain 

Keywords 

A-ATPase; ABC-transporter; ATP synthase; 
F-ATPase; Multidrug transporter; P-ATPase; 
Proton gradient; Proton motive force; Transmem¬ 
brane ATPase; V-ATPase 

Synonyms 

Adenosine S'-triphosphatase; Adenosine 
triphosphatase; ATP phosphohydrolase 


Definition 

Enzymatic activity that catalyzes the decomposi¬ 
tion of adenosine triphosphate (ATP) into aden¬ 
osine diphosphate (ADP) and phosphate (Pi). 
A protein with ATPase activity. 






210 


ATPase 


Overview 

The term ATPase applies to the activity of any 
enzyme’s ability to decompose ATP, including 
metabolic enzymes involved in anabolic pro¬ 
cesses that need energy, as well as enzymes pro¬ 
moting transport across ► membrane. In the 
former case, the enzyme decomposes ATP using 
the energy liberated to do work; for instance, 
enzymes such as DNA helicases, RecA protein, 
AAA proteins, or the muscle contraction protein 
myosin hydrolyze ATP, applying the liberated 
free energy directly to their functions. In other 
cases, i.e., glutamine synthetase, decomposition 
of ATP is performed in two steps, helping to 
perform chemical work, phosphorylating a sub¬ 
strate or enzyme in a first step, and releasing the 
Pi in a second step. Sometimes this type of reac¬ 
tion involves the transfer of pyrophosphoryl or 
adenylyl groups instead. There are many known 
ATPases, which promote ATP hydrolysis 
coupled to transport of solutes across membranes 
into another compartment. These are integral 
membrane proteins called transmembrane 
ATPases, and there are many different types 
found in all kind of organisms, performing func¬ 
tions in which energetic exchanges are quantita¬ 
tively quite relevant. There are at least four 
general types of this kind of ATPases: F, V, 
ABC-multidrug transporters, and P. 

F-ATPases, present in plasma membrane of 
bacteria, mitochondrial inner membrane, and thy- 
lakoid membranes of chloroplasts of photosyn¬ 
thetic eukaryotes, are reversible enzymes that are 
able to promote the generation of a proton motive 
force at the expense of ATP hydrolysis or to 
synthesize ATP from ADP and Pi using a 
preexisting proton gradient. In this type of func¬ 
tion, the enzyme is more appropriately named 
► ATP synthase. This process of ATP synthesis 
is often called oxidative phosphorylation. In the 
case of fermenting bacteria which lack an elec¬ 
tron transport chain (to produce a proton motive 
force) and cannot perform oxidative phosphory¬ 
lation, the enzyme acts as a real ATPase produc¬ 
ing a proton gradient, which is used to energize 
other transport processes. F-ATPases are struc¬ 
turally related to V-ATPases since both kinds of 


enzymes are homologues. In F-ATPases, a F 0 
complex of proteins integral to the membrane is 
a transmembrane proton translocase, and the F x 
protein complex is a molecular machine that can 
either decompose ATP promoting the passage of 
proton through F 0 uphill the gradient or trans¬ 
form the energy liberated by the passage of pro¬ 
ton, downhill the gradient of protons, through F 0 
into chemical energy, thus synthesizing ATP 
from ADP and Pi. Both complexes consist of 
assemblies of several subunits that together 
form a rotary motor (Fig. 1). Binding of protons 
to F 0 causes the rotation of some of the subunits, 
which together with the subunits of F x conform 
three binding sites for ADP and Pi. The complex 
undergoes rotationally conformation changes 
through different affinity states, in one of which 
ADP and Pi can react, before the synthesized 
ATP is released (rotational catalysis). 


H + 

F-ATPase (ATP synthase) 

ATPase, Fig. 1 Model of the structure and function of 
F-ATPases 








ATPase 


211 



f 

H + 

V-ATPase 


ATPase, Fig. 2 Model of the structure and function of 
V-ATPases 


V-ATPases, present in lysosomal or 
endosomal secretory vesicle membranes, are 
proton-transporting proteins that generate a 
lower pH inside the vesicles, thus activating the 
hydrolytic enzymes present in such compart¬ 
ments. V-ATPases are also found in the plasma 
membranes of a wide variety of animal cells, 
including certain tumor cells, where they are 
involved in processes such as pH homeostasis or 
metastasis. V-ATPases have also been found in 
plants and fungi. The structures of these enzymes 
are more complex than those of P-ATPases and 
include a transmembrane proteins complex (V Q ), 
which works as a proton translocase, and a 
peripheral domain (Vi), with the ATPase activ¬ 
ity. The better known is that of yeast in which V Q 
seems to contain six and V i eight different sub¬ 
units (Fig. 2). The ATPases of Archaea 
(sometimes referred to as A-ATPases) are 


structurally and phylogenetically related to the 
V-ATPases. 

In some anaerobic bacteria, extremophiles 
(particularly thermophilic and alkaliphilic), and 
Archaea, the coupling ion used by F and V-types 
ATPases is Na + instead or in addition to H + , and a 
sodium motive force (SMF) substitutes the 
► proton motive force, (PMF). Certain studies 
suggest that the Na + -dependent ATPases came 
first in terms of evolutionary history; however, 
some others consider them as secondary adapta¬ 
tion to survival in extreme environments. 

The ATP-binding cassette (ABC) multidrug 
transporters constitute a large and ubiquitous 
superfamily of integral membrane proteins that 
are responsible for the ATP-powered transloca¬ 
tion of many substrates across membranes, 
existing as both importers and exporters. 
Importers have, to this date, only been found in 
prokaryotes, whereas exporter-type ABC trans¬ 
porters are expressed in the three domains of life. 
The highly conserved ABC structural domains of 
ABC transporters provide the nucleotide- 
dependent engine that drives transport. By con¬ 
trast, the transmembrane domains that generate 
the translocation pathway are more variable. In 
importers, the ABC domains are in separate sub¬ 
units from the transmembrane ones (TMD) while 
in exporters are another domain of the transporter 
protein (Fig. 3). In prokaryotes, the importers 
provide the cell with hydrophilic nutrients, 
while exporters remove different xenobiotics 
and hydrophobic substances from the cell. The 
prokaryotic exporters are responsible for the 
efflux of drugs that cause certain antibiotic resis¬ 
tances, and the eukaryotic ones can prevent the 
inhibitory effect of anticancer drugs by 
preventing their accumulation within the tumor 
cells. For functioning, the importers require a 
substrate-binding protein (SBP). 

P-ATPases are enzymes of plasma or sarco¬ 
plasmic reticulum that promote cation transport; 
these enzymes are reversibly phosphorylated by 
ATP. All members of this family have certain 
amino acid sequence conservation, particularly 
the Asp residue that suffers the phosphorylation/ 
dephosphorylation process, and are inhibited by 
vanadate. Some are a unique polypeptide with 









212 


ATPase 


Exporter Importer 



Hydrophilic nutrients 

| 



Hydrophobic substances 

ABC-multidrug transporters 


ATPase, Fig. 3 Model of the structure and function of ABC-multidrug exporters and importers. TMD transmembrane 
domain, ABC ATP-binding cassette, SBP substrate-binding protein 


multiple membrane-spanning regions, while 
others have a second subunit. This type of 
enzyme is widely distributed and includes repre¬ 
sentatives in animals (Na + K + -ATPase, Ca 2+ - 
ATPase, H + K + -ATPase), plants and fungi 
(plasma membrane H + -ATPase), and bacteria 
(Cd 2+ , Hg 2+ , or Cu 2+ ATPases). Albeit their 
diversity in ion specificity, all P-ATPases are 
homologues (Fig. 4). 

Basic Methodology 

The main methodologies used for the studies on 
ATPases include crystallization and structure 
determination by X-ray diffraction; nuclear mag¬ 
netic resonance (NMR) of particular subunits or 
complexes; electron and fluorescence micros¬ 
copy including visualization of the rotational 
movement of F x -ATPase, after attaching the 
rotating subunit to a fluorescent actin filament; 
and kinetic and binding studies of the enzyme 
activities, as well as genetic studies based on the 
effect of protein sequence modifications. 


Membrane 


Cytoplasm 


ATP ADP + Pi 

P-ATPase 

ATPase, Fig. 4 Model of the structure and function of 
the Ca + -ATPase, a P-ATPase 

Key Research Findings 

Boyer’s group proposed in 1973 that the step 
requiring energy in the synthesis of ATP by 
ATP synthase was the release of the ATP 


















ATPase 


213 


molecule from the enzyme. Three years later, the 
binding change mechanism was proposed by this 
group. The first X-ray structure of an incomplete 
Fi complex was published by Walker’s group in 
1994. In 1997, Yoshida’s group was able to record 
the movement of the Fj complex during ATP 
hydrolysis, now including the gamma subunit 
(the rotating shaft of the enzyme), after attaching 
individual complexes to a surface and looking to a 
fluorescent actin filament attached to the y subunit. 
In 2004, the mechanically driven synthesis of ATP 
by the F x complex was also demonstrated in exper¬ 
iments in which the y subunit inserted in the Fj 
complex was induced mechanically to rotate in the 
presence of ADP and phosphate and ATP was 
afterward released to the medium. 


Future Directions 

Although we begin to have a good view of how 
ATPases work, deeper stmctural analyses are 
needed to determine the mechanisms of ions pass 
through the ATPases domains and of torque gener¬ 
ation. Comparison of the stmctures of ATPases of 
different origins should also help in determining the 
most relevant aspects of this issue. In the 
astrobiological field, the ions that could have been 
used by the first ATPases, in the origin of life, are 
still controversial, and thus research in this field is of 
great interest and will have to be addressed shortly. 

See Also 

► ATP Synthase 

► Bioenergetics 

► Membrane 

► Proton Motive Force 

References and Further Reading 

Abrahams JP, Leslie AG, Lutter R, Walker JE 
(1994) Structure at 2.8 A resolution of Fl-ATPase 
from bovine heart mitochondria. Nature 370:621-628 
Boyer PD, Cross RL, Momsen W (1973) A new concept 
for energy coupling in oxidative phosphorylation 
based on a molecular explanation of the oxygen 
exchange reactions. Proc Natl Acad Sci USA 
70:2837-2839 


Buch-Pedersen MJ, Pedersen BP, Veierskov B, Nissen P, 
Palmgren MG (2009) Protons and how they are 
transported by proton pumps. Eur J Physiol 
457:573-579 

Gruber G, Marshansky V (2008) New insights into 
structure-function relationships between archeal ATP 
synthase (A^q) and vacuolar type ATPase (ViV 0 ). 
Bioessays 30:1096-1109 

Itoh H, Takahashi A, Adachi K, Noji H, Yasuda R, 
Yoshida M, Kinosita K Jr (2004) Mechanically driven 
ATP synthesis by Fi-ATPase. Nature 427:465-468 
Jefferies KC, Cipriano DJ, Forgac M (2008) Function, 
structure and regulation of the vacuolar (H+)- 
ATPases. Arch Biochem Biophys 476:33-42 
Kayalar C, Rosing J, Boyer PD (1977) An alternating site 
sequence for oxidative phosphorylation suggested by 
measurement of substrate binding patterns and 
exchange reaction inhibitions. J Biol Chem 
252:2486-2491 

Krah A, Pogoryelov D, Meier T, Faraldo-Gomez JD 
(2010) On the structure of the proton-binding site in 
the Fo rotor of chloroplast ATP synthases. J Mol Biol 
395:20-27 

Kiihlbrandt W (2004) Biology, structure and mechanism 
of P-type ATPases. Nat Rev Mol Cell Biol 5:282-295 
Locher KP (2009) Structure and mechanism of 
ATP-binding cassette transporters. Philos Trans 
R Soc B 364:239-245 

Madigan MT, Martinko JM, Dunlap PV, Clark DP 
(2008) Brock biology of microorganisms, 12th edn. 
Benjamin Cumming, San Francisco 
Mulkidjanian AY, Makarova KS, Galperin MY, Koonin 
EV (2007) Inventing the dynamo machine: the evolu¬ 
tion of the F-type and V-type ATPases. Nat Rev 
Microbiol 5:892-899 

Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, 
Koonin EV (2008) Evolutionary primacy of sodium 
bioenergetics. Biol Direct 3:13 
Mulkidjanian AY, Galperin MY, Koonin EV (2009) 
Co-evolution of primordial membranes and membrane 
proteins. Trends Biochem Sci 34:206-215 
Nelson DL, Cox MM (2009) Lehninger principles of bio¬ 
chemistry, 5th edn. WH Freeman, New York 
Noji H, Yasuda R, Yoshida M, Kinosita K Jr (1997) Direct 
observation of the rotation of Fl-ATPase. Nature 
386:299-302 

Pedersen PL (2007) Transport ATPases into the year 
2008: a brief overview related to types, structures, 
functions and roles in health and disease. J Bioenerg 
Biomembr 39:349-355 

Pogoryelov D, Yildiz 6, Faraldo-Gomez JD, Meier 
T (2009) High-resolution structure of the rotor ring of 
a proton-dependent ATP synthase. Nat Struct Mol Biol 
16:1068-1073 

Rees DC, Johnson E, Lewinson O (2009) ABC trans¬ 
porters: the power to change. Nat Rev Mol Cell Biol 
10:218-227 

Saroussi S, Nelson N (2009) Vacuolar H + -ATPase an 
enzyme for all seasons. Eur J Physiol 457:581-587 



214 


AU 


AU 

Daniel Rouan 

LESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 

Synonym 

Astronomical unit 


Definition 

AU stands for astronomical unit. It is the average 
Earth-Sun distance, corresponding to 
149.6 x 10 6 km (or approximately 8 light-min 
or 100 Sun diameters). This is one of the basic 
units of astronomy. Other distance units (pc, kpc, 
etc.) are derived from it. 

See Also 

► Parsec 


Austrian Space Agency, Austria 

► ASA 


Autocatalysis 

Olga Taran 1 and Gunter von Kiedrowski 2 
Chemistry and Chemical Biology, Harvard 
University, Cambridge, MA, USA 
2 Lehrstuhl fiir Organische Chemie I, Ruhr- 
Universitat Bochum, Bochum, NRW, Germany 

Keywords 

Catalysis; Origin of life theories; Self-replication 


Definition 

Autocatalysis is catalysis by one or more of the 
products of a reaction. Autocatalysis is often seen 
as the minimal requirement for the emergence of 
► life, as it is at the core of modern biogenetic 
theories based on genetic replicators, metabolic 
networks, and containment reproducers. Autoca¬ 
talysis is one of the pathways for chiral symmetry 
breaking and is also responsible for the formation 
of patterns and ordered periodic behavior in 
chemical reactions. While autocatalytic phenom¬ 
ena have been observed in fields as diverse as cell 
biology and nonlinear physics, their general 
study is the subject of the emergent field of “Sys¬ 
tems Chemistry.” 

Overview 

Autocatalytic reactions are described by the 
equation: 

pP + aA + ...^{p+\)P + ... (1) 

where a and p are reaction orders, P is the 
autocatalyst, and A is a precursor molecule. The 
autocatalytic reaction order p determines the 
“explosivity” of the product growth, which 
increases from parabolic (p = Vi) to exponential 
(p = 1) and hyperbolic (p = 2). Each type of 
growth has distinct evolutionary consequences. 
Competition between two or more 
autocatalysts - for a common resource constitu¬ 
ent A - leads to coexistence (“survival of every¬ 
body”) for parabolic, selection (“survival of the 
fittest”) for exponential, and fixation (“survival of 
the least common”) for hyperbolic growth. 

Typically, the concentration-time curve of for¬ 
mation of an autocatalyst has a sigmoidal form 
(see Fig. 1), which is the result of a self- 
accelerating growth phase followed by decelera¬ 
tion due to the consumption of precursors. 

Coupling of autocatalytic cycles with other 
reactions including autocatalytic ones can lead 
to oscillating behavior and spatiotemporal pattern 
formation. One example is the well-known 
Belousov-Zhabotinsky reaction. 






Autocatalysis 


215 





Autocatalysis, Fig. 1 (a) Typical sigmoidal 
concentration-time curve observed in many autocatalytic 
reactions. Initially, the reaction rate is slow, while the 
catalyst concentration is low. The reaction rate increases 
as more products are formed and then slows down when 
the regents are consumed or inhibition by template takes 
place. The character of the growth phase can be parabolic, 
exponential, or hyperbolic, according to the reaction 
mechanism involved in the process, (b) Periodic 


concentration oscillations of ferroin (Fe (II)) and ferritin 
(Fe (III)) complexes in Belousov-Zhabotinsky reaction. 
Reaction with limited diffusion creates spatial patterns as 
observed in this photo, (c) Scheme of a simple four- 
component cross-catalytic network. Precursors A and 
B can form two autocatalysts AB and BA or a group of 
cross-catalysts AA and BB. The scheme represents the 
reaction mechanism reported by Sievers and von 
Kiedrowski (1994) 


Autocatalysis can be found in both catabolic 
reactions (e.g., hydrolysis of simple esters) and 
anabolic reactions (e.g., template replicators). 
Feedback may result from simple autocatalysis 
by one product, cross-catalysis between two 
products, or an “autocatalytic set” of molecules 
forming a network of mutually catalytic 
interactions. 

Many genetic theories of the origin of life 
(e.g., the “►RNA world” model) demand self¬ 
replication of nucleic acids in the absence of 
enzymes. Self-replication means autocatalysis 
plus information transfer. The latter is usually 


based on a templating principle according to 
which the product transfers its blueprint as con¬ 
stitutional information. It has been demonstrated 
using nucleic acids, peptides, and small organic 
molecules as templates. 

Metabolic theories call for cycles that generate 
larger molecules from small building blocks in an 
anabolic direction, whereas the autocatalysis 
itself results from a catabolic split to yield 
medium-sized intermediates (as in the 
“► Formose reaction”). 

Autopoietic theories require self-reproduction 
of a container as well as the included 












216 


Automaton, Chemical 


components. Experimental examples have been 
found in reactions where lipid molecules forming 
micelles or vesicles are generated from non-lipid 
precursors via phase-transfer autocatalysis. 

Several modem theories for the origin of (bio) 
molecular homochirality are supported by exam¬ 
ples of enantioselective autocatalysis and chiral 
symmetry breaking. 

Current research challenges in the field of 
Systems Chemistry are programmed design of 
autocatalytic systems and their integration into 
dynamic supersystems. 


See Also 

► Autocatalysis 

► Evolution, Molecular 

► Formose Reaction 

► Hypercycle 

► Life 

► RNA World 

► Self-Replication 

► Template-Directed Polymerization 

References and Further Reading 

Bachmann PA, Luisi PL, Lang J (1992) Autocatalytic self- 
replicating micelles as models for prebiotic structures. 
Nature 357:57-59 

Blackmond D (2004) Asymmetric autocatalysis and its 
implications for the origin of homochirality. Proc 
Natl Acad Sci 101:5732-5736 

Eigen M, Schuster P (1979) The hypercycle - a principle 
of natural self-organization. Springer, Berlin 

Epstein IR, Pojman JA (1998) An introduction to 
nonlinear chemical dynamics: oscillations, waves, pat¬ 
terns, and chaos. Oxford University Press, New York 

See the Memorandum of Understanding of the Systems 
Chemistry at European Cooperation in the Field of 
Scientific and Technical Research (COST) site http:// 
w3 .cost.esf .org/index.php?id= 189&action_number= 
CM0703 

Sievers D, von Kiedrowski G (1994) Self-replication of 
complementary nucleotide-based oligomers. Nature 
369:221-224 

Szathmary E (2006) The origin of replicators and repro¬ 
ducers. Philos Trans R Soc Lond B Biol Sci 
361:1761-1776 

Vidonne A, Philp D (2009) Making molecules make 
themselves - the chemistry of artificial replicators. 
Eur J Org Chem 5:593-610 


Automaton, Chemical 

Andre Brack 

Centre de Biophysique Moleculaire CNRS, 
Orleans Cedex 2, France 

Keywords 

Algorithmic chemistry; Autopoiesis; Chemical 
reaction network; Chemoton; Minimal 
metabolism 

Synonym 

Self-replication 

Definition 

There is a remarkable gap between complex 
chemical systems that generate self-organizing 
patterns (e.g., oscillations in Belousov- 
Zhabotinsky types of reactions) and the chemical 
self-construction that any living being achieves 
through its metabolism. Chemical self¬ 
organization mechanisms operate at many differ¬ 
ent levels in biological systems, but the network 
of continuous transformation processes underly¬ 
ing the constitution of an organism is something 
clearly distinct. The idea of a chemical automa¬ 
ton addresses precisely this issue, trying to deter¬ 
mine what an autocatalytic reaction network 
requires to become an autonomous, self- 
producing system. So far we lack experimental 
evidence of chemical automata that are not living 
metabolic systems, but synthetic biology and cur¬ 
rent projects to fabricate artificial cells may soon 
provide interesting insights to this problem, 
which has been extensively explored theoreti¬ 
cally in the past. 

See Also 

► Autocatalysis 




Autotroph 


217 


► Chemical Reaction Network 

► Self-Assembly 

► Self-Replication 

References and Further Reading 

Benner SA, Ricardo A, Carrigan MA (2004) Is there a 
common chemical model for life in the universe? Curr 
Opin Chem Biol 8(6):672-689 

Brack A, Trouble M (2010) Defining life: connecting robot¬ 
ics and chemistry. Orig Life Evol Biosph 40:31-136 

Bro P (1997) Chemical reaction automata. Complexity 
2(3): 3 8-44 

Eigen M, Schuster P (1979) The hypercycle: a principle of 
natural self-organization. Springer, New York 

Fontana W (1992) Algorithmic chemistry. In: Langton 
CG, Taylor C, Farmer JD, Rasmussen S (eds) 
Artificial life II. Addison-Wesley, Redwood City, 
pp 159-209 

Ganti T (1975) Organization of chemical reactions into 
dividing and metabolizing units: the chemotons. 
Biosystems 7:15-21 

Kauffman S (1986) Autocatalytic sets of proteins. J Theor 
Biol 119:1-24 

Rosen R (1991) Life itself: a comprehensive inquiry into 
the nature, origin and fabrication of life. Columbia 
University Press, New York 

Ruiz-Mirazo K, Moreno A (2004) Basic autonomy as a 
fundamental step in the synthesis of life. Artif Life 
10(3):235-259 

Varela FJ, Maturana H, Uribe R (1974) Autopoiesis: the 
organization of living systems, its characterization and 
a model. Biosystems 5:187-196 


Autopoiesis 

Alvaro Moreno 1 and Kepa Ruiz-Mirazo 2 
^epartamento de Logica y Filosofia de la 
Ciencia, Universidad del Pais Vasco, 

San Sebastian, Spain 

department of Logic and Philosophy of Science, 
FICE, UPV-EHU, Biophysics Research Unit 
(CSIC - UPV/EHU), Donostia, San Sebastian, 
Spain 

Synonyms 

Metabolic organization; Minimal autonomy; 
Self-producing network 


Definition 

Autopoiesis is a recurrent set of component pro¬ 
duction processes that creates a physical/topolog¬ 
ical boundary, within which that set of processes 
is continuously realized. 

History 

The term was originally proposed by 
H. Maturana and F. Varela in the early 1970s 
(from Greek: auto , “self,” and poiesis , “produc¬ 
tion”) and proposed as an abstract definition of 
► life. According to these authors, an autopoietic 
system is “organized as a network of processes of 
production (transformation and destruction) of 
components which: (1) through their interactions 
and transformations continuously regenerate 
and realize the network of processes (relations) 
that produce them; and (2) constitute it (the 
machine) as a concrete unity in the space in 
which they (the components) exist, by specifying 
the topological domain of its realization as such a 
network.” 


See Also 

► Automaton, Chemical 

► Cell, Minimal 

► Life 

► Metabolism 


Autotroph 

Elena Gonzalez-Toril 
Laboratorio de Extremofilos, Centro de 
Astrobiologia (INTA-CSIC), Torrejon de Ardoz, 
Madrid, Spain 

Synonyms 

Primary producer 





218 


Autotrophy 


Definition 

Autotroph is an organism capable of 
biosynthesizing all cell material from carbon 
dioxide as the only carbon source. With respect 
to energy, autotrophs can obtain it from two 
sources: (1) photoautotrophs from radiation 
(sunlight) and (2) chemolithoautotrophs from 
the oxidation of reduced inorganic substrates. 
Autotrophs are capable of growth exclusively at 
the expense of inorganic nutrients, and they are of 
vital importance in the cycling of inorganic com¬ 
pounds on Earth including methanogens, which 
produce methane from H 2 and C0 2 , and nitrifiers, 
which convert ammonia to nitrate. Autotrophs 
are the source of reduced carbon substrates for 
the heterotrophs. Autotrophs are key elements of 
the ► carbon cycle. For this reason, autotrophic 
organisms are also called primary producers. 

See Also 

► Autotrophy 

► Calvin-Benson Cycle 

► Carbon Cycle, Biological 

► Carbon Dioxide 

► Carbon Source 

► Chemolithoautotroph 

► Photoautotroph 


Autotrophy 

Elena Gonzalez-Toril 1 and Juli Pereto 2 
^aboratorio de Extremofilos, Centro de 
Astrobiologia (INTA-CSIC), Torrejon de Ardoz, 
Madrid, Spain 

2 Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 

Keywords 

Calvin-Benson cycle; Carboxysomes; 
Chemolithoautotrophy; C0 2 fixation; 
Photoautotrophy; Rubisco 


Synonyms 

Primary production 

Definition 

Autotrophy is a lifestyle in which inorganic com¬ 
pounds provide for all nutritional needs of an 
organism. Implicit in this definition is the capac¬ 
ity of an organism to derive all cell carbon 
from carbon dioxide. Energy can be derived 
from two sources: (1) Photoautotrophs are pho¬ 
tosynthetic and obtain energy from sunlight. 
(2) Chemolithoautotrophs obtain energy by the 
oxidation of inorganic substances. Table 1 shows 
a general classification of organisms on the basis 
of the carbon and energy sources. 

Overview 

Autotrophs are capable of growth exclusively at 
the expense of inorganic nutrients, and they are 
vital in the cycling of inorganic compounds 
(Alberts et al. 1994; Campbell and Reece 2002). 
Such autotrophs not only completely satisfied their 
own needs for reduced carbon monomers from 
inorganic matter but could also feed the already 
existing heterotrophs. Thus, autotrophic organisms 
are also called primary producers. Carbon dioxide 
that is fixed into organic compounds as a result of 
autotrophic activity is available for consumption or 
respiration by animals or heterotrophic microor¬ 
ganism. The end products of respiration in hetero¬ 
trophic organism are carbon dioxide, and this way 
the carbon cycle is completed (Alberts et al. 1994; 
Campbell and Reece 2002). Now it is accepted that 
autotrophy is an extremely important process on 
Earth and autotrophic microorganisms, as primary 
producers, support the growth of non-autotrophic 
organisms (Maier et al. 2000). 

Photoautotrophs 

A large number of microorganisms, as well as the 
green plants, algae, and protists, are 
phototrophic. They use light as energy source in 
the process called photosynthesis. The result of 




Autotrophy 


219 


Autotrophy, Table 1 Classification of metabolisms according to energy, reducing power, and carbon sources 


Metabolism 

Energy source 

Reducing power 

Carbon source 

Chemo-litho-autotrophic 

Oxidation of inorganic compounds 

Inorganic compounds 

co 2 

Photo-litho-autotrophic 

Visible light 

Inorganic compounds 

co 2 

Photo-organo-heterotrophic 

Visible light 

Organic compounds 

Organic compounds 

Chemo-organo-heterotrophic 

Oxidation of organic compounds 

Organic compounds 

Organic compounds 


this mechanism is the generation of a proton 
motive force that can be used in the synthesis of 
ATP and the synthesis of reducing power (e.g., 
NADPH). Most phototrophs use energy conserved 
in ATP and electrons in NADPH for the assimila¬ 
tion of carbon dioxide as the carbon source for 
biosynthesis. These phototrophs are called photo¬ 
autotrophs. There are also phototrophs able to use 
organic compounds as carbon sources with light as 
energy source; they are called photoheterotrophs 
(Table 1) (Campbell and Reece 2002; Maier 
et al. 2000; Madigan et al. 2003). 

Chemolithoautotrophs 

In the 1880s, Sergei Winogradsky (1856-1953) pro¬ 
posed the concept of chemolithotrophy, the oxida¬ 
tion of inorganic compounds as a source of energy 
and electrons for the autotrophic growth. Studying 
sulfur bacteria (Beggiatoa and Thiothrix ), he con¬ 
cluded that these organisms obtained their carbon 
from C0 2 in air, and they were called autotrophs. 
The discovery of autotrophy in chemolithotrophic 
bacteria was of major significance in the advance of 
our understanding of cells physiology because it 
showed that C0 2 could be converted to organic 
carbon without photosynthesis. Chemolithotrophy 
is shown by members of both the Bacteria and 
Archaea domains. Chemolithoautotrophs are impor¬ 
tant in the cycling of inorganic compounds in Earth, 
including methanogens, which produce methane, 
and nitrifiers, which convert ammonia to nitrate 
(Madigan et al. 2003; Ehrlich 2002). 

Basic Methodology and Key Research 
Findings 

Autotrophic Pathways 

Six biochemical mechanisms are known for the 
autotrophic fixation of C0 2 into cell material. 


The pathways differ in the participating enzymes, 
ATP, and reducing power requirements and car¬ 
bon isotope fractionation (Maier et al. 2000; 
Madigan et al. 2003; Berg et al. 2010). 

1. The Calvin-Benson cycle, discovered in the 
1950s in Melvin Calvin’s lab, starts with the 
condensation of a 5-C sugar (ribulose 
1,5-bisphosphate) with C0 2 to yield two mol¬ 
ecules of 3-C (3-phosphoglycerate) (Fig. la). 
From these molecules both the initial 5-C 
sugar is regenerated and organic materials 
are biosynthesized. The cycle is operative in 
plastids of plants, algae, and protists, as well 
as in cyanobacteria, some aerobic or faculta¬ 
tive anaerobic proteobacteria, CO-oxidizing 
mycobacteria, some iron- and sulfur-oxidizing 
firmicutes, and green sulfur bacteria. The abil¬ 
ity to fix carbon by this pathway is conferred 
by the activity of two enzymes (together with 
fragments of central metabolism like gluco- 
neogenesis and the pentose phosphate path¬ 
way): ribulose 1,5-bisphosphate carboxylase- 
oxygenase (► Rubisco) and phosphoribu- 
lokinase (Campbell and Reece 2002; Maier 
et al. 2000; Madigan et al. 2003). Although 
Rubisco activity has been detected in some 
Archaea, it has not been possible to demon¬ 
strate Calvin-Benson-dependent autotrophic 
growth (Berg et al. 2010). 

Several autotrophic prokaryotes that use 
the Calvin-Benson cycle for C0 2 fixation pro¬ 
duce polyhedral cell inclusions called 
carboxysomes. Carboxysomes are made of 
polyhedral protein shells about 80-120 nm in 
diameter (Fig. 2). These compartments are 
surrounded by a thin membrane and consist 
of a tightly packed crystalline array of mole¬ 
cules of Rubisco (Tsai et al. 2007). Thus, the 
carboxysomes would be a mechanism to 












220 


Autotrophy 


Autotrophy, Fig. 1 The 

diversity of autotrophic 
pathways. A scheme of 
stoichiometric 
relationships in (a) the 
Calvin-Benson cycle, (b) 
the Arnon cycle, (c) the 
Wood-Ljungdahl pathway, 
(d) the hydroxypropionate 
bicycle, and (e) the 
hydroxypropionate/ 
dicarboxylate- 
hydroxybutyrate cycles. In 
each case, the identity of 
the net product of 
C fixation, the starting point 
of biosynthesis, is indicated 


3 3 GOg 

3 C5 ^—*6 C3- 




T 


G3 (3 phosp hog 1 yea rate)-► Biosynthesis 


. 5 C3 


C6 


W- 


T 


02 (acetyl-Co A)-► Biosynthesis 


05 * v C4 




COj co 2 


[H] 

C0 2 ' - ■ ► CQ * C2 (acetyl-CoA)-► Biosynthesis 

[H] f 


CO* 


R-CH, 


HC0 3 - HC0 3 - 

02 Vw C3 04 -t—► C2 (glyoxyJate) 

\ _ / ^ * \— 


e 


05- 


"Y" 

C2 


- 03 (pyruvate)-► Biosynthesis 


C0 2 HCOjf 

02 C3^+ 04 ► 02 (acetyl-CoA)-► Biosynthesis 

V_ 


X 



Autotrophy, Fig. 2 (a) A thin-section electron micro¬ 
graph of Halothiobacillus neapolitanus cells with 
carboxysomes inside. In one of the cells shown, arrows 
highlight the visible carboxysomes. (b) A negatively 
stained image of intact carboxysomes isolated from 


H. neapolitanus. The features visualized arise from the 
distribution of stain around proteins forming the shell as 
well as around the Rubisco molecules that fill the 
carboxy some interior. Scale bars indicate 100 nm 
(Figure from Tsai et al. (2007)) 


increase the amount of Rubisco in the cell to 
allow for higher rates of C0 2 fixation. 
Carboxysomes have been found in obligately 
chemolithotrophic sulfur-oxidizing bacteria, 
nitrifying bacteria, cyanobacteria, and 


prochlorophytes. They are not present in fac¬ 
ultative autotrophs like purple anoxygenic 
phototrophs, despite the fact that when these 
organisms grow as photoautotrophs, they use 
the Calvin-Benson cycle to fix C0 2 . Thus, the 












Autotrophy 


221 


carboxysome may be an evolutionary adapta¬ 
tion to life under strictly autotrophic condi¬ 
tions (Madigan et al. 2003). 

2. In the green sulfur bacterium Chlorobium , 
C0 2 fixation occurs by a reversal 
(or reductive) citric acid cycle also known as 
Arnon cycle (Madigan et al. 2003; Evans 
et al. 1966). This is the analogue of a Krebs 
cycle operating in reverse mode (Fig. lb). 
Since the Arnon cycle involves some enzymes 
(e.g., the carboxylating and reducing steps) 
that are inhibited by oxygen, this pathway is 
only found in microorganisms growing under 
anaerobic conditions. These include some 
proteobacteria, green sulfur bacteria, and 
microaerophilic bacteria like Aquifex (Maier 
et al. 2000; Madigan et al. 2003). 

3. In some Gram-positive bacteria and 
methanogenic archaea, the ability to synthe¬ 
size acetyl CoA from CO and/or C0 2 , the 
Wood-Ljungdahl pathway, was identified 
(Madigan et al. 2003; Ljundahl et al. 1965). 
One C0 2 molecule is reduced to CO and 
another one to a methyl group (attached to a 
cofactor). Then, acetyl CoA is synthesized 
from CO and the methyl group (Fig. lc). The 
key enzymes of this pathway are inhibited by 
oxygen; thus it is restricted to obligate anaer¬ 
obic microorganisms. These include some 
proteobacteria, planctomycetes, spirochaetes, 
and archaea (Maier et al. 2000; Madigan 
et al. 2003; Berg et al. 2010). 

4. The 3-hydroxypropionate bicycle is present in 
some green non-sulfur phototrophic bacteria 
like Chloroflexus (Herter et al. 2002). 
A succinyl CoA molecule is synthesized 
from acetyl CoA and two bicarbonate mole¬ 
cules (Fig. Id). Although the same intermedi¬ 
ates as the hydroxypropionate- 
hydroxybutyrate cycle (see below) are used, 
most of the participating enzymes are differ¬ 
ent. The final product of the cycle is 
glyoxylate. Its assimilation requires a second 
metabolic cycle. This pathway is restricted to 
the family Chloroflexaceae and might repre¬ 
sent an early attempt of autotrophy in 
anoxygenic phototrophs (Maier et al. 2000; 
Madigan et al. 2003). 


5. The hydroxypropionate-hydroxybutyrate 
cycle occurs in some aerobic archaea, like 
Sulfolobus. Albeit this pathway is formally 
the same as the 3-hydroxypropionate bicycle, 
the nonhomologous participating enzymes 
indicate that both pathways evolved indepen¬ 
dently in a remarkable case of evolutionary 
convergence in metabolism (Berg 
et al. 2010) (Fig. le). 

6. The dicarboxylate-hydroxybutyrate cycle 
occurs in some anaerobic archaea like the 
Thermoproteales and Desulfurococcales. The 
pathway can be divided into two parts 
(Fig. le): (1) one acetyl CoA, one C0 2 , and 
one bicarbonate are converted into succinyl 
CoA; (2) this C4 molecule is transformed 
into two molecules of acetyl CoA (one serves 
as biosynthetic precursor, the other as acceptor 
of the cycle) (Berg et al. 2010). 

Applications 

Ecology 

Autotrophs are present in all ecosystems. They 
take energy from the environment in the form of 
sunlight or inorganic chemicals and use it to 
create energy-rich molecules such as carbohy¬ 
drates. Thus, they meet their requirements easily 
and can be constitutive around the world. More¬ 
over, autotrophic organisms are primary pro¬ 
ducers and, as a consequence, they are at the 
pyramidal base of the ecosystems. Thus, hetero- 
trophs depend on autotrophs for the energy and 
raw materials they need (Maier et al. 2000). On 
the other hand, autotrophs, as a consequence of 
their poor requirements, have greater adaptabil¬ 
ity; thus, they are especially important in oligo- 
trophic environments, like oligotrophic lakes, 
glaciers and ice, acid waters, geothermal 
systems, etc. 

Rio Tinto (Huelva, Southwestern Spain) is an 
example of an environment dominated by auto¬ 
trophic bacteria. This ecosystem is of great inter¬ 
est for astrobiology (Fig. 3). It is an extreme 
environment with a rather constant acidic pH 
along the entire river and a high concentration 
of heavy metals. The extreme conditions of the 



222 


Autotrophy 


Autotrophy, Fig. 3 Rio 

Tinto as example of an 
ecosystem dominated by 
autotrophic 
microorganisms 



Tinto ecosystem are generated by the metabolic 
activity of chemolithotrophic microorganisms 
thriving in the rich complex sulfides of the Ibe¬ 
rian Pyrite Belt. In this system, more than 70 % of 
the cells are affiliated to autotrophic bacteria 
(iron-oxidizing bacteria), with only a minor frac¬ 
tion corresponding to heterotrophic. The special 
interest shows also autotrophic microalgae, pre¬ 
sent in the river, primary producer, together with 
iron-oxidizing bacteria, of the system (Gonzalez- 
Toril et al. 2003). 

Autotrophy and Early Evolution of Life 

The autotrophic metabolism has emerged inde¬ 
pendently several times during evolution, that is, 
it is a polyphyletic trait (Berg et al. 2010; Pereto 
et al. 1999). The Calvin-Benson cycle seems 
idiosyncratic to bacteria, whereas the Arnon 
cycle and the Wood-Ljungdahl pathway show a 
wider phylogenetic distribution. The different 
versions of the hydroxypropionate pathway 
likely emerged independently (Berg et al. 2010). 
At this moment, phylogenetic analysis of the 
participating enzymes does not allow us to infer 
which one is the older pathway. 

Mainstream hypothesis on the ► origin of life 
postulates that the first prokaryotes were anaero¬ 
bic heterotrophs, for example, fermenters. In the 
beginning, they may have fed on externally avail¬ 
able abiotic organic molecules, either synthe¬ 
sized on Earth or delivered by extraterrestrial 
bodies. It is generally supposed that autotrophic 
metabolism emerged latter. 


Whether the first autotrophs were chemosyn- 
thetic or photo synthetic is currently a matter of 
debate. One school of thought favors chemosyn- 
thetic autotrophs in the form of methanogens, 
which formed methane. Microorganisms 
(methanogenic archaea) with such metabolism 
exist today, and they are strict anaerobes. The 
other school of thought favors photo synthetic 
prokaryotes in the bacterial domain as the first 
autotrophs. This notion is supported by the exis¬ 
tence of the Warrawoona stromatolites, which is 
around 3.5 billion years old. Those microfossils 
have been interpreted, on the basis of comparison 
with modern counterparts, to have been formed 
by cyanobacteria. However, modern 
cyanobacteria are aerobes. Because the primor¬ 
dial atmosphere at this time is thought to have 
been almost free of oxygen, the emergence of 
anaerobic photo synthetic bacteria, of which mod¬ 
ern purple and green bacteria must be a counter¬ 
part, must have preceded that of cyanobacteria 
(Campbell and Reece 2002). 

On the other hand, in 1988, Wachtershauser 
proposed the surface metabolism theory for the 
origin of life (Wachtershauser 1988). According 
to it, life arose as a form of autocatalytic 
two-dimensional chemolithotrophic metabolism 
on a pyrite surface, using the energy and electrons 
of the anaerobic synthesis of FeS 2 (pyrite) from 
FeS and H 2 S. According to this proposal, the 
ancestral carbon fixation pathway would be a 
primitive version of the Arnon cycle 
(Wachtershauser 1990). The Wood-Fjungdahl 




Azulmin 


223 


pathway has also been proposed as a candidate of 
the older autotrophic mechanism (Pereto 
et al. 1999; Russell and Martin 2004). The lack 
of experimental evidences is the weaker aspect of 
the autotrophic hypothesis on the origin of life. 

See Also 

► Calvin-Benson Cycle 

► Chemolithoautotroph 

► Isotopic Fractionation (Interstellar Medium) 

► Origin of Life 

► Photoautotroph 

► Rubisco 

References and Further Reading 

Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD 
(1994) Molecular biology of the cell, 3rd edn. Garland, 
New York 

Berg IA, Kockelkom D, Ramos-Vera WH, Say RF, 
Zarzycki J, Hiigler M, Alber BE, Fuchs G (2010) 
Autotrophic carbon fixation in archaea. Nat Rev 
Microbiol 8:447^-60 

Campbell NA, Reece JB (2002) Biology, 6th edn. Pearson, 
Upper Saddle River 

Ehrlich HL (2002) Geomicrobiology, 4th edn. Marcel 
Dekker, New York 

Evans MCW, Buchanan BB, Arnon DI (1966) A new 
ferredoxin-dependent carbon reduction cycle in a pho¬ 
tosynthetic bacterium. Proc Natl Acad Sci U S 
A 55:928-934 

Gonzalez-Toril E, Llobet-Brossa E, Casamayor EO, 
Amann R, Amils R (2003) Microbial ecology of an 
extreme acidic environment, the Tinto River. Appl 
Environ Microbiol 69(8):4853—4865 
Herter S, Fuchs G, Bacher A, Eisenreich WA 
(2002) A bicyclic autotrophic C0 2 fixation pathway 
in Chloroflexus aurantiacus. J Biol Chem 
277:20277-20283 

Ljundahl L, Irion E, Wood HG (1965) Role of corrinoids 
in the total synthesis of acetate from C0 2 by Clostrid¬ 
ium thermoaceticum. Biochemistry 4:2771-2780 
Madigan MT, Martinko JM, Parker J (2003) Brock biol¬ 
ogy of microorganisms, 10th edn. Pearson, Upper Sad¬ 
dle River 

Maier RM, Pepper IL, Gerba CP (2000) Environmental 
microbiology, 2nd edn. Academic, San Diego 


Pereto J, Velasco AM, Becerra A, Lazcano A (1999) 
Comparative biochemistry of C0 2 fixation and the 
evolution of autotrophy. Int Microbiol 2:3-10 
Russell MJ, Martin W (2004) The rocky roots of the 
acetyl-CoA pathway. Trends Biochem Sci 29:358-363 
Tsai Y, Sawaya MR, Cannon GC, Cai F, Williams EB, 
Heinhorst S, Kerfeld CA, Yeates TO (2007) Structural 
analysis of CsoSlA and the protein shell of the 
Halothiobacillus neapolitanus carboxysome. PLoS 
Biol 5(6):el44 

Wachtershauser G (1988) Before enzymes and templates: 
theory of surface metabolism. Microbiol Rev 
52:452-484 

Wachtershauser G (1990) Evolution of the first metabolic 
cycles. Proc Natl Acad Sci U S A 87:200-204 


Autumnal Point 

► Equinox 


Available Water 

► Water Activity 


Axial Tilt 

► Obliquity and Obliquity Variations 


Azane 

► Ammonia 


Azulmin 

► HCN Polymer 








B 


Background 

Daniel Rouan 

LESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 

Definition 

A background is a diffuse radiation field 
originating from no specific location in the sky. 
When observing a given field, it is that part of the 
signal which is not due to the objects of interest and 
comes from extended or unresolved sources behind 
them. At millimeter wavelengths, the microwave 
background, the fossil emission from the Big Bang, 
is present in any direction of the sky. By extension, 
the molecular glow or the thermal infrared emis¬ 
sion from the atmosphere as well as from the 
telescope that is superimposed on the astronomical 
signal is also called background. 


Bacteria 

Francisco Rodriguez-Valera 
Microbiologia, Universidad Miguel Hernandez, 
Campus San Juan, San Juan, Alicante, Spain 

Keywords 

Cell; Domain; Phylogeny; Prokaryote; Tree of life 

© Springer-Verlag Berlin Heidelberg 2015 
M. Gargaud et al. (eds.), Encyclopedia of Astrobiology, 
DOI 10.1007/978-3-662-44185-5 


Definition 

Bacteria are a large group of single-celled phylo- 
genetically related prokaryotes distinct from 

► Archaea. Bacteria have a wide range of shapes, 
ranging from spheres to rods and spirals. They are 
ubiquitous, growing in soil, water, extreme envi¬ 
ronments, and deep in the Earth’s crust (Vreeland 
et al. 2000; Wanger et al. 2008). There are typi¬ 
cally 40 million bacterial cells in a gram of soil 
and a million bacterial cells in a milliliter of fresh 
water. There are approximately 5 x 10 30 bacte¬ 
ria on Earth, forming much of the world’s bio¬ 
mass (Whitman et al. 1998). Bacteria are vital in 
recycling nutrients and important elements of 
the geobiological cycles. Most have not been 
characterized, and only about half of the phyla 
of bacteria have species that can be grown in the 
laboratory. 

Once regarded as plants constituting the 
class Schizomycetes, bacteria are now classified 
as prokaryotes. Unlike the cells of animals 
and other eukaryotes, bacterial cells do not 
contain a nucleus and rarely harbor membrane- 
bound organelles. Although the term bacteria 
traditionally included all prokaryotes, the 
scientific classification changed after the dis¬ 
covery in the 1970s that prokaryotes consist of 
two very different groups of organisms 
(domains) that evolved independently from 
an ancient ► common ancestor. These evolu¬ 
tionary domains are called bacteria and 

► Archaea. 





226 


Bacteria 


History 

Bacteria were first observed by Antonie van Leeu¬ 
wenhoek in the seventeenth century, using a 
single-lens microscope of his own design (Porter 
1976). He called them “animalcules” and 
published his observations in a series of letters to 
the Royal Society (van Leeuwenhoek 1684). The 
name bacterium was introduced much later, by 
Christian Gottfried Ehrenberg in 1838. 

Louis Pasteur demonstrated in the 
mid-eighteenth century that ► fermentation is 
caused by the growth of microorganisms and that 
this growth is not due to spontaneous generation. 
Along with his contemporary, Robert Koch, Pas¬ 
teur was an early advocate of the germ theory of 
disease. In his research into tuberculosis, Koch 
finally proved the germ theory, for which he was 
awarded a Nobel Prize in 1905. In Koch’s postu¬ 
lates, he set out criteria to test if an organism is the 
cause of a disease, and these postulates are still 
used today. A major step in the study of bacteria 
was the development, in the middle of the last 
century, of molecular biology techniques with 
which much was learned about their biochemistry 
and genetics. In 1977, Carl Woese (Woese and 
Fox 1977) made an important breakthrough in 
our knowledge of evolution, when, in comparing 
the sequences of 16 S ribosomal RNA genes, he 
observed that a group of prokaryotic organisms, 
Archaea, have a separate line of evolutionary 
descent from that of bacteria (Woese et al. 1990). 

Overview 

Bacteria is one of the two types of prokaryotic 
organisms, the other is Archaea. Eukaryotic cells 
actually represent a consortium of cells including 
a host or nucleus cytoplasm and the endosymbi- 
otic organules: mitochondria and chloroplast, 
both of bacterial origin (Dyall et al. 2004). The 
separation between bacteria and Archaea is 
largely derived from molecular biology studies, 
mostly on ► ribosome structure and components 
(proteins and ribosomal RNA) and ► transcrip¬ 
tion machinery (RNA polymerase). Bacteria 
indeed have representatives carrying out most 


known metabolic pathways and driving the func¬ 
tioning of most ecosystems. The only known 
metabolic strategy that is not found in bacteria 
is the archaeal methanogenesis (DeLong and 
Pace 2001). Bacteria can actually close all bio¬ 
geochemical cycles on their own, so that a 
uniquely bacterial biosphere can be envisioned. 
This is not true of either eukaryotes or Archaea 
(at least with the admittedly limited knowledge 
that we have about this group). 

The classification of bacteria has undergone 
frequent changes in the last few years and is 
subject to continuous controversy as is their 
relationship with the other major cellular types. 
The widely accepted classification scheme is 
based on the 16S rRNA sequence comparisons. 
The most recent classification schemes 
describe the following groups of Bacteria: 
► Proteobacteria {Alpha-, Beta-, Gamma-, 
Delta-, Epsilonproteobacteria), Acidobacteria, 
Aquificae, Chlorobi, Bacteroidetes, Chlamydiae/ 
Verrucomicrobia, Planctomycetes, Spirochaetes, 
Actinobacteria, Chloroflexi, Cyanobacteria, 
Firmicutes, Tenericutes, Fusobacteria, 
Synergistetes, Thermotogae, and Deinococcus/ 
Thermus. 

Some of these groups are extremely diverse in 
metabolism, while others are very restricted. 
However, the availability of cultivated species, 
properly studied for their physiology, is very 
uneven (Rappe and Giovannoni 2003). At least 
in some cases, this might influence our perception 
of their true diversity. Cellular organization and 
structure is also highly variable although most 
bacteria have a rigid cell wall consisting of one 
single group of tridimensional polymers, 
mureins, or peptidoglycans. Some bacteria, 
gram-negative bacteria, also have an extra mem¬ 
brane outside the rigid polymer that provides a 
second permeability barrier. The outer mem¬ 
branes of the gram-negative bacteria have a 
very characteristic structure with a long chain 
polysaccharide facing the extracellular environ¬ 
ment and providing a hydrophilic envelope. 
Some groups of gram-positive bacteria also 
have an outer membrane, very different chemi¬ 
cally and more interlinked to the underlying poly¬ 
mer. Sometimes these gram-positive bacteria 



Bacteria 


227 


outer membranes are also quite 
hydrophobic. Finally some bacteria have glyco¬ 
protein S layers as rigid envelopes and some have 
no rigid envelope at all. 

► Motility is common in bacteria and is 
achieved by a characteristic structure, the bacte¬ 
rial flagellum (Kojima and Blair 2004). This 
nanorotor is unique and different structurally 
and phylogenetically from its archaeal and 
eukaryotic counterparts. The archaeal flagellum 
is more similar to a different bacterial structure 
that is actually involved in some types of bacte¬ 
rial motility by gliding. In spirochetes, the flexing 
spiral body rotation is achieved by inward 
directed flagella that are coiled over the cell. 
Some bacteria have other types of motility such 
as gliding over surfaces. This capacity is particu¬ 
larly efficient in social bacteria that move in 
multicellular consortia. This is the case for 
myxobacteria (a group within the 
deltaproteobacteria). 

Although no organelles have been described 
in bacteria, there are examples of fairly complex 
cellular structures, including the presence of 
nuclear membranes, previously considered 
unique to eukaryotes (Fuerst 2005). Other cellu¬ 
lar organule-like structures (Yeates et al. 2008) 
are magnetosomes, peroxisomes, gas vesicles, 
and storage granules. Cell division in bacteria is 
achieved by a cross-divisional cell wall septum, a 
constriction encompassing all the cell envelope 
layers. Although there is no mechanical cell 
machinery such as the mitotic apparatus of 
eukaryotes, bacteria have proteins homologous 
to actin that can produce mechanical modifica¬ 
tion of cell morphology (Shih and Rothfield 
2006). 

Cell shape and size varies widely in bacteria. 
However, most bacterial cells conform to rela¬ 
tively simple geometric shapes based in the cyl¬ 
inder (rod), sphere (coccus), or the spiral coil 
(spirillum) (Young 2006). Cells can vary in size 
from fractions of a micron to many hundreds of 
microns in giant bacteria such as Thiomargarita 
or Epulopiscium (Schulz and Jorgensen 2001). 
Bacterial size is limited by their osmotrophic 
feeding, that is, their need to transport all nutri¬ 
ents across the membrane. This is only efficient 


as long as a high surface/volume ratio is 
maintained. 

Bacterial reproduction is asexual, by clonal 
duplication of the cell, and originates large 
populations of clonal descent. This has been 
used for pure culture isolation and study since 
the origins of microbiology. However, bacteria 
have sex, often referred to as horizontal gene 
transfer or lateral gene transfer. The impact of 
this genetic exchange that has no part in repro¬ 
duction is considered fundamental in the evolu¬ 
tion of bacteria. The absence of meiotic processes 
and zygote formation leads to the possibility of 
genetic exchange among very different partners. 
In this way, the barriers to genetic recombination 
in bacteria are very leaky, if present at all. The 
impact of horizontal gene transfer in the evolu¬ 
tion of the prokaryotic (bacterial and archaeal) 
world is still a matter of controversy, but some 
authors consider that a biologically consistent 
tree of life based on evolutionary relationships 
could simply be a human fabrication. 

See Also 

► Aerobic Respiration 

► Anaerobic Respiration 

► Anoxygenic Photosynthesis 

► Bioenergetics 

► Biofilm 

► Carbon Cycle, Biological 

► Chemolithotroph 

► Chemoorganotroph 

► Common Ancestor 

► Early Archean 

► Fermentation 

► Gram-Negative Bacteria 

► Gram-Positive Bacteria 

► Genotype 

► Lateral Gene Transfer 

► Metabolic Diversity 

► Metabolism, Secondary 

► Microorganism 

► Motility 

► Organelle 

► Peroxisome 

► Phenotype 




228 


Bacterial Microcompartments 


► Photosynthesis 

► Phylogenetic Tree 

► Phylogeny 

► Phylum 

► Prokaryote 

► Proteobacteria 

► Quorum Sensing 

► Respiration 

► Ribosome 

► Sequence Analysis 

► Transcription 

► Translation 

References and Further Reading 

DeLong E, Pace N (2001) Environmental diversity of 
bacteria and archaea. Syst Biol 50:470^178. 
doi: 10.1080/106351501750435040 

Dyall S, Brown M, Johnson P (2004) Ancient invasions: 
from endosymbionts to organelles. Science 
304(5668):253-257. doi: 10.1126/science. 1094884 

Fuerst J (2005) Intracellular compartmentation in 
planctomycetes. Annu Rev Microbiol 59:299-328. 
doi: 10.1146/annurev.micro.59.030804.121258 

Kojima S, Blair D (2004) The bacterial flagellar motor: 
structure and function of a complex molecular 
machine. Int Rev Cytol 233:93-134. doi: 10.1016/ 
S0074-7696(04)33003-2 

Porter JR (1976) Antony van Leeuwenhoek: tercentenary 
of his discovery of bacteria. Bacteriol Rev 40:260-269 

Rappe MS, Giovannoni SJ (2003) The uncultured micro¬ 
bial majority. Annu Rev Microbiol 57:369-394. 
doi: 10.1146/annurev.micro.57.030502.090759 

Schulz H, Jorgensen B (2001) Big bacteria. Annu Rev 
Microbiol 55:105-137. doi: 10.1146/annurev. 
micro.55.1.105 

Shih YL, Rothfield L (2006) The bacterial cytoskeleton. 
Microbiol Mol Biol Rev 70(3):729-754. doi: 10.1128/ 
MMBR.00017-06 

van Leeuwenhoek A (1684) An abstract of a letter from 
Mr. Anthony Leevvenhoek at Delft, dated 17 Sep 
1683, containing some microscopical observations, 
about animals in the scurf of the teeth, the substance 
call’d worms in the nose, the Cuticula consisting of 
scales. Philos Trans (1683-1775) 14:568-574 

Vreeland R, Rosenzweig W, Powers D (2000) Isolation of 
a 250 million-year-old halotolerant bacterium from a 
primary salt crystal. Nature 407:897-900. 
doi: 10.1038/35038060 

Wanger G, Onstott TC, Southam G (2008) Stars of the 
terrestrial deep subsurface: a novel ‘star-shaped’ bac¬ 
terial morphotype from a South African platinum 
mine. Geobiology 6:325-330. doi: 10.1111/j. 1472- 
4669.2008.00163 


Whitman WB, Coleman DC, Wiebe WJ (1998) Prokary¬ 
otes: the unseen majority. Proc Natl Acad Sci USA 
95:6578-6583. doi:10.1073/pnas.95.12.6578 
Woese C, Fox G (1977) Phylogenetic structure of the 
prokaryotic domain: the primary kingdoms. Proc Natl 
Acad Sci U S A 74(ll):5088-5090. doi: 10.1073/ 
pnas.74.11.5088 

Woese CR, Kandler O, Wheelis ML (1990) Towards a 
natural system of organisms: proposal for the domains 
archaea, bacteria, and eucarya. Proc Natl Acad Sci U S A 
87:4576-4579. doi: 10.1073/pnas.87.12.4576 
Xu J (2006) Microbial ecology in the age of genomics and 
metagenomics: concepts, tools, and recent advances. 
Mol Ecol 15:1713-1731. doi: 10.1111/j.1365- 
294X.2006.02882 

Yeates TO, Kerfeld CA, Heinhorst S, Cannon GC, Shively 
JM (2008) Protein-based organelles in bacteria: 
carboxysomes and related microcompartments. Nat 
Rev Microbiol 6:681-691. doi:10.1038/nrmicrol913 
Young K (2006) The selective value of bacterial shape. 
Microbiol Mol Biol Rev 70(3):660-703. doi: 10.1128/ 
MMBR.00001 -06 

Zoetendal E, Vaughan E, de Vos W (2006) A microbial 
world within us. Mol Microbiol 59:1639-1650. 
doi: 10.1111/j. 1365-2958.2006.05056 


Bacterial Microcompartments 

► Carboxysomes, Structure and Function 


Bacterial Spore 

► Endospore 


Bacteriochlorophyll 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, 
Spain 

Synonyms 

Chlorophylls 






Banded Iron Formation 


229 


Definition 

Bacteriochlorophylls are a family of 
magnesium-porphyrin pigments present in 
anoxygenic photosynthetic bacteria and func¬ 
tion both as light receptors and photochemical 
reaction centers. 


See Also 

► Anoxygenic Photosynthesis 

► Photosynthesis 


Bacterirhodopsin 

Ricardo Amils 

Departamento de Biologia Molecular, 
Universidad Autonoma de Madrid, Madrid, 
Spain 

Definition 

Bacteriorhodopsin is a membrane protein that 
captures radiation energy which is used to create 
a proton gradient. It can be found mainly in 
Haloarchea. Bacteriorhodopsin is a membrane 
protein usually found in two-dimensional crystal¬ 
line patches known as purple membrane. The 
repeating element of the hexagonal lattice is com¬ 
posed of three identical protein chains, each 
rotated by 120° relative to the others. Each 
chain has seven transmembrane alpha helices 
and contains one molecule of retinal buried 
deep within. It is the retinal molecule that 
changes its conformation when absorbing a pho¬ 
ton, resulting in a conformational change of the 
bacteriorhodopsin promoting the proton pumping 
action. It can be considered the simplest photo¬ 
synthetic system known. All other phototrophic 
systems (bacteria, algae, chloroplasts) use chlo¬ 
rophylls instead of bacteriorhodopsin to generate 
proton gradients. 


Baly's Experiment 

Stephane Tirard 

Centre Francois Viete d’Histoire des Sciences et 
des Techniques EA 1161, Faculte des Sciences 
et des Techniques de Nantes, Nantes, France 

Definition 

Regarding origin of life, Baly’s experiment (1922) 
is one of the most emblematic organic chemistry 
experiments of the beginning of the twentieth cen¬ 
tury (Baly 1871-1948). It has demonstrated that 
ultraviolet light could act on a solution of water, 
carbon dioxide, and ammonia and produce a lot of 
organic compounds, such as sugars and amino acids. 

J.B.S. Haldane quoted these experiments in his 
famous text in 1929; for him, this was a chemical 
proof of the possibility of a link between mineral 
and organic chemistry in the prebiotic soup. 

See Also 

► Haldane’s Conception of Origins of Life 


Band Scan 

► Molecular Line Survey 


Banded Iron Formation 

A. M. Mloszewska, Rasmus Nielsen Haugaard, 
Ernesto Pecoits and Kurt O. Konhauser 
Department of Earth and Atmospheric Sciences, 
University of Alberta, Edmonton, AB, Canada 

Keywords 

Geobiology; Precambrian; Iron oxides; Chert 








230 


Banded Iron Formation 


Synonyms 

BIF; Itabirite; Taconite 

Definition 

A lithological term applied to a thinly bedded or 
laminated chemical sedimentary rock consisting 
of successive layers of fine-grained quartz, iron 
oxides, carbonates, and/or silicates, typically 
containing 20-40 % iron and 40-50 % silica 
(James 1954; Trendall 2002; Klein 2005) (Fig. 1). 

Overview 

Banded iron formations (BIFs) comprise the larg¬ 
est iron resource on Earth. They formed through¬ 
out much of the Precambrian (~3,800-543 Ma), 
reaching their maximum abundance between 
2,700 and 2,400 Ma ago. Numerous examples 
can be found on almost every continent. Their 
deposition has been linked to significant compo¬ 
sitional changes in the Earth’s atmosphere and 
hydrosphere and possibly even to the diversifica¬ 
tion of the biosphere. 

BIF has been classified on the basis of miner¬ 
alogy, tectonic setting, and depositional environ¬ 
ment (Trendall 2002). The main iron mineral 
phases were used to define four “iron formation 
facies”: oxide, silicate, carbonate, and sulfide. The 
dominant minerals, in their least metamorphosed 
state, are hematite [Fe 2 3+ 0 3 ] and magnetite [Fe 2 
+ Fe 2 3+ 0 4 ] in the oxide facies, greenalite [(Fe 2 
+ Mg) 6 Si 4 Oi 0 (OH) 8 ] and minnesotaite 
[(Fe 2+ Mg) 3 Si 4 Oi 0 (OH) 2 ] in the silicate facies, sid- 
erite [Fe 2+ (C0 3 )] and ankerite [CaFe 2+ (C0 3 ) 2 ] in 
the carbonate facies, and pyrite [Fe 2+ S 2 ] in the 
sulfide facies (Klein 2005). Today, sulfide-facies 
iron formations (i.e., pyritic carbonaceous shale or 
slate) are no longer classified as BIF as they rep¬ 
resent rock types that were deposited in different 
environments and developed in sedimentary suc¬ 
cessions of different ages without systematic asso¬ 
ciation with BIF. 

In terms of their size and lithological associa¬ 
tions, BIF are subdivided into Algoma and 


Superior types. Algoma-type BIFs are compara¬ 
tively small, with lateral extents rarely exceeding 
10 km, thicknesses ranging from 10 to 100 m, and 
primary iron contents typically less than 10 10 t 
(e.g., Condie 1981). They are associated with 
volcanogenic complexes and are inferred to have 
formed close to volcanic centers such as hydro- 
thermal vents, back-arc basins, and intracon¬ 
tinental rift zones. By comparison, Superior-type 
BIFs are hundreds of meters thick, have areal 
extents to the order of 10 5 km 2 , and have total 
primary iron contents that exceed 10 13 t. They 
are typically associated with sedimentary litholo¬ 
gies (dolomite, quartzites, and shales) and are 
inferred to have been deposited on the continental 
shelves and slopes of passive margins (Simonson 
1985). Though the water depth of deposition is still 
poorly constrained, the absence of wave- and 
current-generated features suggests a minimum 
water depth of -200 m (Trendall 2002). 

Banding in BIF is observed on a wide range of 
scales, from coarse meter-thick macrobands and 
centimeter-thick mesobands to millimeter- and 
submillimeter-scale bands. Among the latter is a 
wide variety of varve-like repetitive laminae, 
known as microbands, which may represent 
annual deposits (Trendall and Blockley 1970). 
Some Proterozoic iron formations are also 
found to contain iron granules, oolites, and other 
fragments embedded in a silica matrix (e.g., in the 
Lake Superior Region and the Labrador Trough, 
Canada; Nabberu Basin, Australia; Klein 2005). 
This granular variety, called granular iron forma¬ 
tion, possesses clear detrital textures and is 
thought to represent eroded and redeposited frag¬ 
ments of preexisting BIF (Trendall 2002). 

A third type of BIF, the younger (750-560 Ma) 
Rapitan type, is a special case in that it is linked to 
global glaciations (“► snowball Earth” events). 
The isolation of the oceans from the atmosphere 
by worldwide glacial ice cover led to ocean stag¬ 
nation and buildup of dissolved, hydrothermally 
sourced Fe 2+ . As the ice melted and ocean circu¬ 
lation reestablished itself, the iron became oxi¬ 
dized and formed a suite of iron formations in 
the oxic zone of upwelling areas (Klein 2005). 

Most Eo- and Mesoarchean BIFs belong to 
the Algoma-type and are associated with 



Banded Iron Formation 


231 



Banded Iron Formation, Fig. 1 (a) Outcrop photo¬ 
graph of Algoma-type BIF with layers of magnetite BIF 
interbedded with felsic volcaniclastic rocks from the 
2.9 Ga Itilliarsuk BIF, West Greenland, (b) Outcrop pho¬ 
tograph of weakly folded magnetite-quartz BIF from the 
2.85 Ga Central Slave Cover Group, Slave Craton, North¬ 
west Territories, Canada. Brownish bands are secondary 
iron oxides and iron oxyhydroxides. (c) A pristine BIF 


granite-greenstone belts (volcano-sedimentary 
sequences). They are found in the North Atlantic 
Craton (Northern Labrador, southwestern Green¬ 
land), Guiana Shield (Venezuela, Guyana), 
Kaapvaal Craton (South Africa and Swaziland), 
Liberian Shield (Sierra Leone, Guinea, Liberia, 
and Ivory Coast), and Yilgarn Craton (Western 
Australia). Neoarchean to Proterozoic BIFs are 
mostly of the Superior type and are found in the 


core sample from the Joffre Member, Brockman Iron 
Formation, Hamersley Province, West Australia. Black 
mesobands are composed mostly of dense magnetite, red 
micro- and mesobands are composed of chert + hematite, 
and gray micro- and mesobands are composed of 
chert + magnetite + Fe-rich carbonate (All photos cour¬ 
tesy of Rasmus Haugaard) 


Pilbara Craton (Hamersley Group, Western Aus¬ 
tralia), Kalahari Craton (Transvaal Supergroup, 
South Africa), Sao Francisco Craton 
(Quadrilatero Ferrifero), and the Superior Prov¬ 
ince (Labrador Trough and Lake Superior 
Regions, Canada/USA) (Trendall 2002; Klein 
2005). Major deposits of the Rapitan type include 
the Rapitan Group in northern Canada and those 
in the Urucum district of Brazil (Klein 2005). 








232 


Banded Iron Formation 


Key Research Findings 
BIF Composition 

Iron formations can retain the chemical signa¬ 
tures of the seawater from which they precipi¬ 
tated provided that post-depositional element 
mobility was minimal and may therefore be 
used as potential proxies for ancient seawater 
composition through time. Rare-earth element 
and yttrium (REE + Y) profiles are extensively 
used to determine the origin of iron formations. 
Two aspects of the deviation of BIF REE + Y 
profiles from that of modern seawater, the Eu and 
Ce anomalies of shale-normalized profiles, pro¬ 
vide key information about their depositional 
environments (Fig. 2). 

BIFs typically display positive Eu enrich¬ 
ments which are thought to reflect the relative 
influence of hydrothermal fluids on the seawater 
REE load at the time of deposition (Derry and 
Jacobsen 1990). The more pronounced Eu 


anomalies of Algoma-type BIFs compared to 
their Superior-type counterparts suggest a higher 
hydrothermal component in the former due to a 
higher input of high-temperature hydrothermal 
fluids (>250 °C) to Archean seawater caused by 
a hotter mantle (Arndt 1991). The redox-sensitive 
element Ce is used as a proxy for the redox state 
of ancient seawater. Modern oxygenated seawa¬ 
ter has a negative Ce anomaly due to oxidation of 
soluble Ce +3 to insoluble Ce +4 while the lack of 
Ce anomalies in Archean and early Paleopro- 
terozoic BIF REE + Y profiles suggests that 
they were instead precipitated from anoxic sea¬ 
water (e.g., Alexander et al. 2008 and references 
therein). Negligible fractionation of REE + Y 
during the initial precipitation of the precursor 
BIF iron oxyhydroxide minerals and their ability 
to withstand metamorphic conditions of up to 
amphibolite facies (Bau 1993) make these ele¬ 
ments an invaluable tool for deciphering the evo¬ 
lution of ancient seawater conditions. 


Banded Iron Formation, 
Fig. 2 Typical REE + Y 
distribution in BIF showing 
Eu and Ce anomalies as 
depicted by average values 
of BIF from the 
ca. 3,700 Ga-old Isua 
Supracrustal Belt (southern 
West Greenland), 
compared to the average 
REE + Y signature of high- 
temperature hydrothermal 
fluids and average Pacific 
seawater (Graph modified 
after Alexander 
et al. (2008); see references 
therein) 

















Banded Iron Formation 


233 


To better understand the change in seawater 
chemistry through time and the effects of nutrient 
limitations on early life, recent studies derived 
ancient seawater composition by applying 
laboratory-derived partitioning coefficients 
between trace elements in seawater and iron 
oxyhydroxide particles to the absolute concentra¬ 
tions of these elements in BIF (P, Bjerrum and 
Canfield 2002; Ni, Konhauser et al. 2009; Zn, 
Robbins et al. 2013). Because the partitioning of 
P onto iron oxyhydroxides occurs in a predictable 
way, Bjerrum and Canfield (2002) used BIF to 
infer P concentrations in ancient seawater and its 
availability to ancient organisms. Konhauser 
et al. (2009) showed that Ni concentrations 
through time have changed drastically, with con¬ 
centrations reaching up to 400 nM in the Archean 
(compared to an average 9 nM in modem seawa¬ 
ter) due to an abundance of Ni-rich ultramafic 
rocks produced by a hotter mantle. Based on the 
Zn concentrations in BIF of various ages 
(an essential metal in the metabolism of eukary¬ 
otes), Robbins et al. (2013) suggested that Zn 
concentrations in seawater have remained con¬ 
stant through time, contrary to previously 
accepted ideas (e.g., Saito et al. 2003), forcing a 
reassessment of the influence of this metal on the 
timing of eukaryote evolution. Future studies of 
this kind on other bioessential trace metals will 
advance our understanding of the timing and 
evolution of ancient microbial metabolisms. 

Yet another tool used to understand BIF gen¬ 
esis and the environmental conditions under 
which they precipitated is stable isotopes. The 
main traditional stable isotopes used in BIF stud¬ 
ies are carbon (5 13 C) and oxygen (5 18 0) while 
nontraditional isotopes include iron (5 56 Fe), sili¬ 
con (5 30 Si), and most recently, chromium 
(5 53 Cr), uranium (5 238 U), and germanium 
(5 74 Ge). Carbon isotopes are primarily used as a 
means of understanding the genesis of iron for¬ 
mations. Because the organic carbon fraction in 
BIF is so small (typically <0.5 wt.%; Gole and 
Klein 1981), carbon-isotope studies tend to focus 
instead on the carbonate mineral fraction. The 
5 13 C signature in BIF is typically light, ranging 
from +2.4 %o to —20.0 %o (Johnson et al. 2008). 
While one school of thought interprets this light 


signature as evidence of the direct carbonate pre¬ 
cipitation from an iron-rich, carbon-isotope- 
stratified water column with respect to dissolved 
inorganic carbon (e.g., Beukes and Klein 1990), 
petrographic evidence suggests that much of the 
carbonate mineral fraction in BIF is secondary, 
having grown during diagenesis (e.g., Ayres 
1972). More widely accepted opinions involve 
microbially mediated precipitation of carbonate 
during burial diagenesis, including carbonate 
precipitation through microbially mediated 
remineralization of (naturally isotopically light) 
organic matter or due to the reduction of ferric 
iron and precipitation of carbonate minerals by 
means of the bacterial oxidation of methane (see 
Bekker et al. 2010 and references therein). 

The oxygen isotope (5 18 0) composition of 
cherts in BIF is often used as a paleo-temperature 
proxy of the seawater from which they precipi¬ 
tated because the oxygen isotope fractionation 
between silica and seawater is thought to be tem¬ 
perature dependent. Knauth and Lowe (2003) 
interpreted the depleted 5 18 0 composition of 
synsedimentary to very early diagenetic cherts 
in >3.2 Ga-old BIF (Barberton Greenstone Belt, 
South Africa) as indicative of high ocean temper¬ 
ature values (55-85 °C). This evidence was later 
corroborated by 5 18 0 data from an extensive 
dataset of Archean to Phanerozoic cherts, propos¬ 
ing that sea surface temperatures decreased dras¬ 
tically from about 70 °C at 3,500 Ma ago to about 
20 °C at 800 Ma ago (Robert and Chaussidon 
2006). However, caution must be exercised 
when deriving paleo-seawater temperatures in 
BIF whose origin is associated with 
syndepositional hydrothermal alteration (e.g., 
BIF older than 3,500 Ma), since the derived tem¬ 
peratures will instead reflect local mixing condi¬ 
tions of hydrothermal fluids with overlying 
seawater. 

The study of iron isotopes (5 56 Fe) in BIF has 
gained momentum in recent years (e.g., Dauphas 
et al. 2004; Johnson et al. 2008). While the trace 
element distribution in BIF will be influenced by 
post-depositional processes such as recrystalliza¬ 
tion and metasomatism, the iron isotope system 
has been known to retain its pre-metamorphic 
signature despite such conditions (e.g., Dauphas 




234 


Banded Iron Formation 


et al. 2004). Iron isotope values in BIF span the 
entire natural range (—2.5 %o to +1.0 %o), in con¬ 
trast to the near-constant 5 56 Fe of igneous rocks 
(~0 %o) and other sedimentary rock types. They 
reflect a combination of three main processes: 

(a) mineral-specific equilibrium fractionation, 

(b) variation in the composition of fluids from 
which they precipitated, and (c) the effects of 
bacterial Fe metabolic processing (Johnson 
et al. 2003). Therefore, there are two important 
applications of 5 56 Fe in BIF: to provide informa¬ 
tion on the abiotic and biogenic controls on 
ancient redox processes in the early oceans and 
to determine the origins for heavily metamor¬ 
phosed rocks. 

The 5 30 Si compositions of early diagenetic 
cherts in BIF are often used to decipher the 
genetic processes involved in their deposition 
and infer the ambient surface conditions on 
early Earth (e.g., Andre et al. 2006). Typical 
compositions which range from —2.5 %o to 
—0.5 %o reflect relative inputs by hydrothermal 
(negative 5 30 Si, e.g., Andre et al. 2006) and con¬ 
tinental (positive 5 30 Si, e.g. van den Boom 
et al. 2010) sources into the depositional basin. 
A predominantly hydrothermal silica source can 
manifest itself as correlations in band-scale vari¬ 
ations of Fe and Si isotopes, reflecting the dynam¬ 
ics of the hydrothermal discharge (e.g., 
ca. 2,700 Ma-old Wanderer BIF, Zimbabwe; 
Steinhoefel et al. 2009). However, some of the 
well-studied Superior-type BIFs whose silica 
precipitated from a well-mixed water column 
far away from hydrothermal vents and continen¬ 
tal drainage (e.g., on an isolated continental shelf 
platform) show a uniform 5 30 Si composition 
within a single locality (e.g., the ca. 2,500 Ma- 
old Transvaal BIF, South Africa, and Hamersley, 
Western Australia). 

Analytical advances in stable isotope geo¬ 
chemistry have only recently allowed for high- 
precision measurements of trace element isotopes 
such as Cr, U, and Ge in BIF. Chromium isotope 
(5 53 Cr) compositions in BIF can be used to inves¬ 
tigate the oxygenation of the ancient atmosphere, 
where oxidative weathering will oxidize Cr(III) 
on land to the more mobile Cr(VI) which 
becomes enriched in surface seawater (e.g., Frei 


et al. 2009). It has been recently found that 5 238 U 
in BIF and other marine sediments fractionate 
differently under oxic and suboxic to euxinic 
conditions, making it another novel geochemical 
tracer of the Earth’s redox evolution (Weyer 
et al. 2008). Germanium in the oceans has a 
short residence time (about 10,000 years). As 
Ge/Si ratios in seawater appear to vary in 
response to climate, the 5 74 Ge composition of 
BIF and other marine sediments may offer new 
insight into the Earth’s climate history (Rouxel 
et al. 2006). 

Controls on BIF Deposition 

Because the Fe contents of larger BIF is upward 
of 10 13 t, the potential Fe source must be capable 
of supplying these vast quantities. A widely 
accepted idea stems from classical BIF studies 
by Cloud (1973) and Holland (1973) which 
established that the major components (Fe and 
Si) in these rocks were derived from seawater. 
Additionally, certain aspects of the typical REE 
content in BIF led to the conclusion that these 
components were initially hydrothermally 
sourced and later mixed with overlying seawater 
(e.g., Graf 1978). The characteristic positive Eu 
anomalies found in BIF, a trait shared by modern 
hydrothermal vent fluids, is thought to indicate a 
strong influence of hydrothermal fluids on the 
BIF REE load and, by extension, Fe (Derry and 
Jacobsen 1990). This contrasting behavior of Eu 
to neighboring REE is thought to be related to the 
reduction of Eu 3+ in hydrothermal solutions char¬ 
acterized by high temperatures (>250 °C) and 
low oxidation-reduction potentials. The generally 
positive, mantle-like sNd values in BIF (where 
the sNd notation defines the departure of 
143 Nd/ 144 Nd from the Chondritic Uniform Reser¬ 
voir evolution line), which contrast with the neg¬ 
ative sNd values of seawater, support the idea 
that a large part of the Fe in BIF had been sourced 
from ancient submarine hydrothermal systems 
(Jacobsen and Pimentel-Klose 1988). 

Our knowledge of the other major component 
in BIF, silica, begins with the understanding that 
Precambrian seawater was likely close to super¬ 
saturation with respect to amorphous silica until 
the evolution of organisms which incorporate 



Banded Iron Formation 


235 



1) Oxygenic Photosynthesis 

2Fe rt + ViOj + 5HjO -*■ 2Fe(OH), + 4H* 

6Fe* 2 + Vz0 2 + 16H,0 — [CRO] + 6Fe(OH),+ 12H* 

2) Photoferro trophy 

4Fe* 2 + llHp + C0 2 —*[CH,0] + 4Fe(OH), + 8H* 

3) Photooxidation 

2Fe* 2 + 2H + + bt>~> 2Fe s + H 2 T 


Banded Iron Formation, Fig. 3 Three simplified 
models for the oxidation of Fe 2+ and the deposition of 
banded iron formations: ( 1 ) oxygenic photosynthesis and 
oxidation of Fe 2+ by cyanobacterially produced oxygen in 


the photic zone. (2) Fe(II) oxidation in an anoxic water 
column by photoautotrophs such as green and purple 
sulfur bacteria. (3) Abiotic oxidation of Fe 2+ via 
photooxidation 


silica in their skeletons, such as diatoms and 
radiolaria. The main sources of Si to the oceans 
are hydrothermal fluids and continental runoff, 
which have compositionally distinct Ge/Si ratios 
that can be used to identify the origin of the silica 
in BIF. Hamade et al. (2003) established, using 
the Ge/Si ratios of chert bands in ca. 2,500 Ma 
BIF of the Dales Gorge Member (Hamersley 
Basin, Western Australia), that most of the silica 
in BIF was continentally derived. Frei and Polat 
(2007) later confirmed that this was also true for 
Algoma-type BIFs, proposing that the spread in 
Ge/Si ratios observed in the ca. 3,800 Ma-old Isua 
Supracrustal Belt was due to the interaction of 
hydrothermally iron-fertilized bottom waters 
with silica-rich surface seawaters derived from 
pre-4,000 Ma-old mafic land masses. Silicon iso¬ 
topes have added some complexity to the issue of 


source since they show a perceptible hydrother¬ 
mal signature in some BIFs (e.g., Steinhoefel 
et al. 2009), suggesting that the silica in BIF 
may be derived from mixed hydrothermal and 
continental sources. 

Prerequisites for BIF deposition necessitate 
not only a source of Si and soluble (reduced) Fe 
but also a way to oxidize that Fe 2+ into insoluble 
Fe 3+ (Fig. 3). 

Traditional models of BIF deposition propose 
that Fe 2+ was oxidized in the presence of free 
oxygen derived from oxygenic microbial photo¬ 
synthesis by cyanobacteria (Cloud 1965) and 
later through the direct utilization of 0 2 by aero¬ 
bic chemolithoautotrophic bacteria (Holm 1989): 

2Fe +2 + V 2 O 2 + 5H 2 0 — 2Fe(OH) 3 + 4H+ 



















236 


Banded Iron Formation 


6Fe+ 2 + V 2 O 2 + 16H 2 0 

->■ [CH 2 O] + 6Fe(OH) 3 + 12H+ 

Indeed, the most voluminous BIFs (e.g., 
Hamersley Group, Western Australia; Transvaal 
Supergroup, South Africa) overlap in age with 
the rise of atmospheric oxygen at -2.4 Ga. 
While this suggests that the Fe 3+ component in 
these BIF formed via an oxic mechanism, the low 
atmospheric oxygen concentrations in the 
Archean suggest that the pre-2,400 Ma BIF 
formed via an anoxic mechanism. Both abiotic 
and biogenic BIF formation mechanisms have 
been suggested. In the latter case, the oxidation 
of Fe 2+ into Fe 3+ in an anoxic world can occur via 
anoxygenic phototrophy, whereby some photo¬ 
synthetic bacteria (e.g., green and purple sulfur 
bacteria) can use Fe 2+ as an electron donor for 
carbon assimilation instead of water, thus pro¬ 
ducing Fe 3+ instead of 0 2 (Garrels et al. 1973): 

4Fe 2+ + C0 2 + 11H 2 0 

-► CH 2 0 + 4Fe(OH) 3 + 8H + 

The biogenic precipitation of iron oxides by sev¬ 
eral species of modern phototrophic bacteria has 
been observed in both freshwater and marine 
environments, and laboratory experiments dem¬ 
onstrate that this form of metabolism could gen¬ 
erate sufficient quantities of Fe 3+ to account for 
all the oxidized iron in BIF (Kappler et al. 2005). 

It has also been postulated that the absorption 
of ultraviolet radiation by either Fe 2+ or Fe(OH) + 
in the water column could have triggered the 
hydrolyzation of these species according to the 
following equation (Caims-Smith 1978): 

2Fe 2+ (aq) + 2H+ + hv -> 2Fe 3+ (aq) + H 2 | 

Although laboratory experiments have demon¬ 
strated that this oxidative process could have 
generated enough Fe 3+ to account for all the ferric 
oxides in BIF, the process remains contentious as 
the experiments were not done in solutions that 
actually mimicked Precambrian seawater compo¬ 
sition (Konhauser et al. 2007). 


The signature feature of many iron formations 
is the distinctive banding made by alternating 
assemblages of silica/silicate and iron oxide min¬ 
erals. Two fundamentally different models have 
been proposed as to their formation. The first 
suggests episodic pulsing of an iron-rich plume 
into the shallow waters of a depositional basin. 
During periods of up welling, increased bacterial 
activity in the photic zone would induce the oxi¬ 
dation of Fe 2+ to Fe 3+ , while periods of no 
upwelling corresponded to low iron mineraliza¬ 
tion and high silicification from background 
waters (Morris 1993). Posth et al. (2008) demon¬ 
strated experimentally that banding could also be 
due to natural fluctuations in seawater tempera¬ 
ture. In the summer, the warm waters promote 
increased bacterial Fe 2+ oxidation while 
maintaining Si in solution, while during the win¬ 
ter, the decline in water temperature diminishes 
bacterial activity but induces silicification. The 
second view proposes that banding is the result of 
post-depositional diagenetic processes in which 
Si was remobilized and segregated into bands 
(Trendall and Blockley 1970). Significantly, cou¬ 
pling the reduction of Fe 3+ minerals to the oxida¬ 
tion of organic matter not only explains the 
reduced Fe mineralogy in BIF and the low 
organic-matter content but also explains the 
abundance of light C isotope signatures associ¬ 
ated with the interlayered carbonate minerals 
(Konhauser et al. 2005). 

BIF and Iron Ore 

Apart from being an important proxy for Precam¬ 
brian seawater composition, BIFs are the main 
source of metallic iron for the steel industry. 
Almost all iron extracted from BIF-hosted iron 
ore deposits are used to make pig iron (a mixture 
of iron ore and coke produced in a blast furnace), 
which is the main component in the manufacture 
of steel. 

BIF-hosted iron ore deposits can be divided 
into three classes on the basis of their iron con¬ 
tent: (1) iron-rich primary BIFs containing 
30-45 wt.% Fe, (2) high-grade martite-goethite 
ores with 56-63 wt.% Fe, and (3) high-grade 
hematite ores containing 60-68 wt.% Fe (Clout 
and Simonson 2005). The bulk of iron ore mined 



Banded Iron Formation 


237 



Banded Iron Formation, Fig. 4 Sketch showing typical supergene enrichment of a magnetite-rich BIF leading to a 
high-grade hematite-goethite ore deposit within the weathering zone (Modified from Clout and Simonson (2005)) 


today corresponds to high-grade iron deposits 
(class 1 and 2) formed by supergene iron enrich¬ 
ment of precursor BIFs. The supergene enrich¬ 
ment process (Fig. 4) involves deep weathering 
from the downward movement of oxidizing 
meteoric fluids that leach out the chert and car¬ 
bonate components, leaving a residual accumu¬ 
lation of oxidized and hydrous Fe 3+ phases such 
as hematite, martite, and goethite (Webb 
et al. 2003; Clout and Simonson 2005). Martite 
is often used as a textural term for hematite pseu- 
domorphs after magnetite. The formation of these 
high-grade iron ores took place long after depo¬ 
sition, likely during the Phanerozoic, when the 
concentration of atmospheric oxygen, and thus 
meteoric waters, was sufficient to oxidize precur¬ 
sor mineral phases such as magnetite (Fig. 4). 

In some deposits, however, hydrothermal 
fluids facilitated the formation of high-grade 
iron ore prior to supergene enrichment. Within 
the depositional basin, chert bands were hydro- 
thermally replaced by carbonates, which in turn 
were dissolved and leached during later super¬ 
gene enrichment (e.g., Tayor and Dalstra 2001). 

The world’s leading iron ore producers and 
their historical and future estimated output of Fe 
are shown in Table 1. 

The iron reserves (part of the mineralization 
that is economically feasible to extract at the time 
of determination) for each country as in 2011 are 


also presented. As observed in Table 1, the world 
output of iron is projected to increase from 2010 
to 2013 by about 13 %, that is, from 1.32 billion 
metric tons (Gt) in 2010 to 1.52 Gt in 2013 
(Menzie et al. 2013). The world iron resources 
(parts of the mineralization that is in such form 
and amount that economic extraction is not fea¬ 
sible) reached ca. 800 Gt of crude ore (defined as 
it leaves the mine in an unconcentrated form) 
containing 230 Gt of iron (US Geological Survey, 
Mineral Commodity Summaries, January 2013). 

Superior-type BIF are the largest source of 
iron used in industry, where three of the largest 
deposits in the world are located in the Carajas 
and Quadrilatero Ferrifero iron provinces in Bra¬ 
zil and the Hamersley iron province in Western 
Australia. These provinces account for close to 
40 % of the world’s iron reserves (Table 1). An 
example of the magnitude of these BIF deposits is 
seen within the Hamersley iron province where 
the Paleoproterozoic Brockman Iron Formation 
contains some of the largest single lithostra- 
tigraphic BIF units known. These units are up to 
360 m thick (e.g., the Joffre Member), having an 
areal extent of 10 5 km 2 and estimated initial Fe 
content of 4.3 x 10 13 t at the time of deposition 
(e.g., Trendall and Blockley 1970). 

Table 1 shows that China is the largest pro¬ 
ducer and importer of iron in the world. The main 
iron ore reserves of China, however, possess 










238 


Banded Iron Formation 


Banded Iron Formation, Table 1 The world’s largest producers of iron 2000-2017 (estimated). See text for details. 
Values extracted from Menzie et al. (2013) and US Geological Survey Mineral Commodity Summaries, January 2013 


Reserves in billion 


Fe content in thousand metric tons 


tons (Gt) 


Country 

Average 

ore 

grade (% 
Fe) 

2000 

2005 

2010 

2013 

2015 

2017 

Crude 

ore 

(2011) 

Fe 

content 

Australia 

62 

107,000 

163,000 

271,000 

330,000 

350,000 

370,000 

35,000 

17,000 

Brazil 

66 

141,000 

186,891 

247,772 

250,000 

250,000 

260,000 

29,000 

16,000 

Canada 

64 

22,700 

19,333 

23,300 

28,000 

28,000 

30,000 

6,300 

2,300 

China 

64 

73,600 

134,000 

350,000 

410,000 

420,000 

430,000 

23,000 

7,200 

India 

64 

48,600 

97,500 

166,000 

170,000 

172,000 

174,000 

7,000 

4,500 

Russia 

58 

50,000 

56,100 

58,500 

59,000 

59,500 

60,000 

25,000 

14,000 

South 

Africa 

62-65 

21,570 

24,900 

36,900 

46,700 

48,900 

49,500 

1,000 

650 

Ukraine 

55 

30,600 

37,700 

43,000 

45,000 

48,000 

50,000 

6,000 

2,100 

USA 

- 

39,703 

34,202 

32,000 

32,000 

32,000 

32,000 

6,900 

2,100 

World 

607,000 

837,000 

1,320,000 

1,520,000 

1,660,000 

1,750,000 

170,000 

80,000 


relatively low-grade Fe content (~30 % Fe); 
therefore, high export rates of high-grade iron 
ore are expected from China’s largest suppliers 
in the future (e.g., Australia and Brazil). 

Future Directions 

As marine chemical precipitates, BIFs hold great 
importance as proxies for ancient seawater chem¬ 
istry and, in this regard, may provide new insights 
into the composition of the ancient marine bio¬ 
sphere and, ultimately, the atmosphere, through 
the biogenic gases that ancient plankton emitted. 
Recent studies have begun to examine changing 
Precambrian seawater chemistry in terms of 
bioessential trace metals, and the results obtained 
from the BIF record are being corroborated by the 
record of these trace metals in marine black 
shales (e.g., Zn; Scott et al. 2012). Future work 
on BIF will undoubtedly investigate the temporal 
variations in more metals. Such geochemical 
studies will be enhanced by new analytical devel¬ 
opments in trace metal stable isotopes, whereby 
relatively novel metal isotopes (e.g., 5 53 Cr and 
5 238 U) or multi-isotope surveys (e.g., combining 
5 56 Fe and 5 30 Si; Steinhofel et al. 2009) will 
improve our understanding of the paleoredox 


conditions under which BIF formed. New 
BIF-based studies examining the paleoredox con¬ 
ditions a few million years prior to and after the 
great oxidation event (GOE, ca. 2.45 Ga) indicate 
that this event likely occurred more gradually 
than previously thought. As the products of the 
interplay between the mantle, the ocean, and the 
biosphere, BIFs are important chemical archives 
of ancient seawater composition. They not only 
grant us an understanding into ancient mantle and 
surface process systematics but provide impor¬ 
tant insights into the evolutionary pathways of 
early life as well. 

See Also 

► Archean Environmental Conditions 

► Archean Traces of Life 

► Bacteria 

► Earth’s Atmosphere, Origin and Evolution of 

► Iron Cycle 

► Iron Isotopes 

► Iron Oxides, Hydroxides and Oxy-hydroxides 

► Jaspilite 

► Magnetite 

► Ocean, Chemical Evolution of 

► Oxygenation of the Earth’s Atmosphere 

























Banded Iron Formation 


239 


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Bandpass 

Daniel Rouan 

LESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 

Definition 

The bandpass is a well-defined range of frequen¬ 
cies (or wavelengths) determined by a filter that 
cuts out all other frequencies (or wavelengths) 
above and below this band. In visual and infrared 
photometry, different sets of standard filters with 
well-defined bandpasses have been defined and 
are used to perform color photometry. A given set 
defines a photometric system, the measured 
values in the different filters being generally 
given in ► magnitudes. 

See Also 

► Johnson UBV Bandpasses 


Barberton Greenstone Belt 

Nicholas Amdt 

ISTerre, Universite Grenoble Alpes, France 

Keywords 

Chert; Greenstone belt; Komatiite; Sedimentary 
rocks; South Africa; Traces of life 





Barberton Greenstone Belt 


241 


Definition 

The Barberton greenstone belt in South Africa is 
one of the best-preserved successions of 
mid-Archean (3.57-3.21 Ga) supracrustal rocks 
in the world, together with the ► Pilbara Craton 
in Western Australia. As such, it is a remarkable 
natural laboratory where conditions and pro¬ 
cesses at the surface of the Archean Earth can 
be studied in detail. The volcanic sequences 
include thick flows of ► komatiite, a type of 
ultramafic lava named after the Komati River 
that flows through the belt, and records of large 
phreatomagmatic eruptions. Sedimentary 
sequences include ► cherts, ► banded-iron for¬ 
mations, and barite whose compositions con¬ 
strain the composition and temperature of 
Archean oceans and preserve some of the earliest 
traces of life on Earth. The granitic rocks and 
metamorphic sequences provide information 
about Archean tectonic processes. 

History 

Geological mapping and research has been carried 
out in the Barberton belt over much of the past 
century, but only in the 1970s did its geological 
significance become apparent. Three develop¬ 
ments were particularly important: The first was 
the development of increasingly accurate age dat¬ 
ing that revealed the emplacement of volcanic and 
sedimentary rocks between 3.5 and 3.2 Ga ago 
(e.g., Lopez Martinez et al. 1984; Armstrong 
et al. 1990). This discovery showed that the Bar¬ 
berton terrain, together with those of the Pilbara 
Craton in Western Australia, contained the oldest 
known, well-preserved (i.e., metamorphosed to 
only a low degree) volcanic and sedimentary 
sequences. The second important discovery was 
the recognition by Richard and Morris Viljoen of 
the University of the Witwatersrand that many 
of the ultramafic rocks of the sequence were 
volcanic. They named this new rock type komatiite 
after the Komati River that flows through the belt. 
The geological and tectonic significance of these 
rocks has been developed in numerous publica¬ 
tions (e.g., Viljoen and Viljoen 1969; Anhaeusser 


1980; de Wit et al. 1987; Dann 2000). The third 
important development stemmed from the work on 
clastic and chemical sedimentary rocks. Following 
the recognition of the ancient age of the sedimen¬ 
tary sequences in the 1970s, several research 
groups undertook a systematic search for micro¬ 
fossils in carbonaceous black ► cherts and shales. 
Detailed sedimentological and geochemical stud¬ 
ies followed and led to major advances in the 
understanding of surface processes on the early 
Earth, including the observation of shallow-water 
sedimentary rocks and silicified evaporites (Lowe 
and Knauth 1977), sedimentary barite horizons 
(Heinrichs and Reimer 1977), seafloor alteration 
(Duchac and Hanor 1987), seafloor hot springs 
(de Ronde and Ebbesen 1996), semi-quantitative 
evidence for tides (Eriksson and Simpson 2000), a 
record of temperature of the Archean ocean 
(Knauth and Lowe 2003), and photo synthetic 
microbial mats (Tice and Lowe 2006). In addition, 
it was found that at least four sedimentary beds in 
the Barberton belt contained sand-sized spherical 
particles (sphemles) interpreted to have formed by 
condensation of clouds of impact-generated rock 
vapor and thus represent the oldest terrestrial 
impact deposits (Lowe et al. 2003; Hofmann 
et al. 2006). 

Overview 

The Barberton greenstone belt is a small, cusp¬ 
shaped succession of volcanic and sedimentary 
rocks invaded on all sides by granitoid plutons or 
truncated by ductile shear zones. It is located 
about 350 km east of Johannesburg and is world 
famous for its komatiites, a type of ultramafic 
lava named after the Komati River that runs 
through the southern part of the belt, and for 
thick sequences of sedimentary rocks, which 
have yielded some of the earliest records of 
early life and of Earth’s early surface conditions. 
The greenstone sequences, assigned to the ► Bar¬ 
berton Supergroup, have been subdivided into 
three stratigraphic units. From base to top, these 
are (1) the Onverwacht Group, dominated by 
ultramafic and mafic volcanic rocks; (2) the Fig 
Tree Group, a volcano-sedimentary succession 




242 


Barberton Greenstone Belt 


made up of graywackes (a variety of sandstone 
with a clay-rich matrix), shales, cherts, and felsic 
volcaniclastic rocks; and (3) the Moodies Group, 
characterized by coarse-grained clastic sedimen¬ 
tary rocks, mainly sandstones and conglomerates. 
Geological mapping has provided an increasingly 
clearer picture of the detailed stratigraphy despite 
the complex structure (Lowe et al. 2012). The 
protracted, 350-million-year-long evolution of the 
region encompassed multiple tectonic events that 
include three or more cycles of volcanism and 
sedimentation, deformation, and granite intrusion 
(Lowe and Byerly 1999a). This rich history led de 
Wit et al. (1992) to use the region as the basis of 
their model for the formation of continental cmst. 

Extensive field-based studies in the Barberton 
belt, starting from the early 1960s, provided evi¬ 
dence for the existence, as early as 3.5 Ga, of a rich 
microbial ecosystem. Spherical, coccoidal, 
rod-shaped, and filamentous microscopic struc¬ 
tures made up of carbonaceous matter and 
interpreted as microfossils have been recorded 
from Onverwacht and Fig Tree Group cherts. 
These rocks were deposited in shallow and deep 
marine environments, possibly in part on normal 
Archean oceanic crust and possibly associated with 
hydrothermal activity (Walsh 1992; Altermann 
2001; Westall et al. 2001; Tice and Lowe 2006). 

Domal stromatolites are also present in the Bar¬ 
berton belt (Byerly et al. 1986), but their origin, 
together with other early Archean occurrences, is 
controversial (Lowe 1994). More recently, Fumes 
et al. (2004) reported micrometer-scale tubular 
structures, interpreted to represent bioerosion fea¬ 
tures, in the rims of Onverwacht Group pillow 
basalts. Stable isotopic data have revealed the pos¬ 
sible emergence of diverse groups of prokaryotes 
including carbon-fixing Bacteria and Archaea, 
methanogens, sulfate reducers, and possibly 
photosynthesizers. Structures reminiscent of mod¬ 
em microbial mats in shallow-water sandstones 
are widespread in parts of the Moodies Group 
(Heubeck 2009; Gamper et al. 2012). 

The sedimentary sequences themselves can be 
mapped in detail and measured at high strati¬ 
graphic resolution. They thus provide abundant 
information about conditions at the Earth’s sur¬ 
face: the spatial and temporal sequence of 


depositional systems; the interface between vari¬ 
ous regimes of erosion, transport, and deposition; 
the diagenetic processes near the surface; struc¬ 
tural control on sedimentary composition, thick¬ 
ness, and geometry; the thermal history and 
evolution of sedimentary basins; and thus the 
overall geodynamic setting on the early Earth. 

The ultramafic lavas of the Barberton belt 
have unusual compositions that define the 
Al-depleted or Barberton-type komatiite 
(Nesbitt and Sun 1976; Arndt et al. 2008). 
These rocks are formed through melting under 
unusual conditions in the mantle. Controversy 
surrounds the exact setting: most geologists sup¬ 
port a model in which the melts form in an unusu¬ 
ally hot mantle plume (e.g., Arndt et al. 2008), 
but others advocate melting in cooler conditions 
in an Archean subduction zone (e.g., Grove and 
Parman 2004). Resolution of the issue has impor¬ 
tant implications for our understanding of 
Archean geodynamics. Despite more than 
30 years of research, very few complete chemical 
analyses of Barberton komatiites are available, 
yet this information is crucial if the potential of 
these rocks as tracers of Archean geodynamic 
processes is to be realized. Black and white 
smokers on the Archean ocean floor, the exits of 
hydrothermal fluids that circulated through basal¬ 
tic crust, represent one possible setting for the 
emergence and evolution of life (Russell 
et al. 2005). Examples of these may well exist 
in the Barberton greenstone belt, but, as for most 
of the crucial geological and biological aspects of 
the Archean mentioned above, also these are the 
subject of considerable debate (e.g., de Ronde 
and Ebbesen 1996; Lowe and Byerly 2007). 

Future Directions 

Much of future work in the belt will focus around 
scientific drilling projects that are aimed at recov¬ 
ering continuous sections of well-preserved vol¬ 
canic and sedimentary rocks. Work on the 
sedimentary sequences will provide information 
about erosion and sedimentation on the early 
Earth, the composition and temperature of 
Archean seawater, and possible sites where life 



Barberton Greenstone Belt 


243 


may have emerged and evolved. The study of 
tidal sequences will provide information about 
the dynamics of the Earth-Moon system, and the 
investigation of spherule layers (including impact 
debris) provides information about the nature and 
magnitude of meteorite impacts on the early 
Earth. Work on the ultramafic to felsic volcanic 
rocks will provide new insights into volcanic 
processes, dynamics of the crust and mantle, 
and the interaction between oceanic volcanic 
crust and the hydrosphere and biosphere. The 
sources of hydrothermal fluids on the ocean 
floor, driven by the circulation of seawater 
through the volcanic pile, constitute a second 
habitat of early life. Work on deeper sections 
through the lower parts of the succession will 
provide information about tectonic processes 
that operated during deposition of volcanic, sed¬ 
imentary, and granitic rocks and during accretion 
of these materials to the continent. 


See Also 

► Archean Traces of Life 

► Barberton Supergroup 

► Chert 

► Impact Melt Rock 

► Komatiite 

► Pilbara Craton 

► Stromatolites 

References and Further Reading 

Altermann W (2001) The oldest fossils of Africa - a brief 
reappraisal of reports from the Archean. J Afr Earth 
Sci 33:427-436 

Anhaeusser CR (1980) A geological investigation of the 
Archean granite-greenstone terrane south of the 
boesmanskop syenite pluton Barberton mountain 
land. Trans Geol Soc South Afr 9:73-106 

Armstrong RA, Compston W, De Wit MJ, Williams IS 
(1990) The stratigraphy of the 3.5-3.2 Ga Barberton 
greenstone belt revisited: a single zircon ion micro¬ 
probe study. Earth Planet Sci Lett 101:90-106 

Arndt NT, Bames SJ, Lesher CM (2008) Komatiite. Cam¬ 
bridge University Press, Cambridge 

Dann JC (2000) The komati formation, Barberton green¬ 
stone belt, South Africa, part I: new map and magmatic 
architecture. S Afr J Earth Sci 6:681-730 


de Ronde CEJ, Ebbesen TW (1996) 3.2 b.y. of organic 
compound formation near seafloor hot springs. Geol¬ 
ogy 24:791-794 

de Wit MJ, Hart RA, Hart RJ (1987) The Jamestown 
ophiolite complex, Barberton mountain belt: a section 
through 3.5 Ga oceanic crust. J Afr Earth Sci 
6:681-730 

de Wit MJ, Roering C, Hart RJ, Armstrong RA, de Ronde 
CEJ, Green RWE, Tredoux M, Peberdy E, Hart RA 
(1992) Formation of an Archean continent. Nature 
357:553-562 

Duchac K, Hanor JS (1987) Origin and timing of the 
metasomatic silicihcation of an early Archean 
komatiite sequence, Barberton mountain land, South 
Africa. Precambrian Res 37:125-146 

Eriksson KA, Simpson EL (2000) Quantifying the oldest 
tidal record: the 3.2 Ga moodies group, Barberton 
greenstone belt, South Africa. Geology 28:831-834 

Furnes H, Banerjee NR, Muehlenbachs K, Staudigel H, de 
Wit MJ (2004) Early life recorded in Archean pillow 
lavas. Science 304:578-581 

Gamper A, Heubeck C, Demske D, Hoehse M (2012) 
Composition and microfacies of Archean microbial 
mats (Moodies Group, Ca. 3.22 Ga, South Africa). 
In: Noffke N, Chafetz H (eds) Microbial mats in 
siliciclastic depositional systems through time, Special 
publication 101. SEPM (Society for Sedimentary 
Geology), Tulsa, pp 65-74 

Grove TL, Parman S (2004) Thermal evolution of the 
Earth as recorded by komatiites. Earth Planet Sci Lett 
219:173-187 

Heinrichs TK, Reimer TO (1977) A sedimentary barite 
deposit from the Archean hg tree group of the Barber¬ 
ton mountain land (South Africa). Econ Geol 
72:1426-1441 

Heubeck C (2009) An early ecosystem of Archean tidal 
microbial mats (Moodies Group, South Africa, ca. 3.2 
Ga). Geology 37:931-934 

Hofmann A, Reimold UW, Koeberl C (2006) Archean 
sphemle layers in the Barberton Greenstone Belt, South 
Africa: a discussion of problematics related to the impact 
interpretation. In: Reimold WU, Gibson R (eds) Pro¬ 
cesses on the early Earth, vol 405, Geological Society 
of America special paper., pp 33-56 

Knauth LP, Lowe DR (2003) High Archean climatic tem¬ 
peratures inferred from oxygen isotope geochemistry 
of cherts in the 3.5 Ga Swaziland supergroup, South 
Africa. Geol Soc Am Bull 115:566-580 

Lopez Martinez M, York D, Hall CM, Hanes JA 
(1984) Oldest reliable 40Ar/39Ar ages for terrestrial 
rocks: Barberton mountainland komatiites. Nature 
307:352-354 

Lowe DR, Byerly GR (eds) (1999a) Geologic evolution of 
the barberton greenstone belt, South Africa. Geologi¬ 
cal Society of America special paper 329, p 312 

Lowe DR, Byerly GR (2007) Ironstone bodies of the 
Barberton greenstone belt, South Africa: products of 
a cenozoic hydrological system, not Archean hydro- 
thermal vents! Geol Soc Am Bull 119:65-87 




244 


Barberton Greenstone Belt, Sedimentology 


Lowe DR, Knauth LP (1977) Sedimentology of the 
onverwacht group (3.4 billion years), transvaal, 
South Africa, and its bearing on the characteristics 
and evolution of the early Earth. J Geol 85:699-723 

Lowe DR, Byerly GR, Kyte F, Shukolyukov A, Asaro F, 
Krull A (2003) Spherule beds 3.47-3.24 billion years 
old in the Barberton greenstone belt, South Africa: a 
record of large meteorite impacts and their influence 
on early crustal and biological evolution. Astrobiology 
3:7—48 

Lowe DR, Byerly GR, Heubeck C (2012) Geologic map of 
the west-central Barberton Greenstone Belt, South 
Africa, scale 1:25,000: Geol Soc America Map and 
Chart Series No. 103 

Nesbitt RW, Sun S-S (1976) Geochemistry of Archean 
spinifex-textured peridotites and magnesian and 
low-magnesian tholeiites. Earth Planet Sci Lett 
31:433^153 

Russell MJ, Hall AJ, Boyce AJ, Fallick AE (2005) On 
hydrothermal convection systems and the emergence 
of life. Econ Geol 100:419-138 

Tice MM, Lowe DR (2006) The origin of carbonaceous 
matter in pre-3.0 Ga greenstone terrains: a review and 
new evidence from the 3.42 Ga buck reef chert. Earth 
Sci Rev 76:259-300 

Viljoen MJ, Viljoen RP (1969) Evidence for the existence 
of a mobile extrusive peridotitic magma from the 
Komati Formation of the Onverwacht Group. Trans 
Geol Soc S Afr Spec Publ 21:87-112 

Walsh MM (1992) Microfossils and possible microfossils 
from the early Archean onverwacht Group, Barberton 
mountain land, South Africa. Precambrian Res 
54:271-293 

Westall F, de Wit MJ, Dann JC, van der Gaast S, de Ronde 
CEJ, Gemeke D (2001) Early Archean fossil bacteria 
and biofilms in hydrothermally influenced sediments 
from the Barberton greenstone belt, South Africa. Pre¬ 
cambrian Res 106:93-116 


Barberton Greenstone Belt, 
Sedimentology 

Axel Hofmann 

Department of Geology, University of 
Johannesburg, Auckland Park, Johannesburg, 
South Africa 


Keywords 

Archean Eon; Chert; Sedimentary rock; Exoge¬ 
nous; Onverwacht Group; Fig Tree Group; 
Moodies Group 


Definition 

► Sedimentary rocks can be found throughout the 

► Barberton Supergroup. In the volcano¬ 
sedimentary Onverwacht Group, sedimentary 
rocks make up less than 5 % of the succession. 
They consist of bedded ► cherts, representing a 
variety of silicified clastic, chemical, and biogenic 
sediments. Deep- to shallow-marine, fine-grained 
siliciclastic sedimentary rocks make up the domi¬ 
nant part of the Fig Tree Group. The Moodies 
Group is characterized by relatively coarse¬ 
grained, siliciclastic, alluvial, fluvial, shoreline, 
and shallow-marine deposits. Detailed sedimento- 
logical and geochemical studies of the sedimen¬ 
tary rocks of the Barberton Supergroup have 
provided major advances in the understanding of 
surface processes in the Paleo- and Mesoarchean. 

Overview 

Bedded chert horizons of the Onverwacht Group 
are typically 1-20 m thick and represent interflow 
sedimentary units that were deposited on the sea¬ 
floor between phases of extrusive submarine vol¬ 
canic activity. The cherts consist of a variety of 
silicified sediments (Lowe 1999; Tice and Lowe 
2006; Hofmann et al. 2013). Extensive early silic- 
ification took place as a result of low-temperature 
hydrothermal activity on the seafloor, resulting in 
excellent preservation of the sedimentary strata. 
Silicified volcaniclastic sediments are common 
and include silicified beds of ultramafic to mafic 
ash and accretionary lapilli. Laminated cherts of 
various shades of gray to black represent mix¬ 
tures of volcaniclastic material and carbonaceous 
matter (Fig. 1). Deposition took place in 
low-energy, predominantly sub-wave base set¬ 
tings with episodic, high-energy current events 
during which coarse-grained volcaniclastic mate¬ 
rial and, in rare cases, meteorite impact ► ejecta 
were deposited. Cherts have been used exten¬ 
sively to study surface processes, seawater com¬ 
position, and life in the Archean. 

The Fig Tree Group consists of a 2-3 km 
thick, largely siliciclastic, and volcaniclastic 
sequence that is capped by felsic volcanic and 




Barberton Greenstone Belt, Sedimentology 


245 


Barberton Greenstone 
Belt, Sedimentology, 

Fig. 1 Carbonaceous chert 
with discontinuous layers 
of silicified ultramafic ash 
(gray chert ) showing ripple 
lamination (characteristic 
of subaqueous deposition). 
Onverwacht Group, 
Kromberg Formation, Farm 
Josefsdal 



volcaniclastic rocks (Heinrichs 1980; Lowe and 
Nocita 1999; Hofmann 2005). In the southern 
part of the belt, a variety of siliciclastic 
lithofacies with abundant felsic volcanic detritus 
are present that formed in deep- to shallow-water, 
fan delta, and alluvial environments (southern 
facies). The local presence of beds of jaspilitic 
banded iron formation, chert, and barite indicates 
syndepositional hydrothermal activity. In the 
northern part of the Barberton greenstone belt, 
the Fig Tree Group is mainly characterized by 
turbiditic sandstones and shales that formed in 
relatively deepwater environment (northern 
facies). Several spherule beds of quenched liquid 
silicate droplets in the Fig Tree Group represent 
fallout and partially tsunami-reworked meteorite 
impact deposits (Lowe et al. 2003). 

The ► Moodies Group consists of up to 3.7 km 
thick, quartz-rich, predominantly arenaceous 
rocks, in contrast to the quartz-poor and matrix- 
rich Fig Tree graywackes. It consists of alluvial 
conglomerate, braided fluvial, tidal and shallow- 
marine sandstones, and minor siltstone, jaspilite, 
and banded iron formation (Anhaeusser 1976; 
Heubeck and Lowe 1994). Intertidal sedimentary 
rocks are locally well preserved. Tidal bundles 
and microbial mat-related sedimentary structures 
have been reported (Heubeck and Lowe 1994; 
Eriksson and Simpson 2000). Moodies strata 
may include some of the oldest preserved aeolian 
deposits (Simpson et al. 2012). Deposition of the 
Moodies Group was syntectonic with final green¬ 
stone belt deformation and occurred within only a 


few Ma under initially extensional and later com- 
pressional deformation (Heubeck et al. 2013). 


See Also 

► Archean Environmental Conditions 

► Barberton Greenstone Belt 

► Barberton Greenstone Belt, Traces of Early 
Life 

► Chert 

► Earth, Formation and Early Evolution 

► Ejecta 

► Greenstone Belts 

► Sedimentary Rock 

References and Further Reading 

Anhaeusser CR (1976) The geology of the Sheba hills area 
of the Barberton mountain land, South Africa, with 
particular reference to the Eureka syncline. Trans 
Geol Soc S Afr 79:253-280 

Eriksson KA, Simpson EL (2000) Quantifying the oldest 
tidal record: the 3.2 Ga Moodies Group, Barberton 
greenstone belt, South Africa. Geology 28:831-834 

Heinrichs T (1980) Lithostratigraphische Untersuchungen 
in der Fig Tree Gruppe des Barberton Greenstone Belt 
zwischen Umsoli und Lomati (Siidafrika). Gottinger 
Arb Geol Palaont 22:118 

Heubeck C, Lowe DR (1994) Depositional and tectonic 
setting of the Archean Moodies Group, Barberton green¬ 
stone belt, South Africa. Precambrian Res 68:257-290 

Heubeck C, Engelhardt J, Byerly GR, Zeh A, Sell B, 
Luber T, Lowe DR (2013) Timing of deposition and 
deformation of the Moodies Group (Barberton 






246 


Barberton Greenstone Belt, Traces of Early Life 


greenstone belt, South Africa): very-high-resolution of 
Archaean surface processes. Precambrian Res 
231:236-262 

Hofmann A (2005) The geochemistry of sedimentary 
rocks from the Fig Tree Group, Barberton greenstone 
belt: implications for tectonic, hydrothermal and sur¬ 
face processes during mid-Archaean times. Precam¬ 
brian Res 143:23^19 

Hofmann A, Bolhar R, Orberger B, Foucher F (2013) 
Cherts of the Barberton greenstone belt: petrology 
and trace-element geochemistry of 3.5 to 3.3 Ga old 
silicified volcaniclastic sediments. South African Jour¬ 
nal of Geology 116:297-322 

Lowe DR (1999) Petrology and sedimentology of cherts 
and related silicified sedimentary rocks in the Swazi¬ 
land supergroup. In: Lowe DR, Byerly GR (eds) Geo¬ 
logic evolution of the Barberton greenstone belt, 
vol 329. Geol Soc Am Spec Pap, South Africa, 
pp 83-114 

Lowe DR, Nocita BW (1999) Foreland basin sedimenta¬ 
tion in the Mapepe formation, southern-facies Fig tree 
group. In: Lowe DR, Byerly GR (eds) Geologic evo¬ 
lution of the Barberton greenstone belt, vol 329. Geol 
Soc Am Spec Pap, South Africa, pp 233-258 

Lowe DR, Byerly GR, Kyte F, Shukolyukov A, Asaro F, 
Krull A (2003) Spherule beds 3.47-3.24 billion years 
old in the Barberton Greenstone Belt, South Africa: a 
record of large meteorite impacts and their influence 
on early crustal and biological evolution. Astrobiology 
3:7—48 

Simpson EL, Eriksson KA, Muller WU (2012) 3.2 Ga 
eolian deposits from the Moodies Group, Barberton 
greenstone belt, South Africa: implications for the 
origin of first-cycle quartz sandstones. Precambrian 
Res 214-215:185-191 

Tice MM, Lowe DR (2006) The origin of carbonaceous 
matter in pre-3.0 Ga greenstone terrains: a review and 
new evidence from the 3.42 Ga Buck Reef Chert. Earth 
Sci Rev 76:259-300 


Barberton Greenstone Belt, Traces of 
Early Life 

Frances Westall 

Centre de Biophysique Moleculaire, CNRS, 
Orleans Cedex 2, France 


Keywords 

Early Archaean; Biosignatures; Early life; Pro¬ 
karyotes; Microfossils; Carbon isotopes; Basalt; 
Volcanic sediments; Anaerobic photosynthesis; 
Chemolithotrophy 


Synonyms 

Early Archean; Early life 

Definition 

The Barberton Greenstone Belt of South Africa 
and Swaziland, together with the greenstone belts 
of the Pilbara region in Australia, hosts the oldest 
(3.5-3.3 Ga) well-preserved rocks containing 
fossil signatures of life. These traces occur in 
thin layers of volcaniclastic sediments, 
sandwiched between thick successions of mafic 
to ultramafic volcanic lavas. The remains of 
microbial mats are relatively common in 
shallow-water deposits, while deeper-water 
deposits contain reworked, detrital remains of 
organic matter and microbial mats. Somewhat 
younger clastic sediments of the 3.2 Ga-old 
Moodies Group have yielded relatively large cel¬ 
lular remains of possible planktonic organisms 
and abundant microbial mats. 

Overview 

The early to mid-Archaean (3.5-3.2 Ga) Barber¬ 
ton Greenstone Belt consists of kilometer-thick, 
largely subaqueous volcanic rocks and their ero- 
sional products and of sedimentary rocks includ¬ 
ing Banded Iron Formations (BIFs), cherts, shales, 
barite, siltstones, sandstones, and conglomerates. 
Largely basic to ultrabasic lavas were extruded 
onto relatively shallow-water platforms. Inter¬ 
spersed with the volcanics are thin horizons of 
volcaniclastic and hydrothermal sediments depos¬ 
ited in water depths ranging from littoral to 
sub-wave base. Early diagenetic silicification of 
sediments and underlying volcanics was related to 
circulating hydrothermal fluids (Hofmann and 
Bohlar 2007) and seawater oversaturation with 
respect to silica (Lowe and Byerly 1986). The 
cherts and unsilicified siliciclastic sediments host 
a variety of traces of early life. 

Early studies reported the occurrence of pos¬ 
sible cellular microfossils (e.g., Knoll and 
Barghoorn 1977). Microbial corrosion features, 




Barberton Greenstone Belt, Traces of Early Life 


247 




Barberton Greenstone Belt, Traces of Early Life, 
Fig. 1 (a) Purported microbial tunnels in the vitreous 
rind of an ~3.5 Ga-old pillow lava from the Barberton 
Greenstone Belt (Furnes et al. 2004). (b) Silicified colony 
of chemolithotrophic microorganisms on the surface of a 
volcanic particle in silicified volcaniclastic sediments 
from the Pilbara, Australia (Westall et al. 2006a). (c) 
Thin-section micrograph of possible photosynthetic 


filamentous microbial mat from ~3.4 Ga-old cherts from 
Barberton (Walsh 2004). (d) Well-preserved silicified fil¬ 
aments in a 3.3 Ga-old microbial mat from Barberton 
(Westall et al. 2006b). (e) Acritarch (organic-walled ves¬ 
icle of unknown biological affinity) from 3.2 Ga-old 
siliciclastic sediments from the Moodies Group, Barber¬ 
ton (Javaux et al. 2010) 


typical of those produced by chemolithotrophic 
microorganisms in the vitreous rinds of pillow 
lavas, were described by Fumes et al. (2004, 
2007) from the Kromberg Formation 
(ca. 3.4 Ga), but their biogenicity has yet to be 


confirmed (McLoughlin et al. 2012; Grosch 
et al. 2014). The hollow structures in the surfaces 
of the pillow basalts are lined by Ti-oxides that 
contain early sulfide inclusions showing 5 34 S 
depletions (8-45 %o) which is consistent with an 










248 


Barberton Greenstone Belt, Traces of Early Life 


early microbial origin for the sulfides. No micro¬ 
fossils are associated with these tunnels. Fossil¬ 
ized colonies of chemotrophic organisms that 
could have produced such features have also 
been described in similarly aged strata 
(3.446 Ga) (Westall et al. 2006a, 2011a) from 
the Pilbara, Australia (Fig. 1). 

The surfaces of volcaniclastic sediments 
deposited in shallow-water environments were 
host to microbial mats and biofilms which prob¬ 
ably formed by anaerobic photo synthetic organ¬ 
isms. When observed in petrographical thin 
sections, they are characterized by packets of 
fine-grained, carbon-rich layers that form more 
or less continuous wispy, wavy horizons on sed¬ 
iment surfaces (Walsh 1992, 2004; Walsh and 
Lowe 1999; Tice and Lowe 2004, 2006; Tice 
2009). Tice (2009) demonstrated that environ¬ 
mental factors, such as current energy, controlled 
the style of microbial mats preserved in the 
3.42 Ga-old Buck Reef Chert. Formed at water 
depths between storm base and fair-weather wave 
base, anastomosing and mesh-like mats occur in 
sediments consisting of coarse-grained fluffy car¬ 
bonaceous grains, while finely laminated mats 
occur in finer-grained sediments deposited 
under quiet conditions. 

Rarely, carbonaceous filaments are observed 
in silicified interstitial spaces between mat layers 
(Walsh 1992). Although the organisms forming 
the mats are seldom preserved, a scanning elec¬ 
tron microscope study of an extremely well- 
preserved silicified biofilm documented the 
presence of filaments 0.25 pm in diameter and 
tens of microns in length embedded in chert 
interpreted as thick polymer on the mat surface 
(Westall et al. 2006b). Detailed in situ morpho¬ 
logical and geochemical analysis of this particu¬ 
lar biofilm demonstrated that the biofilm had 
been undergoing incipient calcification, probably 
due to the action of sulfate-reducing microorgan¬ 
isms degrading the lower, dead layers of the 
biofilm prior to early silicification that preserved 
it in three dimensions (Westall et al. 2011b). 

The silicified sediments also contain detrital 
particles of carbon that may be derived from 
microbial colonies. Thus, carbon and sulfur iso¬ 
tope signatures have been interpreted to indicate 


the presence of a variety of microbial organisms 
including photosynthesizers (pelagic as well as 
benthonic), heterotrophs such as methanogens, 
and chemotrophs (see review in Westall 2011). 

Younger littoral sediments from the 3.2 Ga-old 
Moodies Group have revealed a wealth of fossil 
microbial structures. Crinkled, domed, and anas¬ 
tomosing photosynthetic microbial mats occur on 
the surfaces of coarse-grained, tidal-zone sand¬ 
stones (Noffke et al. 2006; Heubeck 2009). Cor¬ 
relative siltstones have yielded compressed 
remains of large (up to 300 pm diameter) organic, 
hollow, spherical structures (acritarchs) 
interpreted as unicellular microorganisms or colo¬ 
nial envelopes (Javaux et al. 2010), thus 
documenting the existence of a diverse biota. 

See Also 

► Anoxygenic Photosynthesis 

► Archean Traces of Life 

► Barberton Greenstone Belt 

► Biomarkers 

► Chemolithotroph 

► Microbial Mats 

► Microfossils 

► Pilbara Craton 


References and Further Reading 

Fumes H, Banerjee NR, Muehlenbachs K, Staudigel H, de 
Wit M (2004) Early life recorded in Archean pillow 
lavas. Science 304:578-581 

Furnes H, Banerjee NR, Staudigel H, Muehlenbachs K, 
McLoughlin N, de Wit M, van Kranendonk M (2007) 
Comparing petrographic signatures of bioalteration in 
recent to Mesoarchean pillow lavas: tracing subsurface 
life in oceanic igneous rocks. Precambrian Res 
158:156-176 

Grosch EG, McLoughlin N, Lanari P, Erambert M, Vidal 
O (2014) Microscale mapping of alteration conditions 
and potential biosignatures in basaltic-ultramahc rocks 
on early Earth and beyond. Astrobiology 14:216-228 

Heubeck C (2009) An early ecosystem of Archean tidal 
microbial mats (Moodies Group, South Africa, ca. 3.2 
Ga). Geology 37:931-934 

Hofmann A, Bolhar R (2007) The origin of carbonaceous 
cherts in the Barberton Greenstone Belt and their sig¬ 
nificance for the study of early life in mid-Archaean 
rocks. Astrobiology 7(2):355-388 



Barberton Supergroup 


249 


Javaux EJ, Marshall CP, Bekker A (2010) Organic-walled 
microfossils in 3.2-billion-year-old shallow-marine 
siliciclastic deposits. Nature 463:934-938 
Knoll AH, Baghoorn ES (1977) Archean microfossils 
showing cell division from the Swaziland system of 
South Africa. Science 198:396-398 
Lowe DR, Byerly GR (1986) Archean flow-top alteration 
zones formed initially in a low-temperature sulphate- 
rich environment. Nature 342:245-248 
McLoughlin N, Grosch EG, Kilbum MR, Wacey D (2012) 
Sulfur isotope evidence for a Paleoarchean subseafloor 
biosphere, Barberton, South Africa. Geology 
40:1031-1034 

Noffke N, Eriksson K, Hazen RM, Simpson EL (2006) 
A new window into early Archean life: microbial mats 
in Earth’s oldest siliciclastic tidal deposits (3.2 Ga 
Moodies Group, South Africa). Geology 34:253-256 
Tice M (2009) Environmental controls on photo synthetic 
microbial mat distribution and morphogenesis on a 
3.42 Ga clastic-starved platform. Astrobiology 9 
(10):989-1000 

Tice M, Lowe DR (2004) Photosynthetic microbial mats 
in the 3,416-Myr-old ocean. Nature 431:549-552 
Tice MM, Lowe DR (2006) The origin of carbonaceous 
matter in pre-3.0 Ga greenstone terrains: a review and 
new evidence from the 3.42 Ga Buck Reef Chert. Earth 
Sci Rev 76:259-300 

Walsh MM (1992) Microfossils and possible microfossils 
from the early Archean Onverwacht Group, Barberton 
Mountain Land, South Africa. Precambrian Res 
54:271-293 

Walsh MM (2004) Evaluation of early Archean 
volcaniclastic and volcanic flow rocks as possible 
sites for carbonaceous fossil microbes. Astrobiology 
4:429-437 

Walsh MM, Lowe DR (1999) Modes of accumulation of 
carbonaceous matter in the early Archaean: a petro¬ 
graphic and geochemical study of carbonaceous cherts 
from the Swaziland Supergroup. In: Lowe DR, Byerly 
GR (eds) Geologic evolution of the Barberton green¬ 
stone belt, South Africa. Geological Society of Amer¬ 
ica Special Paper, 329, Boulder, Colorado, pp 115-132 
Westall F (2011) Early life. In: Gargaud M (ed) Origins of 
life, an astrobiology perspective. Cambridge Univer¬ 
sity Press, Cambridge, pp 391^-13 
Westall F, de Vries ST, Nijman W, Rouchon V, Orberger B, 
Pearson V, Watson J, Verchovsky A, Wright I, Rouzaud 
J-N, Marchesini D, Anne S (2006a) The 3.466 Ga 
Kitty’s Gap Chert, an early Archaean microbial ecosys¬ 
tem. In: Reimold WU, Gibson R (eds) Processes on the 
early Earth, vol 405, Geological Society of America 
Special Paper. Geological Society of America, Boulder, 
pp 105-131 

Westall F, de Ronde CEJ, Southam G, Grassineau N, 
Colas M, Cockell C, Lammer H (2006b) Implications 
of a 3.472-3.333 Ga-old subaerial microbial mat from 
the Barberton greenstone belt, South Africa for the UV 
environmental conditions on the early Earth. Philos 
Trans R Soc London Ser B 361:1857-1875 


Westall F, Foucher F, Cavalazzi B, de Vries ST, 
Nijman W, Pearson V, Watson J, Verchovsky A, 
Wright I, Rouzaud JN, Marchesini D, Anne S 
(2011a) Early life on Earth and Mars: a case study 
from ~3.5 Ga-old rocks from the Pilbara, Australia. 
Planet Space Sci 59:1093-1106 
Westall F, Cavalazzi B, Lemelle L, Marrocchi Y, Rouzaud 
JN, Simionovici A, Salome M, Mostefaoui S, 
Andreazza C, Foucher F, Toporski J, Jauss A, 
Thiel V, Southam G, MacLean L, Wirick S, 
Hofmann A, Meibom A, Robert F, Defarge 
C (201 lb) Implications of in situ calcification for pho¬ 
tosynthesis in a ~3.3 Ga-old microbial biofilm from the 
Barberton greenstone belt, South Africa. Earth Planet 
Sci Lett 310:468^179 


Barberton Supergroup 

Axel Hofmann 

Department of Geology, University of 
Johannesburg, Auckland Park, Johannesburg, 
South Africa 


Synonyms 

Swaziland Supergroup (outdated) 

Definition 

The volcano-sedimentary sequence that forms 
the Barberton greenstone belt has been grouped 
stratigraphically as the Barberton Supergroup, 
renamed from the Swaziland Supergroup of 
older literature. The Barberton Supergroup 
formed ca. 3.55-3.22 Ga ago and is subdivided 
in ascending order into three major stratigraphic 
units: (1) The Onverwacht Group dominantly 
consists of submarine ultramafic-mafic volcanic 
rocks and minor felsic volcanic and silicified 
► sedimentary rocks. (2) The Fig Tree Group is 
comprised of shale, graywacke, and felsic 
volcaniclastic rocks with minor conglomerate, 
chert, baryte, and banded iron formation. 
(3) The Moodies Group consists of shallow 
marine to fluvial sandstone and conglomerate 
with minor felsic and mafic volcanics, shale, 
and banded iron formation. These groups have 





250 


Barophile 


been subdivided in to a number of formations 
which differ in lithology, thickness, and facies 
across the major fault zones that separate the 
Barberton greenstone belt into discrete fault- 
bounded segments. The excellent degree of pres¬ 
ervation and exposure, continuous outcrop of 
mostly subvertically dipping strata, and the high 
lithologic variability made possible the detailed 
mapping of the units of the Barberton Super¬ 
group. This in turn provided the base for targeted 
sampling and major contributions to the under¬ 
standing of the Archean. 

See Also 

► Archean Environmental Conditions 

► Barberton Greenstone Belt 

► Barberton Greenstone Belt, Sedimentology 

► Barberton Greenstone Belt, Traces of Early 
Life 

► Earth, Formation and Early Evolution 

► Greenstone Belts 


Barophile 

► Piezophile 


Barycenter 

David W. Latham 

Harvard-Smithsonian Center for Astrophysics, 
Cambridge, MA, USA 

Synonyms 

Center of mass 


Definition 

In astronomy, the barycenter is the center of mass 
of a system of two or more bodies. For the 


purposes of most calculations, the system can be 
considered to be concentrated at the position of 
the barycenter, with a total mass equal to the sum 
of the masses of the individual objects. The 
barycentric radial velocity of an object, such as 
a star, as measured by a terrestrial observer is 
calculated relative to the center of mass of the 
Solar System. This is slightly different from the 
heliocentric velocity of such a star, which is cen¬ 
tered on the Sun and varies slightly with time 
according to the position of the planets (since 
the motion of the planets produces slight changes 
in the Solar System’s barycenter). 

See Also 

► Astrometric Planets 


Barycenter Velocity 

► Center of Mass Velocity 


Barite 

Christoph Heubeck 

Institut fur Geowissenschaften, Friedrich- 
Schiller-Universitat Jena, Jena, Germany 

Definition 

Barite (also Baryte), BaS04, is a widespread, 
usually white or colorless mineral which can be 
deposited by biogenic, hydrothermal, and evapo- 
ritic processes. In sedimentary environments, the 
main sources of barium ions are submarine 
hydrothermal vents; the sulphate ion is common 
in Phanerozoic seawater. 

The origin of primary stratiform bladed baryte 
crystals on Archean sea floors (“crystal lawns”) is 
debated because the highly oxidized sulfate ion is 
generally thought to have been in short supply in 
Archean oceans. However, some of these barite 







Basic and Acid Rock 


251 


deposits may have formed from sulfate which had 
been generated photolytically as aerosols in the 
Archean atmosphere and then washed into the 
oceans. Others may be late-diagenetic pseudo- 
morphs after calcium sulphate. Studies on 
S isotopes indicate that some barite played a 
role in bacterial sulphate reduction, one of the 
earliest metabolic processes. 


Basalt 

Nicholas Arndt 

ISTerre, Universite Grenoble Alpes, France 


Definition 

Basalt is a fine-grained, dark-colored mafic volca¬ 
nic rock composed of plagioclase, ortho- or 
clinopyroxene, and minor Fe-Ti oxides, with or 
without olivine. Porphyritic samples contain large 
crystals (phenocrysts) of olivine, pyroxene, or pla¬ 
gioclase dispersed in a fine-grained glassy matrix, 
also called groundmass. Gas-rich samples contain 
abundant vesicles. Basalt contains 45-52 % Si0 2 
and 40-90 % ferromagnesian minerals. Basalt 
empts as pillow lava, thick sheet flows, or frag¬ 
mental scoria. It is the most common rock of the 
Earth’s ► oceanic cmst and in lunar maria (ancient 
flood-basalt plains corresponding to the dark sur¬ 
faces of the ► Moon). Basalt is also present in the 
cmst of ► Mars and ► Venus. It forms by partial 
melting of the mantle and erupts in diverse tec¬ 
tonic settings: mid-ocean ridges, oceanic islands, 
subduction zones, continental rifts, and volcanic 
plateaus. 


See Also 

► Igneous Rock 

► Mafic and Felsic 

► Mars 

► Moon, The 

► Oceanic Crust 

► Venus 


Basaltic Flood Plains 

► Mare, Maria 

► Trapps 


B 


Base Pair 

Juli Pereto 

Institut Cavanilles de Biodiversitat i Biologia 
Evolutiva, Universitat de Valencia, Valencia, Spain 


Definition 

Base pair is a pair of nucleic acid bases each in a 
different nucleotide monomer in the same 
(intramolecular) or different (intermolecular) 
► nucleic acid strands and linked to one another 
by specific hydrogen bonds. The canonical base 
pairs in ► DNA (Watson-Crick pairs) contain one 
purine and one pyrimidine in antiparallel posi¬ 
tions: adenine binds thymine in DNA - uracil in 
RNA (through two hydrogen bonds) - and gua¬ 
nine binds cytosine (through three hydrogen 
bonds). There are also many examples of 
non-Watson-Crick pairing, especially in three- 
dimensional structures of RNAs. 


See Also 

► Anticodon 

► Codon 

► DNA 

► Genetic Code 

► Nucleic Acid Base 

► Nucleic Acids 

► RNA 

► Wobble Hypothesis (Genetics) 


Basic and Acid Rock 

► Mafic and Felsic 








252 


Bathybius Haeckelii 


Bathybius Haeckelii 

Stephane Tirard 

Centre Francois Viete d’Histoire des Sciences et 
des Techniques EA 1161, Faculte des Sciences et 
des Techniques de Nantes, Nantes, France 

Definition 

In June 1857, the Britannic ship “The Cyclops” 
found a very special matter on the bottom of the 
North Atlantic Ocean. Some chemists and biolo¬ 
gists considered that is was a very simple living 
matter and thought that it resolved the problem of 
the origin of life. Indeed, according to them, it 
constituted an example of spontaneous genera¬ 
tion and a link between inert matter and living 
matter. Thomas Huxley (1825-1895) himself 
named it Bathybius haeckelii. However, in 
1876, a chemist revealed that it was calcium 
sulfate and not living matter. 

Discussions about Bathybius took place dur¬ 
ing the period of the debate about spontaneous 
generations. Therefore, during few years the pos¬ 
sibility of the production of this matter, very 
closed to living matter, was highly considered 
by many chemists and biologists. 

See Also 

► Huxley’s Conception on Origins of Life 

► Protoplasmic Theory of Life 


Beagle 2 

Frances Westall 

Centre de Biophysique Moleculaire, CNRS, 
Orleans, Cedex 2, France 

Definition 

The Beagle 2 lander, named after the famed ship in 
which Charles Darwin traveled the world, was part 


of the ► European Space Agency’s Mars Express 
mission. It was launched in June 2003 and was 
supposed to land in December 2003. Unfortu¬ 
nately, all contact with the 33.2 kg lander was 
lost a few days before touchdown, and its fate 
remains a mystery. The lander was a compact 
assemblage of instruments designed to address sci¬ 
ence questions ranging from the search for traces of 
past and extant life, measurement of the composi¬ 
tion of the atmosphere and other environmental 
parameters, the oxidation state at the surface, and 
analysis of the geomorphology of the landing site 
in a sedimentary Basin of Isidis Planitia. 

Overview 

The lander was constmcted by a British consortium, 
coordinated by Prof. Colin Pillinger of the Open 
University. It was equipped with a 75 cm long 
robotic arm holding at its end an array of instru¬ 
ments called the PAW (Payload Adjustable Work¬ 
bench) that included stereo cameras, a Mossbauer 
spectrometer to measure the oxidation states of 
iron-containing compounds, an X-ray spectrometer 
for determining mineral composition, and a 
(dentist’s) drill for collecting samples. Also 
onboard the lander was a gas analysis package 
(GAP) that included a gas chromatograph-mass 
spectrometer to analyze carbon isotopes as a signa¬ 
ture for life. Finally, a “mole” or subsurface sam¬ 
pler (PLUTO - Planetary Undersurface Tool) was 
designed to penetrate beneath the loose regolith 
surface to obtain samples for analysis. 

The 1 m diameter lander was equipped with a 
UHF radio antenna, telecommunications, a bat¬ 
tery, electronic processors, heaters, solar panels, 
and other payload instruments, such as radiation 
and oxidation sensors to address the environmen¬ 
tal objectives of the mission. Upon arrival, the 
lander was supposed to have broadcast a piece of 
music specially composed by the British rock 
band Blur. 

Various hypotheses involving malfunctioning 
of various pieces of equipment have been put 
forward to explain the failure of the mission. 
The lander could have bounced off the atmo¬ 
sphere of Mars and burned up, or the parachute 





Benthic Mats 


253 


Belcher Group, 
Microfossils, Fig. 1 The 

mat-building colony of the 
cyanobacteria 
Eoentophysallis 
belcherensis, preserved in 
stromatolites of the 1.5 Ga 
Bil’yakh Group, Siberia 
(Photograph courtesy of 
A. Knoll) 



failed to deploy and/or the airbags did not func¬ 
tion and the lander crashed onto the Martian 
surface, or perhaps the backshell became 
entangled with the parachute, the parachute 
could have covered the lander, thus preventing 
it from opening. At the beginning of 2015 it was 
announced that the orbital camera around Mars, 
HiRISE, had found the lander intact on the mar¬ 
tian surface, within the expected landing ellipse 
in Isidis Planitia but, unfortunately, it appeared to 
be only partially deployed. However, it can be 
demonstrated that the entry, descent and landing 
system did indeed work. 

References and Further Reading 

http://www.beagle2.com/index.htm 


Belcher Group, Microfossils 

Emmanuelle J. Javaux 
Palaeobiogeology-Palaeobotany- 
Palaeopalynology, Geology Department, 
Universite de Liege, Liege, Belgium 

Definition 

The Belcher Group comprises ► sedimentary 
rocks from the Belcher Islands, Canada, dated at 


1.9 Ga. These rocks include ► chert lenses and 
nodules in silicified ► stromatolites growing 
in tidal and shallow subtidal waters on a carbon¬ 
ate platform. The cherts contain tridimensionally 
preserved filamentous and coccoidal (spheroidal) 

► microfossils, including fossilized colonies of 
microscopic pigmented cells. The distribution 
and pattern of division of these later microfossils 
(called Eoentophysallis belcherensis) suggest 
a relationship to the extant genera of 

► cyanobacteria Entophysallis. These microfos¬ 
sils represent some of the oldest remains of 
identified cyanobacteria, together with cyst-like 
cyanobacteria microfossils (akinetes) from 
Gabon dated at 2.1 Ga (Fig. 1). 


See Also 

► Chert 

► Cyanobacteria 

► Fossilization, Process of 

► Microbial Mats 

► Microfossils 

► Sedimentary Rock 

► Stromatolites 


Benthic Mats 

► Microbial Mats 






254 


Benzene 


Benzene 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 

Synonyms 

C 6 H 6 ; Cyclohexa-l,3,5-triene 

Definition 

Benzene is an ► aromatic hydrocarbon in which 
the six carbon atoms are arranged in a ring, with 
all carbon bonds equal and intermediate in length 
between single and double bonds. Under standard 
laboratory conditions benzene is a colorless and 
highly flammable liquid with a sweet smell. Ben¬ 
zene is a known carcinogen and has various toxic 
effects on humans. 

History 

Benzene was first isolated by the English chemist/ 
physicist Michael Faraday in 1825, although the 
natural aromatic resin that contains benzene comes 
from Southeast Asia and was known to Arab 
traders during the Middle Ages. The cyclic struc¬ 
ture of benzene was announced in 1865 by the 
German chemist Friedrich A. Kekule, with the 
data on carbon bond lengths coming from X-ray 
diffraction measurements. An astronomical detec¬ 
tion in the protoplanetary nebula CRL 618 has 
been reported by Cemicharo et al. (2001) from 
mid-infrared observations, and the measured abun¬ 
dance is matched by chemical models (Woods 
et al. 2003). In the Solar System benzene has 
been observed in the atmospheres of Jupiter, Saturn 
and Saturn’s moon Titan (Fouchet et al. 2005). 

See Also 

► Aromatic Hydrocarbon 

► Molecules in Space 


► Planetary Nebula 

► Titan 


References and Further Reading 

Cemicharo J, Heras AM, Tielens AGGM, Pardo JR, 
Herpin F, Guelin M, Waters LBFM (2001) Infrared 
space observatory’s discovery of C 4 H 2 , C 6 H 2 , and 
benzene in CRL 618. Astrophys J 546:L123-L126 
Fouchet T, Bezard B, Encrenaz T (2005) The planets and 
titan observed by ISO. Space Sci Rev 119:123-139 
Woods PM, Millar TJ, Herbst E, Zijlstra AA (2003) The 
chemistry of protoplanetary nebulae. Astron 
Astrophys 402:189-199 


Bernal's Conception of Origins of Life 

Stephane Tirard 

Centre Francis Viete d’Histoire des Sciences et 
des Techniques EA 1161, Faculte des Sciences et 
des Techniques de Nantes, Nantes, France 

Keywords 

Clays; Catalysis 

History 

John Desmond Bernal was a pioneer of diffrac¬ 
tion X-ray method. His interest for biology 
increased during the 1930s and the 1940s, prob¬ 
ably in relation with the study of biological mol¬ 
ecules (peptides, nucleic acids, etc.) with this new 
physical method. 

His work on the origin of life was marked by 
his first publication on this topic in 1951: a little 
book entitled The Physical Basis of Life, which 
came from a previous lecture (1947) and from a 
paper published in 1949 in the Proceedings of the 
Physical Society. 

In this text, Bemal gave a synthesis of previ¬ 
ous theories, that is, Oparin’s (1924, 1938), 
Haldane’s (1929), or Dauvillier’s (1947) ones. 





Beta Pictoris b 


255 


Such as he claimed that primitive atmosphere of 
earth contained C0 2 , he described the possibility 
of a progressive production of organic molecules 
and finally of life. 

His main and original assumption regarded 
problems of dispersion and catalysis. Indeed, 
Bernal claimed that fundamental reactions could 
exist on clay deposits, marine, and freshwater, 
which could insure confinement and catalysis. 

During the 1950s and 1960s, he actively par¬ 
ticipated in the scientific debates on the origin of 
life and was very active in the diffusion of ideas 
on the origin of life. 

See Also 

► Haldane’s Conception of Origins of Life 

► Oparin’s Conception of Origins of Life 

► Origin of Life 


References and Further Reading 

Bernal JD (1951) The physical basis of life. Routledge and 
Kegan Paul, London 

Bernal JD (1967) The origin of life. Weidenfeld and 
Nicholson, London 

Dauvillier A (1947) Genese, nature et evolution des 
planetes. Hermann, Paris 

Haldane JBS (1929) The origin of life. The Rationalist 
Annual , London, pp 242-249 

Oparia AI (1924) Proishkozhdeute Zhiui (The origin of 
life), Auu Syage Tvaus. In: Bemol JD (ed) The origin 
of Life. Weidenfeld and Nicolson, London, 1967 

Operia AI (1938) The origin of life. MacMillan, 
New York 


Bet Pic b 

► Beta Pictoris b 


Beta Electrons 

► Beta Rays 


Beta Pictoris b 

Daniel Rouan 1 and Nader Haghighipour 2 
^ESIA, Observatoire Paris-Site de Meudon, 
Meudon, France 

institute for Astronomy, University of Hawaii- 
Manoa, Honolulu, Hawaii, HI, USA 


Synonyms 

Bet Pic b 


Definition 

Beta Pictoris b is a massive exoplanet directly 
detected around the A-star Beta Pic, on an orbit 
with a semimajor axis between 8 and 10 astro¬ 
nomical units. This is the smallest orbital distance 
known so far among the small set of exoplanets 
observed by direct imaging. The star which is at a 
distance of 20 pc (60 light years) is one of the 
best-known examples of a star surrounded by a 
dusty ► debris disk. The disk was the first to be 
imaged and is now known to extend up to about 
1,000 AU. The planet has a mass of about 9 Jupi¬ 
ter masses and the right mass and location to 
explain the observed warp in the inner parts of 
the disk (Fig. 1). 

A team led by A.M. Lagrange used the NAOS- 
CONICA instrument, an ► adaptive optics 
corrected near-infrared imaging system mounted 
on one of the 8.2-m Unit Telescopes of ESO’s 
Very Large Telescope (► VLT), to observe Beta 
Pic once in 2003 and then several times after 
2008. On 2003 images, a faint source inside the 
disk was seen, but it was not considered as a 
planet as it could have been a background star. 
On the images taken in 2008 and spring 2009, the 
source had disappeared, while in the observations 
taken during autumn 2009 and later, the object 
appeared on the other side of the disk after a time 
fully consistent with the object being an 
exoplanet orbiting its host star. The size of the 
orbit was also consistent with this hypothesis. 







256 


Beta Rays 


Beta Pictoris b. 

Fig. 1 Beta pictoris 



Since then, the spectral energy distribution in 
the infrared was obtained which showed the 
planetary parameters to be fully consistent with 
the first evaluation of the orbit and mass and 
pointed to a dusty planetary atmosphere at 
1,700 K. 

Because the host star is young (12 million 
years old), this discovery is considered as a strong 
indication that ► gas giant planets can form 
within protoplanetary disks in only a few million 
years, a short time compared, for instance, to the 
age of the solar system (4.5 Gyr). 

See Also 

► Adaptive Optics 

► Debris Disk 

► Direct-Imaging, Planets 

► Exoplanets, Discovery 

► Gas Giant Planet 


► HR 8799: The First Directly Imaged Multi¬ 
planet System 

► VLT 


Beta Rays 

Jun-Ichi Takahashi 

NTT Microsystem Integration Laboratories, 
Atsugi, Japan 

Keywords 

Beta decay; Chirality; Radioactive particles; 
Weak interaction 

Synonyms 

Beta electrons 






Big Bang Nucleosynthesis 


257 


Definition 

A beta ray is a stream of beta particles (electrons 
or positrons). In nuclear physics, beta decay is a 
type of radioactive decay in which a beta particle 
is emitted. 

Overview 

In the case of electron emission, the decay is 
referred to as beta minus ((3 _ ), while in the case 
of a positron emission as beta plus ((3 + ). In beta 
minus decay, a neutron is converted to a proton, 
an electron, and an antineutrino; in beta plus 
decay, a proton is converted to a neutron, a pos¬ 
itron, and a neutrino: 

ft^/? + e - +v e - 

p —> n + e + + v e 

If the proton and neutron are part of an atomic 
nucleus, these decay processes transmute one 
chemical element into another. Beta decay does 
not change the number of nucleons in the nucleus 
but changes only its charge. For example: 

90 Siw 90 Y + e“ + v e 

The kinetic energy of beta particles has a contin¬ 
uous spectrum ranging from 0 to maximal avail¬ 
able energy, which depends on parent and 
daughter nuclear states participating in the 
decay. A typical maximal available energy is 
around 1 MeV, but it can range from a few keV 
to a few tens of MeV. The most energetic beta 
particles are ultra-relativistic, with speeds very 
close to the speed of light. 

The spin of the electrons or positrons in beta 
rays is longitudinally polarized due to parity 
nonconservation in the weak interaction medi¬ 
ated by charged W particles. The helicity of a 
beta electron, that is, the spin angular momentum 
component of the kinetic momentum direction, is 
negative (left-handed), and that of a beta positron 
is positive (right-handed). 


From the standpoint of astrobiology, one of 
the hypotheses for the origin of biomolecular 
► chirality, the so-called cosmic scenario, states 
that asymmetric energy sources in space-induced 
asymmetric chemical reactions of precursors in 
interstellar dust, resulting in the ► enantiomeric 
excess of terrestrial bioorganic compounds. It has 
been proposed that beta rays are one of the can¬ 
didates for the source of such asymmetric chem¬ 
ical reactions, which might lead to the origin of 
biomolecular chirality in terrestrial organic 
compounds. 


See Also 

► Alpha Rays 

► Asymmetric Reaction, Absolute 

► Enantiomeric Excess 

► Gamma Rays 

► Homochirality 


BIF 

► Banded Iron Formation 


Big Bang Nucleosynthesis 

Alain Coc 

Centre de Sciences Nucleates et de Sciences 
de la Matiere (CSNSM) CNRS/IN2P3, 
Universite Paris Sud 11, UMR 8609, 

Orsay, France 

Keywords 

Big bang, Deuterium, Helium; Lithium; 
Nucleosynthesis 






258 


Big Bang Nucleosynthesis 


Synonyms 

Primordial nucleosynthesis 

Definition 

The nucleosynthetic process that took place 
within the first 20 min after the Big Bang is called 
Big Bang Nucleosynthesis (BBN) or Primordial 
Nucleosynthesis. At this early epoch, the Uni¬ 
verse was dense and hot enough to allow for 
nuclear reactions to take place, producing the 
“light elements”: 4 He, 2 H (=D, i.e., deuterium), 
3 He, and 7 Li, starting from neutrons and protons. 
The comparison between the primordial abun¬ 
dances of these isotopes, deduced on one hand 
from observations and on the other hand from 
model calculations, is one of the main supports 
of the Big Bang model. 

History 

Prominent landmarks in the development of the 
Big Bang Nucleosynthesis theory include works 
by Gamow in the 1940s (out of equilibrium 
nucleosynthesis in an expanding Universe domi¬ 
nated by radiation), Peebles in 1966 (Big Bang 
Nucleosynthesis calculations up to 4 He), and 
Wagoner in 1973 (Big Bang Nucleosynthesis 
calculations including 7 Li). 

Overview 

The Big Bang model is supported by three pieces 
of observational evidence: the expansion of the 
Universe, the ► cosmic background radiation, 
and the Primordial or Big Bang Nucleosynthesis. 
In the framework of an expanding Universe, with 
uniform temperature and density that decrease 
with time, a temperature of 10 11 K is reached a 
fraction of a second after the Big Bang. 
According to our present knowledge, the only 
particles present in the Universe at this time 
were photons, electrons, positrons, neutrinos, 
and antineutrinos, all in equivalent numbers, 


and a tiny fraction of neutrons and protons. 
Weak reactions (with electrons and neutrinos) 
maintained equilibrium between the number of 
protons and neutrons until the Universe cooled 
down to 10 10 K. This occurred because the rate of 
weak reactions became slower than the rate of 
space expansion. Consequently, the ratio of the 
number of neutrons to protons became frozen. 
When the temperature dropped to 10 9 K, the 
fusion of a proton and a neutron leading to a 
deuterium nucleus became favored compared to 
deuterium dissociation by high-energy photons. 
This was the starting point of primordial nucleo¬ 
synthesis that stopped, after «20 min, with the 
formation of 7 Li because no nucleus with mass 
8 (or 5) exists and because of the decreased den¬ 
sity and temperature. Only the 4 He, D, 3 He, and 
7 Li isotopes are produced in Standard Big Bang 
Nucleosynthesis, involving a dozen main nuclear 
reactions. 

The comparison between the calculated Big 
Bang Nucleosynthesis isotopic abundances and 
those deduced from observations in primitive 
astrophysical sites was used to determine the 
density of ordinary matter in the Universe. It is 
now more precisely deduced from the observa¬ 
tions of the anisotropies of the cosmic back¬ 
ground radiation. Despite the fact that the 
primordial abundances of these light isotopes 
span nine orders of magnitude, the agreement 
between calculations and observations is good 
with the, yet unexplained, exception of 7 Li (but 
within a factor of «3-5). According to models, 
the Big Bang Nucleosynthesis contributions to 
the solar system abundances amount to «90 % 
for 4 He and «25 % for 7 Li and are uncertain for 
3 He but are remarkably the only source of 
present-day deuterium. 

All the parameters of the Standard Big Bang 
Nucleosynthesis are now known from other 
sources. It is now used as a probe of nonstandard 
physics in the early Universe. 

See Also 

► Cosmic Background Radiation 

► Nucleosynthesis, Explosive 



Binary Stars, Young 


259 


► Nucleosynthesis, Neutrino - 

► Nucleosynthesis, Stellar Binary Stars, Young 


References and Further Reading 

Coc A, Goriely S, Xu Y, Saimpert M, Vangioni E (2012) 
Standard big bang nucleosynthesis up to CNO with an 
improved extended nuclear network. Astrophys 
j 744(1-18): 158 

Fields BD (2011) The primordial lithium problem. Annu 
Rev Nucl Part Sci 61:47-68 

Iocco F, Mangano G, Miele G, Pisanti O, Serpico PD 
(2009) Primordial nucleosynthesis: from precision 
cosmology to fundamental physics. Phys Rep 472:1-76 

Peebles PJE (2009) Finding the big bang. Cambridge 
University Press, Cambridge. ISBN 13:978- 
0521519823 

Weinberg S (2008) Cosmology. Oxford University Press, 
Oxford. ISBN 13: 978-0198526827 


Bimolecular Reaction 

Steven B. Chamley 

Solar System Exploration Division, Code 691, 
Astrochemistry Laboratory, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 


Synonyms 


Steven W. Stahler 

Department of Astronomy, University of 
California, Berkeley, CA, USA 


B 


Keywords 

Star formation 


Definition 

Most stars are not isolated objects, but have an 
orbiting companion. This basic fact holds not only 
for mature stars but also for objects at an earlier 
stage of evolution. Indeed, several young star clus¬ 
ters have a higher fraction of binaries than do main- 
sequence stars generally. Young binaries exhibit a 
very broad range in separations and therefore 
orbital periods. In the widest pairs, the orbits are 
highly eccentric. Conversely, the tightest pairs are 
locked into circular orbits. Planet-forming disks are 
absent in these latter systems, apparently because of 
the disturbing influence of the companion. 


Two-body reaction 


Overview 


Definition 

A bimolecular reaction is a chemical process 
involving two reactants. Reactants may be elec¬ 
trons or atoms and molecules existing in various 
combinations of charge states (neutral, anionic, 
or cationic). The most important reactant combi¬ 
nations for interstellar chemistry are ion-neutral, 
neutral-neutral, anion-neutral, electron-neutral, 
and electron-ion. 

See Also 

► Anion 

► Interstellar Chemical Processes 


Astronomers have long known that most stars 
have binary partners, that is, companions locked 
gravitationally into orbit. About 60 % of solar- 
type, main-sequence stars have at least one such 
companion. The vast majority of these multiple 
systems are binaries, but triples and even quadru¬ 
ples also exist. Binarity is also common for stars 
of other spectral types. 

Some binary companions are so close together 
that one can detect the induced wobble in the 
stars’ motion, through a periodic Doppler shift 
in the wavelength of spectral lines. Such spectro¬ 
scopic binaries are relatively rare. Most systems 
are discovered because the two stars share a com¬ 
mon spatial motion. This implies that their 
pairing is physical and not a chance superposi¬ 
tion. Overall, the observed range of periods is 






260 


Binding Constant 


vast, from less than a day to millions of years, 
corresponding to separations from 0.01 to 
10,000 AU. 

The fact that most mature stars have compan¬ 
ions naturally leads us to wonder if this situation 
held further back in time. Are ► pre-main- 
sequence stars, those too young to fuse hydrogen 
into helium, also preferentially found in binaries? 
What about even younger objects, those still 
gathering mass from their parent molecular 
clouds? Since the 1980s, many researchers have 
investigated the matter, and the answer is now 
clear. Pre-main-sequence stars are also very 
likely to have a binary companion. Indeed, the 
binary fraction in some young clusters is even 
greater than for main-sequence stars in the field. 

The systems being found show a wide range in 
orbital separations. Some are tight enough to be 
detected as spectroscopic binaries. Most young 
binaries, however, are noticed because they 
exhibit a common spatial velocity within their 
parent stellar group. On the whole, pre-main- 
sequence binaries span a wide range of separations 
and periods, just as do main-sequence systems. 

Many individual pre-main-sequence stars 
have planet-forming disks, as evidenced by their 
excess infrared and millimeter emission. The 
same is true for stars within binaries, but with a 
significant caveat: if the binary separation is less 
than about 100 AU, corresponding to a period of 
about 1,000 years, then the excess emission is 
absent. Apparently, the relatively nearby com¬ 
panion star prevents formation of any circumstel- 
lar disk. For periods as low as a few days, the 
primary and its companion are locked into per¬ 
fectly circular orbits. 


See Also 

► Pre-Main-Sequence Star 

References and Further Reading 

Duquennoy A, Mayor M (1991) Multiplicity among solar- 
type stars in the solar neighborhood II: distribution of 
orbital elements in an unbiased sample. Astron 
Astrophys 248:485 


Ghez AM, Neugebauer G, Matthews K (1993) The multi¬ 
plicity of T Tauri stars in the star-forming regions 
Taurus-Auriga and Ophiuchus-scorpius: A2, 2 micron 
speckle imaging survey. Astron J 106:2005 
Jensen ELN, Mathieu RD, Fuller GF (1994) A connection 
between submillimeter continuum flux and separation 
in young binaries. Astrophys J 429:F29 
Zinnecker H, Mathieu RD (eds) (2001) The formation of 
binary stars. Astronomical Society of the Pacific, San 
Francisco 


Binding Constant 

► Affinity Constant 


Binding Energy 

Steven B. Charnley 

Solar System Exploration Division, Code 691, 
Astrochemistry Laboratory, NASA Goddard 
Space Flight Center, Greenbelt, MD, USA 

Definition 

Binding energy is the energy required to disas¬ 
semble an entity into its constituent parts. This 
corresponds to the mechanical work which must 
be done in acting against the forces which hold 
the entity together. The binding energy of an 
atom is that required to disassemble an atom 
into free electrons and a nucleus, acting against 
the electromagnetic force. The nuclear binding 
energy is that required to disassemble a nucleus 
into its constituent neutrons and protons, acting 
against the strong nuclear force. The term is also 
used in other contexts, for example, for the 
energy involved in attaching a gaseous molecule 
to an ► interstellar dust grain upon collision. In 
this case, the magnitude depends on both the 
physical nature of the molecule (e.g., polarizabil¬ 
ity) and of the grain surface. Binding energies for 

► physisorption (through van der Waals bond¬ 
ing) are generally much lower than those of 

► chemisorption. 





Biobarrier 


261 


See Also 

► Chemisorption 

► Interstellar Dust 

► Physisorption 


Bioastronomy 

► Astrobiology 


Bioastronomy (IAU Commission 51) 

William M. Irvine 

University of Massachusetts, Amherst, MA, USA 

Definition 

In current usage, bioastronomy is both a synonym 
for astrobiology (although the term was intro¬ 
duced before NASA coined “astrobiology”) and 
the former title of Commission 51 of the Interna¬ 
tional Astronomical Union (► IAU). Commis¬ 
sion 51, which has recently been renamed 
Astrobiology and which may be re-numbered 
following the IAU General Assembly in August, 
2015, defines its field to be the study of the origin, 
evolution, and distribution of life in the universe. 
In this context, bioastronomy/astrobiology 
encompasses the search for extant life, evidence 
of past life, or evidence of prebiotic chemistry on 
solar system bodies, including Mars, Europa, 
Titan, and Enceladus; the search for planets 
around other stars and potential spectroscopic 
evidence for habitability and biological activity; 
the origin of the biogenic chemical elements and 
the study of biologically relevant molecules in 
the interstellar medium and in primitive solar 
system objects such as comets, undifferentiated 
asteroids, and some meteorites; the search for 
intelligent signals of extraterrestrial origin 
(► SETI); the study of the origin, early evolution, 
and environmental constraints for life on Earth; 
the coordination of efforts in all these areas at the 


international level; and the establishment of col¬ 
laborative programs with other international sci¬ 
entific societies with related interests. 

In the International Astronomical Union, this 
Commission is part of Division F, which was 
renamed in 2012 to be Planetary Systems and 
Bioastronomy. 


History 

The International Astronomical Union’s Commis¬ 
sion 51 was established in 1982 as “Bioastronomy: 
Search for Extraterrestrial Life”, was renamed 
simply “Bioastronomy” in 2006, and renamed 
again “Astrobiology” in 2015. From an early con¬ 
centration on ► SETI, bioastronomy has expanded 
its interests as described above. 


See Also 

► IAU 

► SETI 


Biobarrier 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 

Definition 

In ► planetary protection, a biobarrier is a 
mechanical barrier to protect a spacecraft or asso¬ 
ciated component(s) against microbial 
recontamination following the application of 
► bioburden reduction procedures. 


See Also 

► Bioburden 

► Bioburden Reduction 

► Planetary Protection 







262 


Biobloc 


Biobloc 

► Biostack 


Bioburden 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 


Definition 

In ►planetary protection, the bioburden is the 
total amount of viable microorganisms sitting 
on the surface and inside a spacecraft. The 
bioburden is evaluated using ► assays in or on 
items of interest. To evaluate or measure the 
bioburden, the assays can be standardized by 
specific procedures. 


See Also 

► Assay 

► Microorganism 

► Planetary Protection 


Bioburden Reduction 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 

Definition 

Bioburden reduction involves any activities 
designed to remove or destroy ► microorganisms 
that are performed in order to reduce ► bioburden 
levels on or in an item of interest. These activities 
could involve cleaning and wiping with appropri¬ 
ate alcohol or chemical solutions, dry heat 


microbial reduction (► DHMR), ultraviolet or 
y-ray irradiation, and treatment with a 
sterilizing gas. 


See Also 

► DHMR 

► Pasteurization 

► Planetary Protection 

► Sterilization 


Bioburden-Controlled Environment 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 

Definition 

In ► planetary protection, a bioburden-controlled 
environment is a place where the number of via¬ 
ble ► microorganisms, and therefore the poten¬ 
tial for contaminating spaceflight hardware, is 
controlled and minimized. ► Clean rooms, lami¬ 
nar flow hoods or cabinets, and other environ¬ 
ments in which the quantity of microorganisms 
and/or particulates is monitored and maintained 
at a specified level are considered “bioburden 
controlled.” 


See Also 

► Bioburden 

► Clean Room 

► Planetary Protection 


Biodetection System 

► Biosensor 








Biodiversity 


263 


Biodiversity 

Simon Tillier and Guillaume Lecointre 
Departement Systematique et Evolution, UMR 
7138 CNRS-MNHN-UPMC-IRD, Museum 
National d’Histoire Naturelle, Paris, France 

Keywords 

Ecology; Ecosystem services; Environment; 
Evolution; Systematics; Taxonomy 

Synonyms 

Diversity of life 

Definition 

Biodiversity designates the condition of life on 
Earth in terms of its variation at all levels of 
biological organization, from genes to ► ecosys¬ 
tems. By extension, it is used to designate life on 
Earth itself, most generally at the ► species level 
but often also at all organization levels altogether. 
The political impact of the term led to a definition 
adopted by the International Convention on Bio¬ 
logical Diversity (Art.2): “Biological diversity’ 
means the variability among living organisms 
from all sources including, inter alia, terrestrial, 
marine and other aquatic ecosystems and the 
ecological complexes of which they are part; 
this includes diversity within species, between 
species and of ecosystems” (Convention on Bio¬ 
logical Diversity 1992). 

History 

Although first introduced in the end of the 1960s, 
the word biodiversity, as a contraction of biolog¬ 
ical diversity, has been coined by Walter 
G. Rosen while preparing a national US scientific 
forum held in Washington in 1986. The objective 
of this forum was to discuss the importance of the 


quality and variety of living organisms in relation 
with the threats constituted by ► environment 
degradation, species extinction, and potential 
losses of socioeconomic benefits (Wilson 1988). 
In parallel, the convergence of interest from the 
scientific community, from the nature conserva¬ 
tion organizations, and from the southern coun¬ 
tries, who want to control the economic benefit 
from their living resources, led the United 
Nations Environment Programme (UNEP) to 
explore the need for an international convention 
on biological diversity. This approach led to an 
international legal instrument for the conserva¬ 
tion and sustainable use of biological diversity: 
the Convention on Biological Diversity was 
opened for signature on June 5, 1992, at the 
United Nations Conference on Environment and 
Development, better known as the Rio “Earth 
Summit,” and was adopted by 168 countries 
within the next year. In terms of scientific orga¬ 
nization and programming, an international 
research program on biodiversity, named 
Diversitas, was established in 1991 jointly by 
UNESCO, SCOPE (Scientific Committee on 
Problems of the Environment or the International 
Council of Scientific Unions), and the IUBS 
(International Union of Biological Sciences) to 
“promote an integrative biodiversity science, 
linking biological, ecological and social disci¬ 
plines in an effort to produce socially relevant 
new knowledge; and provide the scientific basis 
for the conservation and sustainable use of biodi¬ 
versity.” Ten years after Rio, the second Earth 
Summit held in Johannesburg in 2002 set the 
so-called 2010 target: “to achieve by 2010 a 
significant reduction of the current rate of biodi¬ 
versity loss at the global, regional and national 
level as a contribution to poverty alleviation and 
to the benefit of all life on Earth.” Clearly the 
target has not been met, in the absence of instru¬ 
ments of measure as well as of effective policies. 

However, the conjunction of scientific interest 
and social pressures has modified how ecologists, 
taxonomists, population geneticists, paleontolo¬ 
gists, and social scientists of environment situate 
their own disciplines, toward an integrated vision 
where most see themselves as contributors to 
biodiversity research. 





264 


Biodiversity 


Overview 

Biodiversity science is above all integrative. The 
central problem of biodiversity research is to 
understand how diversity of life, that is, the var¬ 
iation in quality and quantities of living things at 
any scale, relates to the functioning and evolution 
of ecosystems including the human populations 
and societies. In consequence, all population- 
level research may be relevant at any scale, 
from any local group of living organisms to all 
past, present, and future life. Taxonomists 
(or systematists, including paleontologists) 
explore and describe the patterns of biodiversity, 
present and past, proposing scenarios illustrating 
“how” - in terms of a suite of inferred historical 
events - biodiversity reached its present state at 
the largest scales. Evolutionary biologists aim at 
understanding “how” - in terms of biological 
processes - biodiversity reached its present state 
at genetic and population levels. Ecologists 
explore the patterns of species interactions in 
ecosystems and the mechanisms of ecosystem 
functioning; and social scientists explore the rela¬ 
tionships between human populations and socie¬ 
ties and nonhuman biodiversity. Focus on 
socioeconomic benefits, which were already 
encompassed by the initial thoughts in the 
1980s, has brought emphasis of the concept of 
ecosystem services, that is, the part of the ecosys¬ 
tem functions and products that is used by our 
species. 

We understood as late as in the 1980s that the 
number of living species is probably tenfold the 
previous estimates, in the 1CM-0 million living 
species range, rather than 1-2 million (Erwin 
1982 and subsequent papers). In parallel, it has 
become progressively evident that unprecedented 
losses and changes in biological diversity are 
taking place at the genetic, species, and ecosys¬ 
tem levels, particularly in nonmarine groups of 
organisms so far. Comparison with major extinc¬ 
tion crises in the geological history of the Earth 
reveals that the current rate of extinction is at 
least in the same order of magnitude and several 
hundred times greater than the average between 
crises (Dirzo and Raven 2003). The present 
extinction crisis does not strike us because it is 


not catastrophic at the scale of the human 
lifespan, but rather in a time span of several 
millennia, which we do not perceive directly but 
is still a very short instant in the more than 3.5 
billion year-long history of life on Earth. This 
crisis, sometimes referred to as the Sixth Extinc¬ 
tion, is likely the direct result of human activities. 

Understanding the patterns and processes of 
biodiversity loss and change is crucial for our 
species, not only because of the aesthetic, ethical, 
or cultural values attached to biodiversity but also 
because it could have numerous far-reaching con¬ 
sequences for our own life-support system. Even 
the chemical composition of the air we breathe 
and of seawater depends upon biological activity 
well beyond the increase of carbon dioxide in the 
atmosphere and of acidity in the seawater, which 
results directly from human activities. 

One of the likely consequences of 
man-induced changes in the environment is the 
reduction in the capacity of natural and managed 
ecosystems to deliver ecological services, such as 
the production of food and fiber, carbon storage, 
nutrient cycling and resistance to climate, and 
other environmental changes. Assessing the 
causes and consequences of biodiversity changes 
and establishing the bases for the conservation 
and sustainable use of biodiversity are major 
scientific challenges of our time. The major ques¬ 
tions that research is facing are summarized in the 
Diversitas research program (Diversitas 2002, 
2010 ). 

How Did Biodiversity Evolve in Space and 
Time to Reach the Current State? 

There are two kinds of sciences answering the 
“how” questions. The first one is focusing on the 
biological processes by which living matter 
diversifies its forms (see the entry Evolution 
(biological)). The way these scientists demon¬ 
strate their statements is close to that of chemistry 
or physics. By manipulating populations of 
organisms with very short generation times, it is 
possible to develop a hypothetico-deductive 
experimental approach to these “how” questions: 
population genetics is of first importance in the 
field. But there are also other experimental sci¬ 
ences like causal embryology or physiology that 



Biodiversity 


265 


participate to the understanding of this “how,” 
though without any population approach. 

The second approach is the historical “how.” 
A set of sciences like descriptive and compara¬ 
tive embryology and anatomy, paleontology, and 
systematics participate in a historical interpreta¬ 
tion of how life arrived to its present state. The 
present distribution of organisms is explained by 
a suite or series of events, not necessarily linked 
to each other by causal relations. ► Phylogeny 
provides part of the information needed for the 
ordering of events through time. Other data, pale¬ 
ontological, stratigraphical, geological, etc., also 
participate in our knowledge of the history of 
biodiversity. The answer to the historical “how” 
has made decisive progress in the last two 
decades through the association of the phyloge¬ 
netic method introduced by Willi Hennig 
(Hennig 1966) with informatics and use of DNA 
sequences: phyloinformatics now allows 

processing large data sets, whether molecular or 
morpho-anatomical. Thanks to phylogenetic 
methods applied to molecular characters, our 
vision of the tree of life has been radically mod¬ 
ified within the last 25 years and is still evolving. 
Within 25 years, our vision of the tree of life has 
shifted from five “kingdoms” to three main 
branches or clades, of which two are bacteria 
domains diverging from each other just as much 
as from ours, the eukaryotes (the organisms con¬ 
stituted by one to many cells with a nucleus). 
Convincing evidence has been brought to explain 
the origin of eukaryotes by multiple bacterial 
endosymbioses: our own cells, their mitochon¬ 
dria, and plasmids originate indeed from as 
many bacterial lineages. It is now admitted that 
lateral ► gene transfer (i.e., gene transmission 
between two otherwise independent lineages) is 
a relatively frequent phenomenon at least in bac¬ 
teria and may well influence significantly their 
evolution. 

At the ecosystem level, “how” is also a ques¬ 
tion from both points of view: from an ecological 
processes point of view, not only chance, that is, 
the initial conditions, but also species interactions 
doubtless shape the local communities in time, 
even though we are hardly able to understand and 
even less to predict the change when more than 


very few species interact. The historical “how” 
may be easier to grasp, thanks to both paleonto¬ 
logical observations and, possibly, by combining 
the phylogeny of the species composing a com¬ 
munity with the composition of the latter through 
time. An objective is to relate ecosystem change 
with causal factors such as climate change, entry 
of a clade into a new region, or the origin of 
innovations in a clade. 

How Much Biodiversity Exists and How Does 
Its Change or Loss Affect the System 
as a Whole? 

A prerequisite to the “how” is the “what,” that is, 
documenting biodiversity. Understanding how 
little we know about the existing species implies 
that traditional methods and techniques are inap¬ 
propriate, and new strategies are developed to 
increase the efficiency of field sampling, the qual¬ 
ity and accessibility of collections for fieldwork, 
the collection and curation of voucher specimens, 
the technologies for imaging and DNA sequenc¬ 
ing, the digitization of legacy data, and the devel¬ 
opment, maintenance, and connectivity of 
relevant databases. The need for rapid-capture 
technologies for identifying known species and 
discovering new ones has led to the development 
of the “Barcode of Life” initiative, which aims at 
providing IT tools for identifying species through 
short DNA sequences obtained from specimens 
identified by an expert and kept in legacy collec¬ 
tions (Consortium Barcode of Life 2010; Golding 
et al. 2009). The need for access to the informa¬ 
tion on species occurrences and on the collec¬ 
tions, which may well soon include the only 
remaining specimens of many species in view of 
the current rate of extinctions, has led to the 
constitution of the so-called GBIF (Global Bio¬ 
diversity Information Facility 2010; Edwards 
et al. 2000), which is an international informatics 
infrastructure that allows the interoperability of 
the innumerable databases on collection speci¬ 
mens and species occurrences worldwide. 

A serious problem for assessing species diver¬ 
sity is the uneven distribution of expertise among 
taxa and countries: groups of very high diversity 
and ecological importance, such as nematode 
worms, acarians, most insects, or microbes, in 




266 


Biodiversity 


general, are notoriously understudied and very 
poorly known, whereas groups that are closer to 
us in terms of body organization, size, and appeal 
to imagination may even have more specialists 
than species, as is the case of birds or elephants. 
In parallel, expertise is located mainly in Western 
developed countries, principally in Europe and 
North America, whereas most megadiverse trop¬ 
ical countries have very few specialists and insuf¬ 
ficient research infrastructures: biodiversity is in 
the South but expertise and infrastructures are in 
the North. 

For their own biodiversity assessments and in 
response to the environmental concerns, which are 
at the origin of environmental regulations, rich 
countries have developed observation networks 
that are feeding large observational databases, 
managing billions of observational data. These 
databases provide the basic tool for the application 
of environmental regulations regarding species 
and habitats but also constitute a tool for research 
when standardized and made interoperable, inter 
alia, thanks to the GBIF. Their weakness is that 
they necessarily concentrate on taxa for which 
there are a number of observers, that is, principally 
higher plants and vertebrates. However, when 
enough data have been collected in the medium 
and long term, it has been possible to show such 
phenomena as the decline of populations of com¬ 
mon birds in Europe or the shift in distribution 
toward the north of bird and plant species as a 
consequence of global warming. In the domain 
of fisheries, fishing data collected since the end 
of the nineteenth century have allowed us to show 
that overfishing started at least more than one 
century ago, leading to constant diminution of 
tonnage and size of the fish at the world level and 
unpredictable consequences over the food web 
and equilibrium of the global ocean. 

However, assessing is not enough in both sci¬ 
entific and societal terms: we want to be able to 
predict the change, for scientific reasons as well 
as for decision making in environmental policy. 
The solution lies in modeling, operationally 
based so far upon statistics on species distribution 
in terms of environmental parameters. This 
approach, called niche modeling, allows one to 
calculate an ecological envelope that can be 


projected on a map to delimit species’ potential 
distribution in space. It is then easy to modify 
some environmental parameters, including cli¬ 
matic ones, to predict the consequences of 
changes on species occurrences and, to some 
extent, on the composition of communities. This 
approach has proved very powerful to define pol¬ 
icies and strategies regarding invasive pest spe¬ 
cies in Mexico or the design of protected areas; 
but it is somewhat rudimentary by not taking into 
account ecological structures and processes, nor 
metapopulation dynamics, habitat fragmentation, 
etc. The ultimate goal is not just to understand but 
to predict biodiversity change, developing biodi¬ 
versity scenarios that predict biodiversity change 
at the landscape, regional, and global scales in 
response to various scenarios of how anthropo¬ 
genic drivers will change in the future. 

How Does Biodiversity Correspond to the 
Delivery of Ecosystem Functions and Services 
and What Is the True Value of These 
Commodities? 

Over two decades of research in ecology have 
shown that the combination of abiotic (physical 
and chemical) factors together with biological 
interactions determines the limit of biodiversity 
in a community and that the composition of this 
community influences, in turn, the way it func¬ 
tions. A large number of experiments since the 
beginning of the 1990s have confirmed that gen¬ 
erally the increase in biodiversity has a positive 
effect on ecosystem functioning. 

Three mechanisms have been proposed to 
explain this positive effect. The first is a simple 
sampling effect: species-rich ecosystems would 
produce more biomass, simply because the prob¬ 
ability for including a highly productive species 
is higher as the number of species is increased. 
The second is the functional complementarity of 
species resulting from a favorable pattern of traits 
in the community: by increasing diversity, one 
increases the number of effective ecological 
functions as more ecological niches are 
exploited. For example, two plant species having 
different root lengths extending down to the 
ground will better exploit resources in the soil 
and then produce more biomass together, than a 



Biodiversity 


267 


single of them. Finally, interaction of two spe¬ 
cies, then called facilitation, may have a positive 
effect on production: for example, brambles in a 
meadow may create favorable conditions for 
smaller species that need moisture and shade, 
such as arum lilies, and doing so favors the 
increase in productivity of the system. 

These mechanisms may be effective at any 
time and space scale, from bacteria and fungi in 
a piece of cheese to the entire tropical forests and 
oceans. However, for practical reasons, most 
experiments have been based on plant communi¬ 
ties, including the two best known, the European 
BIODEPTH and the American Cedar Creek 
experiments, which both have shown a positive 
effect of diversity upon biomass accumulation in 
the communities. 

The relationship between diversity and stabil¬ 
ity of ecological communities has also been stud¬ 
ied, showing at least theoretically that some 
species may have a key role for the persistence 
of the community when facing environmental 
disruption: roughly, having more species 
increases the chance of having at least one or a 
few able to develop under modified conditions 
and in so doing allow persistence of the commu¬ 
nity. Few experiments have tested this conclu¬ 
sion, but these few confirm so far the theoretical 
prediction of a relation between diversity and 
stability of ecosystem functioning. 

However, most experiments neglect the tro¬ 
phic relationships between species, which we 
know are very complex in species-rich ecosys¬ 
tems, from predation and parasitism to mutual 
dependence such as in pollination processes. 
A starting point may be the top-down effect, 
through which a predator controls the density of 
prey, which themselves control production at 
lower trophic levels. Diminution in density at 
the top levels may allow an indirect increase in 
production at the lowest levels; but it may also 
have just the opposite effect when top levels 
participate significantly in nutrient recycling, 
which itself increases productivity: this may 
well be what happens as mankind clearly exploits 
and overexploits large predators. 

Overall, we know now that diversity favors 
ecosystem resilience and biomass production. It 


is also suspected that diversity favors diversity. 
An illustration of this is, for example, the recent 
discovery of very high levels of horizontal or 
lateral transfers of DNA in microbial communi¬ 
ties, in a way that genomes exhibit functional- 
environmental patterns as well as historical pat¬ 
terns. Horizontal heritage is far more important 
than previously thought, compared to “classi¬ 
cal” vertical heritage. These networks of perma¬ 
nent DNA exchanges among a diversity of 
microbial “species” in a given environment 
(either marine, lacustrine, or terrestrial) stabilize 
the role played by these environmental commu¬ 
nities in the biosphere. Generally speaking, the 
question of positive feedback of diversity is fun¬ 
damental in view of the present changes in eco¬ 
systems and still requires further research at 
various levels of ecosystem organization. If it 
is true, human activities endanger self¬ 
regulation of ecosystems, of which many are at 
risk of collapsing with unavoidably serious risk 
for our own species. 

How Can Scientific Investigation Support 
Policy and Decision Making to Encourage 
More Sustainable Use of Biodiversity? 

In view of the societal needs for a better under¬ 
standing of the functions of biodiversity for 
human beings (and well-being where possible), 
communicating scientific results to relevant polit¬ 
ical levels is crucial. Researchers are trained in 
research and communication with other 
researchers, but not in communication toward 
decision makers, which results in numerous mis¬ 
understandings. This renders the formation of an 
ad hoc mechanism a necessity. Based on the 
example of the IPCC (Intergovernmental Panel 
on Climate Change), the United Nations and the 
G8 have endorsed in 2010 the creation of such a 
mechanism, called the Intergovernmental 
Science-Policy Platform on Biodiversity and 
Ecosystem Services (IPBES 2010; Larigauderie 
and Mooney 2010) as initially proposed by 
France in 2005. The IPBES progresses at an 
intergovernmental pace, which is slower than 
species extinctions and ecosystem change, but 
will hopefully allow progress in the implementa¬ 
tion of the necessary policies. 




268 


Biodiversity 


Key Research Findings 

Since the beginning of the 1980s, a few points 
have been understood: 

• First is a revolution in our vision of the tree of 
life and of the origin and diversification of 
eukaryotes. All eukaryotes are no more nor 
less than each of the two main “prokaryotic” 
clades (Bacteria and Archaea), fungi and ani¬ 
mals now appear as originating from a common 
ancestor not shared with other groups, and 
humans are nothing more than the tip of a tiny 
twig among all mammals, which occupy noth¬ 
ing more than a small branch of the small clade 
constituted by all animals in the tree of life. 

• Next is the change of paradigm in both taxon¬ 
omy and ecology: we now know that we know 
nothing about most living species and that the 
way we interact with biodiversity is not sus¬ 
tainable for the present ecosystems at any 
level, whether marine or land based. 

• The whole biosphere is changing at all levels, 
possibly faster than ever, and surely through a 
process without precedent, which is provoked 
by our species: destruction of whole ecosys¬ 
tems and modification of others through 
anthropic activities including transport of spe¬ 
cies are realities that we have to face. 

• In scientific terms, we understand better how 
biodiversity acts in the functioning of the whole 
ecosystems: biodiversity favors both produc¬ 
tion and stability of ecosystems and likely has 
a positive feedback on diversity itself. 

Future Directions 

On the purely scientific point of view, the main 
future direction to maintain our understanding of 
biodiversity is to keep all contributing sciences 
visible at the political level. The study of biodi¬ 
versity is not merely a matter of counting the 
species that are found in a given area or proposing 
models predicting responses of ecosystems to 
anthropic perturbations. The future in studies 
and understanding of biodiversity must keep 


systematics and evolutionary biology as central 
disciplines along with inventories and ecological 
modeling. 

Systematics is important in understanding the 
reasons why we classify living and fossil organ¬ 
isms as we do. Systematics provides the reason 
why the platypus is classified well apart among 
mammals. Phylogenetic systematics explains 
why the collection of traits exhibited by the platy¬ 
pus is so unique. If a decision has to be made 
concerning the preservation of the platypus, the 
ecological role of the platypus is going to have a 
negligible weight compared to the argument from 
systematics. The platypus (or the coelacanth, 
choose the one you prefer) is negligible in terms 
of biomass, and its role in its environment could 
be replaced by another imported species. In terms 
of what organisms do in their environment, the 
platypus (or the coelacanth) can perfectly well be 
sacrificed. By contrast, phylogenetic systematics 
will provide the arguments to regard this species 
as a very important one. Phylogeny will show that 
the platypus is the product of a very ancient 
mammal lineage represented today by three spe¬ 
cies only. The characters exhibited by the platy¬ 
pus show this: it lays eggs and it has a bizarre 
anatomy of the temporal area. In parallel, the 
lineage gained characters on its own branch, 
such as a duck-like beak or venomous fangs on 
the posterior limbs. The combination of the 
whole set of properties makes the platypus a 
kind of unique evolutionary heritage - a rare 
combination of characters. Protecting species 
should therefore be considered in terms of what 
they have (systematics), not only through what 
they do (ecology). 

Evolutionary biology is also important 
because we cannot pretend to understand and 
properly protect biodiversity without having a 
deep knowledge of the processes that generate 
biological diversity at all levels. This is going to 
be important because it is not sufficient to save 
the present state of nature as if it would not be 
going to change again. Life is continuously 
changing. It is important to protect the potential 
ability to get adapted to new conditions, so 
maintaining genetic variability and our 



Biodiversity 


269 


knowledge about processes that generate it (and 
select it afterward) is of key importance. 

The second relevant direction for our knowl¬ 
edge and action is to consider human societies 
and their products as parts of biodiversity. There 
is a philosophical tradition that keeps humankind 
separated from an undefined nonhuman “nature” 
or an undefined category of “animal” and that 
keeps culture separated from nature. In contrast, 
we are not only trying to change the world to save 
the diversity of this wonderful life but also to save 
the cultural-material heritage for the few next 
human generations. 

Although the economics of biodiversity is a 
rapidly expanding field, and understanding the 
relationship between biodiversity and ecosys¬ 
tem functioning is still seen as a research prior¬ 
ity, for practical reasons focus is presently made 
on observations and monitoring. Not only scien¬ 
tists but also all kinds of decision and policy 
makers need reliable information on what is 
happening and projections of what may happen, 
both locally and globally. Decreases of coral 
reefs and more generally ecological conse¬ 
quences of acidification of the oceans, changes 
in the composition of the atmosphere, invasion 
of exotic species, changes in the species distri¬ 
bution resulting from climate warming and 
transportation by humans, and destruction of 
habitats under anthropogenic pressures are all 
happening and hardly evaluated due to the lack 
of appropriate instruments. This observation 
calls for at least two lines for action from the 
scientific community: 

• The first one is improving our capacity for the 
analysis and prediction of the change in biodi¬ 
versity. Operational models based upon niche 
modeling that are already in use to assist 
decisions should be developed further. The pre¬ 
dictive value of models could doubtless still be 
improved by incorporation of ecosystem 
functional parameters, as ambitioned by many 
ecologists; however, this development is 
impeded so far by the weakness of the concepts 
relating to ecosystem functions, which still 
requires a qualitative jump forward. 


• Complementary and necessary for develop¬ 
ment of modeling is documenting what occurs 
and what happens, because without reliable 
data we may hardly hope to understand what 
is happening globally. Even local predictions 
require global data sets because, like in mete¬ 
orology, operational modeling is based upon 
statistical approaches of which precision and 
reliability are in proportion to the amount of 
observations available. This need for data and 
monitoring is taken into account by the 
projected construction of the Global Earth 
Observation Biodiversity Observation Net¬ 
work (GEO BON), which is a program for 
the coordination of observations on biodiver¬ 
sity promoted by Diversitas. GEO BON is a 
component of the Global Earth Observation 
System of Systems (GEOSS), an initiative 
led by the World Meteorological Organization 
(Scholes et al. 2008). 

Clearly, biodiversity research is shifting from 
traditional fundamental questions on what is 
there, why it is there, and how it works to ques¬ 
tions relating directly to societal concerns guided 
by the central question of where mankind is going 
in a context of radical ecological change at the 
global scale. So far, this shift is beneficial rather 
than detrimental to fundamental research; and 
indeed the questions raised by society regarding 
its own future as a constituent of biodiversity will 
not find their answers if progress is not going on 
in fundamental ecology, systematics, and evolu¬ 
tionary biology. 

To conclude on a positive note, we are right 
to be concerned by the ongoing Sixth Extinction. 
However, life has to be considered in the very 
long term. The Sixth Extinction is a problem of 
our responsibility for the next 2 to some 
200 human generations, but it is not a problem 
for life itself. Several drastic extinctions have 
taken place in the past million years; there will 
be others. Our theoretical framework allows us 
to predict that biodiversity will be recovered, as 
rich as ever or more, and life and Earth will 
continue to change together as time will con¬ 
tinue going by. 




270 


Biodiversity (Planetary Protection) 


See Also 

► Adaptation 

► Domain (Taxonomy) 

► Ecosystem 

► Environment 

► Evolution, Biological 

► Gene 

► Genome 

► Lateral Gene Transfer 

► Phylogenetic Tree 

► Phylogeny 

► Species 


References and Further Reading 

Convention on Biological Diversity (1992) N°30619. 

United Nations, treaty series, 1760, 1993. pp 142-308 
Consortium Barcode of Life (2010) http://www. 
barcodinglife.org/ 

Dirzo R, Raven PH (2003) Global state of biodiversity and 
loss. Annu Rev Environ Resour 28:137-167 
Diversitas (2002) Diversitas science plan. Diversitas, Paris 
Diversitas (2010) An international programme of biodiver¬ 
sity science, http://www.diversitas-intemational.org 
Edwards JL, Lane MA, Nielsen ES (2000) Interoperability 
of biodiversity databases: biodiversity information on 
every desktop. Science 289(5488):2312-2314 
Erwin TL (1982) Tropical forests: their richness in Cole- 
optera and other arthropod species, 3Coleopterists\ 
Bulletin 36:74-75 

GBIF (2010) Global Biodiversity Information Facility. 
http://www.gbif.org. 

Golding GB, Hanner R, Hebert P (eds) (2009) Special 
issue on barcoding. Mol Ecol Resour 9(supplement) 
1:1-267 

Hennig W (1966) Phylogenetic systematics. University of 
Illinois Press, Urbana 

IPBES (2010) Intergovernmental science-policy platform 
for biodiversity and ecosystem services. http://IPBES.net 
Larigauderie A, Mooney HA (2010) The intergovernmen¬ 
tal science-policy platform on biodiversity and ecosys¬ 
tem services: moving a step closer to an IPCC-like 
mechanism for biodiversity. Curr Opin Environ Sus¬ 
tain 2:1-2 

Millennium Ecosystem Assessment (2005) http://www. 
maweb.org 

Naeem S, Bunker D, Hector A, Loreau M, Perrings 
C (2009) Biodiversity, ecosystem functioning and eco¬ 
system services. Oxford University Press, Oxford 
Scholes RJ et al (2008) Toward a global biodiversity 
observation system. Science 321:1044-1045 
Wilson EO (ed) (1988) Biodiversity. National Academy 
Press, Washington, DC 


Biodiversity (Planetary Protection) 

Catharine A. Conley 

NASA Headquarters, Washington, DC, USA 

Definition 

For ► planetary protection, the biological diver¬ 
sity (biodiversity) in an environment is the inven¬ 
tory of types of ► microorganisms identified as 
being present. For microorganisms, the identifi¬ 
cation depends also on the ► assay which is used. 
For instance, to prepare future missions to 

► Mars, the space agencies are conducting stud¬ 
ies in the clean rooms to be used for instrument 
and spacecraft assembly. 

See Also 

► Bioburden 

► Bioburden Reduction 

► Planetary Protection 


Bioenergetics 

Ricardo Amils 

Departamento de Biologia Molecular, 
Universidad Autonoma de Madrid, Madrid, 
Spain 

Keywords 

Active transport; ATP; ATP synthesis; ATPase; 
Chemical energy; Electrical potential; Enthalpy; 
Entropy; Energy; Osmotic work; Photosynthesis; 
Proton motive force; Radiation; Respiration 

Definition 

Bioenergetics is the part of biochemistry dealing 
with ► energy flow through living systems. Life 





Bioenergetics 


271 


is dependent on energy transformation reactions. 
The ability to harness energy from a variety of 
metabolic pathways is a property of all living 
organisms. 

Overview 

Life and Energy 

Life implies work. All life systems perform work: 
chemical work is needed for the synthesis of 
macromolecules, osmotic work is required for 
the maintenance of cellular concentrations, and 
electrical work is necessary for the generation of 
► proton motive force. Energy is the capacity to 
do work. Until the principle of the conservation 
of energy, the first law of thermodynamics, was 
enunciated in the middle of the nineteenth century, 
progress in bioenergetics was extremely slow. 

The second law of thermodynamics estab¬ 
lishes that in an isolated system, entropy 
(a measure of molecular disorder) can never 
decrease. The second law was enunciated for 
inanimate matter; however, a violation of this 
principle by living organisms has never been 
observed. Therefore, on empirical grounds, the 
validity of the second and first laws of thermody¬ 
namics for living organisms is generally 
accepted. Nevertheless, it must be kept in mind 
that living beings are open systems. 

Not all processes permitted by the second law 
of thermodynamics can be used by living sys¬ 
tems, for example, they cannot use the differ¬ 
ences in temperature generated by combustion. 
The source of energy to perform biological work 
is chemical, and only few classes of chemical 
reactions can be used for these purposes. 

The Earth is in a steady state. The intake of 
energy is just compensated by its loss. Energy 
intake and energy loss occur entirely through 
radiation. In a steady state, the entropy content 
of the Earth must be also constant. Entropy is 
gained in the form of solar radiation and loss as 
electromagnetic radiation. Entropy is also pro¬ 
duced through irreversible processes. The rate 
of production of entropy must be equal to the 
net loss. Thus, in balance, the Earth emits 
entropy, and this entropic compensation is also 


operative in the biosphere. While organisms give 
just as much energy as they gain, the entropy 
associated with the energy released must exceed 
the entropy associated with the energy taken 
up. Organisms can develop if they interpose 
themselves into a gradient of entropy between 
incoming and outgoing energies. 

Entropy is absorbed by live systems in the 
form of chemical substrates and radiation. In a 
chemical process, in ideal conditions, the sum of 
the entropies of the reacting chemical system and 
the environment remains constant all the time. In 
ideal conditions, the process is carried out revers¬ 
ibly, but a small change in the parameters, for 
example, concentration, could reverse the direc¬ 
tion of the process. 

In living systems, work generated from chem¬ 
ical substrates is not produced by way of heat. 
Chemical energy is transformed into other forms 
of energy (e.g., ► Proton Motive Force, ► ATP) 
without passing through a heat stage. The small 
gradients of temperature that might exist within 
organisms are never used for work. In general, 
live systems work isothermally and isobarically. 

In bioenergetics, the concept of free energy is 
very useful. The molar free energy, G, is defined 
as 

G = H -TS 

where H is the molar energy content, T is the 
temperature, and S the molar entropy content. 
Strictly, in an isobaric system, H should be called 
enthalpy and G free enthalpy. But in isobaric 
conditions, the volume changes are so small that 
the difference between enthalpy and energy dis¬ 
appears. The energetics of the reaction can be 
described in terms of the differences between 
products and reactants as 

AG = AH - TAS 

The free enthalpy change AG has a negative 
value when the reaction is written in the direction 
in which it proceeds spontaneously, i.e., an exer- 
gonic reaction. In the opposite direction, the reac¬ 
tion is endergonic, and not spontaneous. The 
maximum work that can be obtained from a 




272 


Bioenergetics 


chemical reaction is given by AG, and it is 
obtained when the reaction is performed revers¬ 
ibly. But when a reaction has an irreversible 
component, some of the energy is dissipated as 
heat and then additional entropy is generated. 
While AH is mostly measured by calorimetry, 
AG and TAS are normally derived from measure¬ 
ments of chemical equilibrium. AG is related 
with the equilibrium concentrations of products 
(c pl , C P 2 > • • •) and reactants (c r i, c r2 , ...) and their 
actual concentrations (c*i, c p2 —, c* 1 , c* 2 —): 

AG = —RTln CplCp2 '" + RTln CplCp2 

CrlC r2 • • • ^rl^r2 * * * 

provided that activities can be replaced by con¬ 
centrations. For physicochemical standard 
conditions (pH value 0), the value AG is called 
AG°. For physiological standard conditions 
(pH value 7), AG is by definition AG 0/ . 

The equilibrium constant K is defined as 

g _ c pl c p2 • • • 

GlTr2 • • • 

Therefore, for standard conditions, 

AG = —RTln K 
and 

AG' = —RTln K' 

As AG ° (or AG 0/ ) is a measure of the tendency 
for a reaction to occur in standard conditions, it is 
also known as the reaction affinity. The greater 
the affinity, the more exergonic the reaction and 
the more negative AG ° (or AG 0/ ). It has to be 
underlined that the exergonicity or endergonicity 
of a reaction, in a given condition, is not deter¬ 
mined by the standard values (AG ° or AG 0/ ) but 
the values of AG. The work obtainable from a 
reaction is influenced by the actual concentra¬ 
tions, more exactly activities, of the reactants 
and the products. 

As mentioned in the ideal case of reversible 
reactions, no entropy is generated. However, 


reactions cannot proceed fully reversible if they 
have finite velocities. Metabolism cannot be too 
slow. Therefore, full reversibility cannot be 
attained and entropy must be generated. Hence, 
entropy is certainly generated when organisms do 
external work. 

Experimental work shows that antagonistic 
catabolic and anabolic processes always proceed 
along different pathways. Catabolic reactions are 
usually exergonic; thus, the corresponding ana¬ 
bolic reactions cannot proceed spontaneously, at 
least not in the same conditions. Therefore, dif¬ 
ferent pathways, which proceed at the expense of 
additional energy, are used for anabolism. In 
general, more energy in useful form is needed 
for anabolism than the energy obtained in catab¬ 
olism. Often, no useful energy is obtained at all in 
the catabolic reactions of dynamic states. In this 
case, energy is dissipated as heat. 

Active Transport 

One of the most important dynamic states of the 
cell is the so-called active transport. Active trans¬ 
port is related with the transport of molecules and 
ions across the ► cell membrane against a con¬ 
centration gradient. It requires osmotic work. To 
perform osmotic work, free energy is required. 
When the concentration of a solute in one side of 
the membrane is different from the concentration 
in the other side, diffusion to equilibrate the con¬ 
centrations in both sides of the membrane occurs. 
The direction of the transport is given by the 
change in free energy: 

AG = RTln — 

«i 

a being the thermodynamic activity, which as we 
mentioned before in most cases can be approxi¬ 
mated to concentration. In diffusion AG is nega¬ 
tive. In active transport AG is positive; this is the 
reason why osmotic work must operate to allow 
the solute to cross the membrane against a con¬ 
centration gradient. If the solutes have a charge 
(ions), then an additional term related with the 
electrical potential must be considered. 

Through active transport, large differences in 
concentration of molecules (i.e., glucose) and 






Bioenergetics 


273 


ions (i.e., H + , Na + ) can be set up between the 
cytoplasm and the environment or between dif¬ 
ferent cell compartments in eukaryotic cells. 
Obviously if a difference in concentration across 
the membrane is generated by active transport, 
diffusion will operate in the opposite direction; 
thus, work must be performed all the time to 
maintain a steady state. Solutes are pumped 
across the membrane by specific mechanisms. 
Specificity is extremely important in active trans¬ 
port to ensure that the cell invests energy in 
transporting useful compounds. As has been 
pointed out, dynamic states are very important 
for life systems. No organism is known to be able 
to develop without dynamic states. The complex 
mechanisms to maintain and regulate dynamic 
states are rather universal. One of the biggest 
surprises that is emerging from the analysis of 
whole-genome sequences is the high percentage 
of genomic information devoted to active trans¬ 
port, which underlines its importance. 

Active transport is also the basis of cell bioen¬ 
ergetics. Most ► energy conservation reactions 
are directly or indirectly related with active trans¬ 
port systems. From an energetic point of view, 
active transport can be classified as transport 
reactions that generate useful energy for the cell 
(primary active transport) and those that require 
energy for its functioning (secondary active 
transport). Examples of primary active transport 
are ► respiration, ► photosynthesis, the transport 
of the fermentation products, and the ► ATPase 
activity, all of them coupled to the generation of 
► proton motive force. Examples of secondary 
active transport are the transport of nutrients to 
the cell, the maintenance of homeostatic ionic 
concentrations inside and outside of the cell, the 
bacterial flagellar movement produced, and the 
synthesis of ATP, all of them coupled to the 
dissipation of the ► proton motive force. 

In respiration (see ► Respiration), an electron 
donor gives electrons to an appropriated electron 
acceptor through the use of an electron transport 
chain located in the ► cell membrane in prokary¬ 
otes and in the mitochondrial membrane in 
eukaryotes. The passage of electrons through 
the chain promotes the translocation of protons, 
generating a gradient of protons between both 


sides of the membrane. The difference in poten¬ 
tial energy (chemical energy) between the elec¬ 
tron donor and the acceptor is transformed in 
proton motive force, a universal storage system 
of cellular energy. 

In ► photosynthesis, the photo synthetic reac¬ 
tion center is excited (oxidized) by radiation, and 
the excited electron is trapped by a constituent of 
an associated electron transport chain, and as in 
the respiration, the passage of the excited electron 
through the different components of the chain can 
promote (i) the translocation of protons produc¬ 
ing a gradient of protons (proton motive force) or 
(ii) the generation of cellular reducing power, 
depending of the type of photosynthesis. In the 
first case, the same excited electron goes back to 
the oxidized reaction center to reduce it to the 
ground state (cyclic ► anoxygenic photosynthe¬ 
sis). In the second case, an electron donor must 
donate an electron to the reaction center to bring 
it to the ground state (oxygenic photosynthesis, 
noncyclic anoxygenic photosynthesis), getting in 
both cases ready for another excitation reaction 
using radiative energy. In the photosynthesis, the 
source of energy is radiation and is transformed 
through a more or less complex system 
(depending on the type of photosynthesis) in cel¬ 
lular energy (proton motive force and/or reducing 
power). 

Fermentation is the only bioenergetic system 
that does not make use of an electron transport 
chain to conserve energy (see ► Fermentation); 
instead cytoplasmic soluble enzymatic reactions 
are able to generate cellular useful energy (ATP) 
from chemical energy (reduced carbon sub¬ 
strates). Interestingly enough, because fermenta¬ 
tion is the main source of energy for these 
organisms, an important amount of substrate 
must be fermented for growth, and as a conse¬ 
quence, a high concentration of fermentation 
products are produced (i.e., ethanol, organic 
acids). If the organism is able to couple the trans¬ 
location of the fermentation products to the gen¬ 
eration of a proton gradient, then the potential 
energy stored as a concentration gradient of fer¬ 
mentation products, which is not useful to fuel 
energy requiring cellular reactions, is 
transformed in proton motive force, a useful 




274 


Bioenergetics 


cellular energy source. In the absence of coupling 
between both transports, only diffusion applies 
and the potential energy is lost. It has been cal¬ 
culated that up to one third of the cellular energy 
used by fermentation organisms can be generated 
by this peculiar active transport system. 

All these are examples of primary active trans¬ 
port systems because they can transform different 
► energy sources in proton motive force. Once 
there is enough energy stored as proton motive 
force, it can be used to promote reactions that 
require work. The best-known example is the 
translocation of cellular substrates (i.e., glucose) 
to the interior of the cell against a concentration 
gradient. Normally, organisms, especially pro¬ 
karyotes, live in habitats with extremely low con¬ 
centration of useful substrates to obtain energy. 
The required concentrations of these substrates 
inside the cell for metabolic reactions to proceed 
are several orders of magnitude higher than their 
concentration in the environment. Thus, very 
active transport system is required to concentrate 
these substrates inside the cell. To do this osmotic 
work, energy in the form of proton motive force is 
used. In this case, the translocation of a specific 
substrate is coupled to the dissipation (transport) 
of proton motive force. 

Similarly, proton motive force can be used to 
maintain a high concentration of K + or a low 
concentration of Na + inside the cell. Due to sim¬ 
ple diffusion, the high concentration of potassium 
stored inside the cell and required for an optimal 
performance of the different functional enzy¬ 
matic activities licks out because the concentra¬ 
tion of this cation is rather low outside of the 
cells. To maintain a high concentration of potas¬ 
sium in the cytoplasm, an active transport is 
required, because it has to be performed against 
a concentration gradient. The coupling between 
the translocation of potassium to the interior of 
the cell with the dissipation of the proton motive 
force allows maintaining the optimal cellular 
potassium concentration. A similar situation can 
be found with the sodium concentration. In this 
case, the optimal cellular condition is a lower 
concentration of this cation in the cytoplasm 
than in the environment. In this case, simple 
diffusion licks sodium to the cytoplasm, so the 


active transport required to pump sodium out of 
the cell can be performed using the energy stored 
as proton motive force through the coupling of 
both transport systems. 

But energy stored in the form of proton motive 
force can be used for other cellular functions 
different than transport, like the bacterial move¬ 
ment of flagella. In this case the dissipation of the 
proton motive force is used to perform a mechan¬ 
ical work: the rotation of the flagella or the 
reverse transport of electrons in the electron 
transport chain to generate reducing power for 
microorganisms that need it and cannot produce 
it by other means (many chemolithoautotrophs). 

A special case of active transport that requires 
attention is related with a membrane enzymatic 
complex involved in the synthesis and hydrolysis 
of ATP (see ► ATPase and ► ATP Synthase). 
The membrane-bound synthesis of ATP from 
ADP and phosphate is an endergonic reaction 
that requires energy. This reaction, named 
► ATP synthase, can be fuelled by the use of 
the energy stored as proton motive force. In this 
case, it will perform as a secondary active trans¬ 
port system. But the same enzymatic complex 
can perform in the opposite direction: hydrolyz¬ 
ing ATP and using the released energy to promote 
the translocation of protons outside the mem¬ 
brane, generating proton motive force. In this 
case it is performing as a primary active transport 
system. The reversibility of this reaction is the 
core of the bioenergetic regulation of prokaryotic 
cells. Experimentally, it can be shown that there 
is a linear relationship between the intracellular 
concentration of ATP and the proton motive 
force. If the proton motive force measured as 
membrane potential corresponds to the concen¬ 
tration of ATP measured inside the cell, no activ¬ 
ity can be detected. If the proton motive force is 
lower than the value that will correspond to a 
given concentration of ATP, then ATP is hydro¬ 
lyzed to generate proton motive force until both 
systems are equilibrated. If the proton motive 
force is higher than the value that should corre¬ 
spond to the ATP concentration, then the proton 
motive force is dissipated to increase the ATP 
concentration until both systems reach equilib¬ 
rium. With only one metabolic activity, 



Biofilm 


275 


prokaryotes can regulate in an efficient manner 
and with little genomic investment the bioener¬ 
getics of the cell. 

See Also 

► Anoxygenic Photosynthesis 

► ATP 

► ATPase 

► ATP Synthase 

► Cell Membrane 

► Electrochemical Potential 

► Energy 

► Energy Conservation 

► Energy Sources 

► Metabolism 

► Mitochondrion 

► Oxidation 

► Photosynthesis 

► Proton Motive Force 

► Proton Pump 

► Reduction 

► Respiration 

References and Further Reading 

Allen JF, Martin W (2007) Evolutionary biology: out of 
thin air. Nature 445:610-612 
Bryant DA, Frigaard NU (2006) Prokaryotic photosynthe¬ 
sis and phototrophy illuminated. Trends Microbiol 
14:488^196 

Buch-Pedersen MJ, Pedersen BP, Veierskov B, Nissen P, 
Palmgren MG (2009) Protons and how they are 
transported by proton pumps. Eur J Physiol 
457:573-579 

Gruber G, Marshansky V (2008) New insights into 
structure-function relationships between archeal ATP 
synthase (AxA 0 ) and vacuolar type ATPase (ViV 0 ). 
Bioessays 30:1096-1109 

Heathcote P, Fyfe PK, Jones MR (2002) Reaction centers: 
the structure and evolution of solar power. Trends 
Biochem Sci 27:79-87 

Itoh H, Takahashi A, Adachi K, Noji H, Yasuda R, 
Yoshida M, Kinosita K Jr (2004) Mechanically driven 
ATP synthesis by F r ATPase. Nature 427:465-468 
Kiang NY, Siefert J, Govindjee, Blankenship RE (2007a) 
Spectral signatures of photosynthesis. I. Review of 
Earth organisms. Astrobiology 7:222-251 
Kiang NY, Segura A, Tinetti G, Govindjee, Blankenship 
RE, Cohen M, Siefert J, Crisp D, Meadows VS (2007b) 
Spectral signatures of photosynthesis. II. Coevolution 


with other stars and the atmosphere on extrasolar 
worlds. Astrobiology 7:252-274 
Krah A, Pogoryelov D, Meier T, Faraldo-Gomez JD 
(2010) On the structure of the proton-binding site in 
the Fo rotor of chloroplast ATP Synthases. J Mol Biol 
395:20-27 

Kiihlbrandt W (2004) Biology, structure and mechanism 
of P-type ATPases. Nat Rev Mol Cell Biol 5:282-295 
Madigan MT, Martinko JM, Dunlap PV, Clark DP 
(2008) Brock biology of microorganisms, 12th edn. 
Benjamin Cumming, San Francisco 
Mulkidjanian AY, Makarova KS, Galperin MY, Koonin 
EV (2007) Inventing the dynamo machine: the evolu¬ 
tion of the F-type and V-type ATPases. Nat Rev 
Microbiol 5:892-899 

Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, 
Koonin EV (2008) Evolutionary primacy of sodium 
bioenergetics. Biol Direct 3:13 
Nelson DL, Cox MM (2009) Lehninger principles of bio¬ 
chemistry, 5th edn. WH Freeman, New York 
Nicholls DG, Ferguson SJ (2002) Bioenergetics 3. Aca¬ 
demic, London 

Noji H, Yasuda R, Yoshida M, Kinosita K Jr (1997) Direct 
observation of the rotation of FI-ATPase. Nature 
386:299-302 

Pennazio S (2008) Photosynthesis: the years of light. Riv 
Biol 101:443-162 

Renger G, Kuhn P (2007) Reaction pattern and mecha¬ 
nism of light induced oxidative water splitting in pho¬ 
tosynthesis. Biochim Biophys Acta 1767:458—471 
Stephan E, Giovanni F, Francis-Andre W (2008) The 
dynamics of photosynthesis. Annu Rev Genet 
42:463-515 

Voet D, Voet JG (2004) Biochemistry, 3rd edn. Wiley, 
New York 

White D (1999) The physiology and biochemistry of pro¬ 
karyotes, 2nd edn. Oxford University Press, New York 
Xion J, Bauer CE (2002) Complex evolution of photosyn¬ 
thesis. Annu Rev Plant Biol 53:503-521 
Xiong J (2006) Photosynthesis: what color was its origin? 
Genome Biol 206:1465-6914 


Biofilm 

Jana Kviderova 

Institute of Botany, Academy of Sciences of the 
Czech Republic, Trebon, Czech Republic 

Keywords 

Adaptation; Biofilm; Biomarkers; Community; 
Extreme environment; Microorganisms; Species 
composition; Structure 





276 


Biofilm 


Synonyms 

Microbial mats; Periphyton 

Definition 

Biofilm is a layer of microorganism(s) or micro¬ 
bial communities growing on a solid surface, 
usually of thicknesses ranging between several 
pm to several mm. The thicker biofilms are also 
referred as ► microbial mats. 

Overview 

Biofilm communities are found in various aquatic 
and subaerial ecosystems or even in the human 
body (e.g., dental plaque) at liquid-solid or aerial- 
solid interfaces (Fig. 1). Typical biofilms develop 
on stones in streams and rivers or at the bottom of 
lakes. They participate in nutrient and energy 
cycling in the given ► ecosystem and could 
serve as a substrate for colonization by other 
species. Repeated sedimentation of inorganic 
material on the growing biofilm leads to layered 
structure resembling stromatolites (Krumbein 
et al. 2003). 

Biofilms are usually formed by various 
microorganisms that include autotrophs as well 
as heterotrophs, eukaryotes, bacteria, and, in the 
most extreme conditions, archaea (Aguilera 
et al. 2007a). The organization level of the bio¬ 
film species can range from unicellular flagel¬ 
lates to multicellular filaments (Fig. 2). If the 
biofilm is formed by several layers of microor¬ 
ganisms, gradients of physical and chemical 
factors (e.g., light, pH, 0 2 ) are established and 
influence its structure and species composition. 
The microenvironment within the mature bio¬ 
film could be different from that of the surround¬ 
ings and could provide protection to more 
sensitive species (Ferris et al. 2005). For exam¬ 
ple, acidophilic red alga Cyanidium sp. is more 
tolerant to pH values above 3 than to those 
below 1, probably due to adaptation to elevated 
pH in biofilm interior (Kviderova 2012). It is 



Biofilm, Fig. 1 Biofilms in the acidic waters of Rio 
Tinto, SW Spain 


possible that microorganisms within biofilms 
communicate by chemical signals. Such com¬ 
munication has been detected in biofilms of 
pathogenic bacteria, but in natural communities 
very little is known of this phenomena (Kellner 
and Surette 2006). 

The development of a biofilm starts by accu¬ 
mulation of amorphous particles containing inor¬ 
ganic grains and bacteria. The cells divide, 
produce extracellular polymeric substances, 
form microcolonies, and provide substrate for 
further colonization by fungi and small eukary¬ 
otic heterotrophs like amoebas. The flagellates 
also participate at the initial formation. The ses¬ 
sile genera are observed later and could require 
establishment of some organic matrix to be 
attached on. Filamentous microorganisms are 
last to appear. Small pieces of mature biofilm 
detach either due to internal signals or external 
factors, like water flow, and could colonize a new 
surface (Aguilera et al. 2007b). 






Biofilms 


277 



Biofilm, Fig. 2 Example of a photosynthetic biofilm 
consisting in the association of unicellular red alga 
Cyanidium caldarium, filamentous green alga 
Klebsormidium sp., and pennate diatom Pinnularia 
sp. from Rio Tinto, Spain 

Biofilms are the new microbial ecology frontier. 
Biofilms have not been studied in a systematic way 
until recently due to lack of appropriate methodol¬ 
ogies. Confocal microscopy and in situ hybridiza¬ 
tion techniques allow to study intact biofilms and 
appreciate their complex stmctural diversity. For 
evaluation of photochemical performance of auto¬ 
trophic biofilms, methods using variable chloro¬ 
phyll fluorescence are applied in field (Gomez 
et al. 2011; Marteinsson et al. 2013) and in detailed 
laboratory (Kviderova 2012) studies. 

An important part of microbial life on Earth is 
associated to bio films. Biofilms and microorgan¬ 
isms from ► extreme environments are consid¬ 
ered interesting astrobiological model systems 
(Aguilera et al. 2007b; Gomez et al. 2011; Krai 
et al. 2004), specially as biomarkers of extinct or 
extant life in habitable planets like Mars or on 
Galilean moons. 


See Also 


► Microorganism 

► Rio Tinto 

► Stromatolites 


References and Further Reading 

Aguilera A, Souza-Egipsy V, Gomez F, Amils R (2007a) 
Development and structure of eukaryotic biofilms in 
an extreme acidic environment, Rio Tinto (SW, 
Spain). Microb Ecol 53:294-305 
Aguilera A, Amaral-Zettler L, Souza-Egipsy V, Zettler E, 
Amils R (2007b) Eukaryotic community structure 
from Rio Tinto (SW, Spain), a highly acidic river. In: 
Seckbach J (ed) Algae and cyanobacteria in extreme 
environments. Springer, Dordrecht 
Ferris MJ, Sheehan KB, Kiihl M, Cooksey K, 
Wiggleswoth-Cooksey B, Harvey R, Henson JM 
(2005) Algal species and light microenvironment in a 
low-pH geothermal microbial mat community. Appl 
Environ Microbiol 71:7164-7171 
Gomez F, Walter N, Amils R, Rull F, Klingelhofer AK, 
Kviderova J, Sarrazin P, Foing B, Behar A, Fleischer I, 
Parro V, Garcia-Villadangos M, Blake D, Martin 
Ramos JD, Direito S, Mahapatra P, Stam C, 
Venkateswaran K, Voytek M (2011) Multidisciplinary 
integrated field campaign to an acidic Martian Earth 
analogue with astrobiological interest: Rio Tinto. Int 
J Astrobiol 10:291-305 

Kellner L, Surette MG (2006) Communication in bacteria: 
an ecological and evolutionary perspective. Nat Rev 
Microbiol 4:249-258 

Krai T, Bekkum C, McKay C (2004) Growth of 
methanogens on a Mars soil simulant. Orig Life 
Evol Biosph 34:615-626 

Krumbein WE, Paterson DM, Zavarzin GA (2003) Fossil 
and recent biofilms: a natural history of life on earth. 
Kluwer Academic Publishers, Dordrecht 
Kviderova J (2012) Photochemical performance of the 
acidophilic red alga Cyanidium sp. in a pH gradient. 
Orig Life Evol Biosph 42:223-234 
Marteinsson V, Vaishampayan P, Kviderova J, Mapelli F, 
Medori M, Calfapietra C, Aguilera A, Hamisch D, 
Reynisson E, Magnusson S, Marasco R, Borin S, 
Calzada A, Souza-Egipsy V, Gonzalez-Toril E, 
Amils R, Elster J, Hansch R (2013) A laboratory of 
extremophiles: Iceland Coordination Action for 
Research Activities on Life in Extreme Environments 
(CAREX) field campaign. Life 3:211-233 


► Colonization, Biological 

► Concentration Gradients - 

► Ecosystem BiofillTIS 

► Extreme Environment 

► Microbial Mats ► Microbial Mats 











278 


Biogenicity 


Biogenicity 

Nicola McLoughlin 

Department of Earth Science and Centre for 
Geobiology, University of Bergen, Bergen, 
Norway 

Keywords 

Biosignatures and traces of life; History and ori¬ 
gins of life; Life detection 

Synonyms 

Biosignature 

Definition 

Biogenicity refers to any chemical and/or mor¬ 
phological signature preserved over a range of 
spatial scales in rocks, minerals, ice, or dust par¬ 
ticles that are uniquely produced by past or pre¬ 
sent organisms. This includes elemental and 
isotopic signatures diagnostic of life, which can¬ 
not be formed by purely abiotic processes. These 
may be accompanied by textural remains with 
shapes, orientations, and abundances that 
uniquely result from the growth or decay of 
(once) living organisms. Further support for 
biogenicity can be shown if the distribution and 
abundance of this evidence is controlled by bio¬ 
logically significant primary variables such as 
light, temperature, and nutrient gradients. 

Overview 

Biogenicity criteria are used to assess the likeli¬ 
hood of a biological origin for candidate traces of 
life. Biogenicity criteria address observable and 
quantifiable features that can be broadly divided 
into three types: (1) the morphological complex¬ 
ity and size distribution of textural traces of life; 
(2) the elemental composition, bonding, 


symmetry, and isotopic composition of chemical 
traces of life; and (3) the environmental distribu¬ 
tion or geological context of traces of life. These 
three approaches to investigating the biogenicity 
of candidate traces of life are mutually 
reinforcing and should be accompanied by efforts 
to falsify potential abiotic explanations for the 
observations. The so-called ► dubiofossils or 

► pseudofossils are features that are highly ques¬ 
tionable traces of life and more likely explained 
by abiotic processes that can mimic life 
(Hofmann 1971). 

Specific biogenicity criteria have been tailored 
for the different classes of biosignatures found on 
Earth. For ► microfossils in the rock record, 
biogenicity criteria have been proposed by 
Buick (1990) and Brasier et al. (2004), and in 
summary these focus on the size distribution of 
the population; morphological features such as 
branching, septation, evidence for cell walls, 
nuclei, or extracellular polymeric substances; 
their orientation, especially evidence of colonial 
behavior, tiering, or phototaxis; and lastly evi¬ 
dence of primary environmentally controlled dis¬ 
tribution and/or subsequent decay. The 
importance of such criteria has been highlighted 
by abiotic experiments that produce microfossil¬ 
like filamentous biomorphs in the laboratory 
(Garcia-Ruiz et al. 2003). These microfossil 
biogenicity criteria have also been adapted for 
meteorite samples, especially for those purported 
to contain fossilized ► magnetobacteria 
(Thomas-Kerpta et al. 2001). 

For laminated sedimentary stru