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Handbook of Astrobiology
Handbook of Astrobiology
Edited by
Vera M. Kolb
University of Wisconsin-Parkside, USA
CRC Press
Taylor & Francis Group
6000 Broken Sound Parkway NW, Suite 300
Boca Raton, FL 33487-2742
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Chapter 1.2 Astrobiology Goals: NASA Strategy and European Roadmap .......................................................................... 15
David J. Des Marais
Chapter 1.3 Online, Classroom and Wilderness Teaching Environments: Reaching Astrobiology Learners of All
Ages Around the World ...................................................................................................................................... 27
Bruce W. Fouke, Kyle W. Fouke, Tom Murphy, Colleen N. Cook, Bruce F. Michelson, Joseph L. Cross,
Lizanne DeStefano, Glenn A. Fried, Killivalavan Solai, Jacalyn Wittmer Malinowsky, Susan B. Kelly,
Claudia C. Lutz, Erin Louer, Courtney C. Fenlon, Nicholas P. Vasi, Adrienne M. Gulley, and Mayandi
Sivaguru
Chapter 2.2 A Generalized and Universalized Definition of Life Applicable to Extraterrestrial Environments .................. 65
Benton C. Clark
v
vi Contents
Chapter 3.1 Philosophical Aspects of the Origin-of-Life Problem: Neither by Chance Nor by Design ............................. 109
Iris Fry
Chapter 3.2 Charles Darwin and the Plurality of Worlds: Are We Alone? .......................................................................... 125
Michael Ruse
Chapter 4.2 Formation and Delivery of Complex Organic Molecules to the Solar System and Early Earth ...................... 165
Sun Kwok
Chapter 4.3 Organic Molecules in Meteorites and Their Astrobiological Significance ...................................................... 177
Zita Martins
Chapter 4.5 Atmosphere on Early Earth and Its Evolution as It Impacted Life ................................................................... 207
James F. Kasting
Chapter 5.2 Prebiotic Chemical Pathways to RNA and the Importance of Its Compartmentation ..................................... 235
Peter Strazewski
Chapter 5.3 The Hydrothermal Impact Crater Lakes: The Crucibles of Life’s Origin ........................................................ 265
Sankar Chatterjee
Contents vii
Chapter 5.5 Prebiotic Reactions in Water, “On Water,” in Superheated Water, Solventless, and in the Solid State ............331
Vera M. Kolb
Chapter 5.6 The Origin and Amplification of Chirality Leading to Biological Homochirality .......................................... 341
Kenso Soai, Arimasa Matsumoto, and Tsuneomi Kawasaki
Chapter 5.7 Phosphorus in Prebiotic Chemistry—An Update and a Note on Plausibility .................................................. 355
Alan W. Schwartz
Chapter 5.8 Phosphorylation on the Early Earth: The Role of Phosphorus in Biochemistry and Its Bioavailability .......... 361
Carolyn Lang, Jennifer Lago, and Matthew A. Pasek
Chapter 6.1 Transitions: RNA and Ribozymes in the Development of Life ........................................................................ 379
Eric J. Hayden, Niles Lehman, and Peter J. Unrau
Chapter 6.2 Three Ways to Make an RNA Sequence: Steps from Chemistry to the RNA World ...................................... 395
Paul G. Higgs
Chapter 6.5 The Origin of Life as an Evolutionary Process: Representative Case Studies ................................................. 437
Iris Fry
Chapter 8.1 The Progenote, Last Universal Common Ancestor, and the Root of the Cellular Tree of Life ....................... 521
Johann Peter Gogarten
Chapter 8.3 Viruses in the Origin of Life and Its Subsequent Diversification ..................................................................... 535
Luis P. Villarreal and Frank Ryan
Chapter 8.4 Carl R. Woese and the Journey toward a Universal Tree of Life ..................................................................... 555
Bruce W. Fouke, Killivalavan Solai, Shelby L. Jones, Elizabeth M. Smith, Kyle W. Fouke,
Kaitlyn E. Fouke, Claudia C. Lutz, Mayandi Sivaguru, and Glenn A. Fried
Chapter 8.6 Biomarkers and Their Raman Spectral Signatures: An Analytical Challenge in Astrobiology ...................... 597
Howell G.M. Edwards
Chapter 8.7 Fossilization of Bacteria and Implications for the Search for Early Life on Earth and Astrobiology
Missions to Mars ............................................................................................................................................... 609
Frances Westall and Keyron Hickman-Lewis
Chapter 9.1 Extremophiles and Their Natural Niches on Earth .......................................................................................... 635
Aharon Oren
Chapter 9.3 Virus Evolution and Ecology: Role of Viruses in Adaptation of Life to Extreme Environments ................. 677
Marilyn J. Roossinck
Chapter 11.1 Mind in Universe: On the Origin, Evolution, and Distribution of Intelligent Life in Space .......................... 701
David Dunér
Chapter 11.2 Where Are They? Implications of the Drake Equation and the Fermi Paradox .............................................717
Nikos Prantzos
Chapter 12.1 Exoplanets: Methods for Their Detection and Their Habitability Potential .................................................. 759
Ken Rice
Chapter 12.2 Solar System Exploration: Small Bodies and Their Chemical and Physical Conditions ............................... 775
Hikaru Yabuta
Chapter 12.3 Solar System Exploration: Icy Moons and Their Habitability ....................................................................... 787
Steven D. Vance
Chapter 12.4 Searching for Extraterrestrial Life in Our Solar System................................................................................ 801
Benton C. Clark
xi
xii Preface
Section 10 deals with habitability and characterization of This brief overview of the topics covered in the handbook
habitable planets. These topics and the evolution of habitabil- illustrates the comprehensive approach to astrobiology which
ity are discussed in a single chapter in this section. I desired and hopefully have achieved.
Section 11 includes four chapters on putative intelligent Thanks are expressed to the authors of the chapters, whose
life in the universe; the history and philosophy of this subject; contributions made this handbook possible, and to the edi-
and SETI (Search for Extraterrestrial Intelligence). Specific torial and production staff of the publisher, notably Rebecca
topics include philosophical approaches to the origin, evolu- Davies and Georgia Harrison, who facilitated the process of
tion, and distribution of intelligent life in space; implications producing the handbook in the record time, thus ensuring that
of the Drake equation and the Fermi paradox on the search its content stays current.
for intelligent life elsewhere; SETI and its goals and accom- I dedicate this handbook to the memory of my father, Dr.
plishments; and humanistic implications of discovering life Martin A. Kolb, and my mother, Dobrila Kolb, who encour-
beyond Earth. aged my early love for science and supported me in my path
The final section of the handbook, Section 12, has five towards becoming a scientist. This dedication extends to my
chapters which focus on exoplanets, exploration of the solar loved ones, Vladimir, Mirjana, and Natasha Kolb.
system, the search for extraterrestrial life, and planetary pro- Finally, special acknowledgment is due to my teachers of
tection. Specifically, topics include methods for detection of astrobiology, who generously shared their knowledge with me,
exoplanets and their habitability potential; small bodies in the satisfied my thirst for knowledge, inspired my dreaming about
solar system and their chemical and physical conditions; icy this exciting field, and carried me, so to speak, on their wings.
moons and their habitability; searching for extraterrestrial life There were many, too many to list here, but the very special
on Mars and in our solar system in general; and the history, ones are Leslie Orgel, Stanley Miller, Gustaf Arrhenius, and,
goals and objectives of the planetary protection program. most recently, Benton Clark.
Colour versions of figures can be downloaded from the CRC
Press website https://www.crcpress.com/9781138065123. The Vera M. Kolb
password to access the figures is: 9781138065123 Kenosha, Wisconsin
June 15, 2018
Editor
Vera M. Kolb earned a BS in Creative Activity. During her second sabbatical (2002–2003)
chemical engineering and an she studied sugar organo-silicates and their astrobiological
MS in organic chemistry from importance with Joseph Lambert, at Northwestern University,
Belgrade University, Beograd, Evanston, Illinois. Dr. Kolb was inducted in the Southeastern
Serbia, followed by a PhD in Wisconsin Educators’ Hall of Fame in 2002. She is a recipient
organic chemistry at Southern of numerous research and higher education grants and awards
Illinois University at from the Wisconsin Space Grant Consortium/NASA, among
Carbondale, Illinois. She was others. At this time, she has published over 150 articles,
a chemistry professor at the including patents and books, in organic chemistry, medicinal
University of Wisconsin–Parkside, Kenosha, Wisconsin, from chemistry, and astrobiology. She has edited a book,
1985 to 2016, and is now a professor Emeritus. During her Astrobiology, An Evolutionary Approach, for CRC Press,
first sabbatical leave (1992–1994), she received training in which was published in 2014. Her second book, Green
astrobiology (then termed exobiology) at the NASA Organic Chemistry and its Interdisciplinary Applications, was
Specialized Center of Research and Training (NSCORT) in published in 2016, also by CRC Press. Since both astrobiology
San Diego, where she has worked with Leslie Orgel at the and green chemistry study organic reactions in water, as in the
Salk Institute, and Stanley Miller, at the University of primordial soup for astrobiology and as a benign solvent in
California, San Diego, California. She has worked in the field green chemistry, the relationship between these two fields
of astrobiology ever since. In 1992 she received the University speaks of their true interdisciplinary character.
of Wisconsin–Parkside Award for Excellence in Research and
xiii
Contributors
Jessica C. Bowman Colleen N. Cook
School of Chemistry and Biochemistry Online and Continuing Education
Georgia Institute of Technology University of Illinois at Urbana-Champaign
Atlanta, Georgia Urbana, Illinois
and
Antoni Camprubí Innovative Education
Departamento de Procesos Litosféricos University of South Florida
Instituto de Geología Tampa, Florida
Universidad Nacional Autónoma de México
Mexico City, Mexico Joseph L. Cross
Carl R. Woese Institute for Genomic Biology
Sankar Chatterjee University of Illinois at Urbana-Champaign
Geosciences Urbana, Illinois
Museum of Texas Tech University
Lubbock, Texas
Punam Dalai
Aditya Chopra Department of Polymer Science
Planetary Science Institute University of Akron
Research School of Astronomy & Astrophysics Akron, Ohio
Research School of Earth Sciences
Australian National University David J. Des Marais
Canberra, Australia Exobiology Branch
NASA—Ames Research Center
Benton C. Clark Moffett Field, California
Space Science Institute
Boulder, Colorado
Lizanne DeStefano
Center for Education Integrating Science
Vanessa Colás Mathematics and Computing
Departamento de Procesos Litosféricos Georgia Institute of Technology
Instituto de Geología Atlanta, Georgia
Universidad Nacional Autónoma de México
Mexico City, Mexico
Steven J. Dick
María Colín-García Scientific Advisory Board
Departamento de Dinámica Terrestre Superficial SETI Institute
Instituto de Geología Board of Directors, METI International
Universidad Nacional Autónoma de México
Mexico City, Mexico David Dunér
Division of History of Ideas and Sciences
Catharine A. Conley Division of Cognitive Semiotics
New Mexico Institute of Mining and Technology Lund University
Socorro, New Mexico Lund, Sweden
xv
xvi Contributors
Vera M. Kolb
CONTENTS
1.1.1 Introduction ...................................................................................................................................................................... 3
1.1.2 Astrobiology: Definition, Scope, and a Brief History ...................................................................................................... 3
1.1.3 Classification of Astrobiology as a Field of Study ........................................................................................................... 4
1.1.4 A Brief Overview of Selected Key Developments in Astrobiology ................................................................................. 5
1.1.4.1 Understanding the Concept of Life ................................................................................................................. 5
1.1.4.2 Chemicals in the Universe and Their Delivery to the Early Earth ................................................................. 5
1.1.4.3 Prebiotic Chemistry and the Ribonucleic Acid World .................................................................................... 6
1.1.4.4 Prebiotic Reactions in Hydrothermal Vents .................................................................................................... 7
1.1.4.5 Prebiotic Reactions in Water and in the Solid State........................................................................................ 7
1.1.4.6 Phosphorus in Prebiotic Chemistry ................................................................................................................. 7
1.1.4.7 Prebiotic Evolution of Homochirality ............................................................................................................. 7
1.1.4.8 Approaches to Reconstructing the Origin of Life ........................................................................................... 8
1.1.4.9 Abiotic-to-Biotic Transition ............................................................................................................................ 8
1.1.4.10 Early Compartmentalization and Development of Protocells......................................................................... 8
1.1.4.11 Astrobiology and Evolution of Life ................................................................................................................. 9
1.1.4.12 Biosignatures and Detection of Life................................................................................................................ 9
1.1.4.13 Life Under Extreme Conditions ...................................................................................................................... 9
1.1.4.14 Habitability Within the Solar System and Beyond ......................................................................................... 9
1.1.4.15 Some Rapidly Advancing Astrobiology Areas ............................................................................................... 9
1.1.5 Summary ........................................................................................................................................................................ 10
Dedication ................................................................................................................................................................................... 10
References ................................................................................................................................................................................... 10
1.1.1 INTRODUCTION the future of life on Earth and beyond. Astrobiology scope is
delineated in the NASA’s astrobiology roadmap (Des Marais
In this chapter, the definition, scope, and a brief overview et al. 2008). Specific goals include understanding the emer-
of astrobiology are given. Classification of astrobiology as gence of life on Earth, determining how the early life on
a field of study, its specific goals, its multidisciplinary and Earth interacted and evolved with its changing environment,
interdisciplinary nature, and selected key developments are understanding the evolutionary mechanisms and environmen-
described. Astrobiology includes numerous research themes, tal limits of life, exploring habitable environments in our solar
which are expanding as the field evolves. Thus, it is not pos- system and searching for life, understanding the nature and
sible to cover all the developments in a single chapter, even distribution of habitable environments in the universe, and
briefly. Instead, an overview of selected astrobiology develop- recognizing signatures of life on the early Earth and on other
ments is presented, which is only a sampler of what is offered worlds. The NASA’s astrobiology map is being updated as
in this handbook. the astrobiology field advances. A similar roadmap has been
developed for astrobiology research in Europe (Horneck et al.
1.1.2 ASTROBIOLOGY: DEFINITION, 2015, 2016). The topic of these roadmaps is further discussed
and updated in Section 1 of this handbook.
SCOPE, AND A BRIEF HISTORY
Astrobiology is a young science that acquired its name
Astrobiology is defined as the study of the origin, evolution, only in 1995 (named by Wes Huntress from NASA; Catling
distribution, and future of life in the universe (NASA’s defini- 2013). Astrobiology evolved from its predecessor, exobiol-
tion; Des Marais et al. 2008). Astrobiology seeks to answer ogy, which is the study of the origin of life and of possible
fundamental questions about the beginning and evolution of life outside Earth (Dick and Strick 2004; Dick 2007). The
life on Earth, possible existence of extraterrestrial life, and term exobiology was coined in 1960 (by Joshua Lederberg).
3
4 Handbook of Astrobiology
The difference between the two fields is that astrobiology is (Miller and Orgel 1974; Mason 1991; Brack 2000; Zubay
broader and notably includes the evolution of life on Earth. 2000; Chela-Flores 2001, 2011; Fenchel 2002; Lurquin 2003;
The exobiology era coincided with the space missions, nota- Gilmour and Sephton 2004; Luisi 2006; Sullivan and Baross
bly the Viking mission on Mars in 1976, which followed a 2007; Sullivan and Carney 2007; Kolb 2014a; Longstaff
series of reconnaissance missions in the 1960s and early 2015). New developments on chemical origins of life and pre-
1970s. The Viking mission searched for the microbial life on biotic chemistry are covered in Section 5 of this handbook.
Mars (DiGregorio 1997; Jones 2004), but it did not confirm
its existence. The early experiments that used radio astron- 1.1.3 CLASSIFICATION OF ASTROBIOLOGY
omy to search for extraterrestrial intelligence by the Search
AS A FIELD OF STUDY
for Extraterrestrial Intelligence (SETI) program (Tarter 2007)
did not result in positive findings. In 1996, the analysis of the Astrobiology is commonly referred to as a field of study
Martian meteorite ALH84001, which was found in Antarctica, rather than a discipline. Dick (2012) examined the ques-
indicated possible presence of the fossils of bacterial life tion if astrobiology is a separate discipline and if it should
(Goldsmith 1997; Jones 2004), but the results were not con- be considered as such. This question is still open to discus-
vincing enough. Disappointments regarding a lack of positive sion. Astrobiology as a discipline would include origins of
results in the search for extraterrestrial life (Dick and Strick life (interstellar molecules, complex organics, development
2004; Dick 2007, 2012) continue to this date. The only life we of laboratory experiments, life in extreme environments,
know of is the life on Earth. Search for extraterrestrial life and genomics/phylogenetic relationships), planetary systems (the-
extraterrestrial intelligence is further discussed in Sections 10 oretical studies, atmospheric biosignatures, extrasolar planets,
through 12 of this handbook. circumstellar disks), planetary science (rock biosignatures,
While astrobiology is a new science, it comes from biogeochemistry, geochemistry exploration of Mars, Europa,
a very old and long history of ideas, which go all the way moons, etc.), and SETI (Dick 2012). A common approach is
back to the antiquity. The history of one of the core ideas that astrobiology is not a discipline itself but draws upon other
of astrobiology, a possibility of extraterrestrial life, is disciplines, subdisciplines, and specialized areas of research.
described in the books: “Plurality of worlds: The origins Physics, chemistry, biology, geology, and astronomy were the
of the extraterrestrial life debate from Democritus to Kant” initial disciplinary pillars of astrobiology. Rapid developments
(Dick 1984), “The extraterrestrial life debate, 1750–1900” in astrobiology and astrobiology-relevant disciplines led to
(Crowe 1999), “Medieval cosmology: Theories of infinity, an expanded list, which included cosmology, atmospheric
place, time, void, and the plurality of worlds” (Duhem 1987), science, oceanography, evolutionary science, paleontology,
and other sources. A comprehensive coverage of the ideas planetary science, biochemistry, molecular biology, microbi-
about extraterrestrial intelligent life is covered in the books: ology, and ecology. Astrobiology also seeks insights from his-
“Extraterrestrials: Science and alien intelligence” (Regis tory of science and philosophy (Fry 2000). The latter approach
1987), “Extraterrestrials: Where are they?” (Zuckerman is also covered in Section 3 of this handbook.
and Hart 1995), “Beyond contact: A guide to SETI and An all-encompassing goal for astrobiology is to understand
communicating with alien civilizations” (McConnell 2001), cosmic evolution. NASA embraced the idea of cosmic evo-
and “Civilizations beyond Earth: Extraterrestrial life and lution, comprising the following evolutionary sequence: Big
society” (Vakoch and Harrison 2013), among other sources. Bang, galaxies, stars, biogenic elements, planets, chemical
The future of life on Earth and its potential uniqueness are evolution, origin of life, pre-Cambrian biology, complex life,
discussed in the books “The life and death of planet Earth: intelligent life, cultural evolution, civilization, science and
How the new science of astrobiology charts the ultimate fate technology, and the study of life in the universe (Dick 2007).
of our world” (Ward and Brownlee 2002), and “Rare Earth: This formidable goal adds many more disciplines and sub-
Why complex life is uncommon in the universe” (Ward and disciplines of various fields of study for astrobiology to rely
Brownlee 2004). Search for exoplanets, some of which may upon. It becomes clearer why it would be difficult to classify
be habitable, is a subject of recent studies (Kasting 2010; astrobiology as a single discipline.
Summers and Trefil 2017). This subject is further covered in NASA classified astrobiology as a field of study that is
Section 12 of this handbook. multidisciplinary in its content and interdisciplinary in its
The major hypothesis about the origin of life on Earth, execution. Astrobiology requires a close coordination of not
which later became accepted as a key foundation of both exo- only various disciplines but also programs, including space
biology and astrobiology, was proposed independently by A.I. missions (Race 2007).
Oparin in 1924 and J. B. S. Haldane in 1929 (Oparin 1965, The distinction between multidisciplinary and interdis-
1968, 1994; Deamer and Fleischaker 1994; Haldane 1994). ciplinary studies is described in the book “Interdisciplinary
This hypothesis states that the origin of life on Earth can be research, process and theory” by Repko (2012). Both types of
understood based only on the laws of chemistry and physics. studies are used to investigate complex problems and issues,
Life arose in Earth’s distant past by chemical reactions and which are beyond the ability of any single discipline. These
physical processes under the specific conditions on the early studies are thus well suited for astrobiology. Repko addresses
Earth and over a long period of time. Numerous rapid devel- the “multi,” “inter,” and “disciplinary” parts of these terms. A
opments based on the Oparin–Haldane proposal followed brief account is given here. In a multidisciplinary approach,
Astrobiology 5
a problem is studied from the perspective of several disci- a challenge. A choice taken here is to focus on the themes that
plines at one time. This approach tends to be dominated by are most closely related to the central focus of astrobiology as
the method and theory preferred by the main discipline of the a study of the origin and evolution of life and on a possibility
investigator. This prevents effective integration of the insights of life elsewhere.
from all the disciplines that were consulted. In contrast, the
interdisciplinary approach successfully integrates disciplin-
1.1.4.1 Understanding the ConCept of Life
ary insights to construct a more comprehensive understanding
of the problem. While employing a research process that sub- Among key problems that astrobiology is yet to solve is to
sumes the methods of relevant disciplines, interdisciplinary define life (Popa 2014). Many such definitions have been pro-
research does not privilege any disciplinary method or theory. posed, but none is universally accepted (Popa 2014). While
Thus, the interdisciplinary approach is more powerful but not each definition addresses some features of life, none appears
always easy to achieve (Repko 2012). inclusive of all the features. Even the most inclusive defini-
Although the modern astrobiology field is commonly per- tions may only describe what life does but may not state what
ceived as mostly based on the developments in the natural sci- life is (Catling 2013). We may not know enough about the the-
ences and technology, contribution to astrobiology from other ory of life to define it properly (Cleland and Chyba 2007). Our
disciplines needs to be considered equally. This is demon- ability to define life is also dependent on our understanding
strated in a review paper by Dick (2012) titled “Critical issues of the origin of life. Currently, the NASA’s operational defini-
in the history, philosophy, and sociology of astrobiology”. tion of life that is used most often is: “Life is a self-sustained
In its study of some complex problems, such as the future chemical system capable of undergoing Darwinian evolution”
of life and the humanistic implications of discovery of extra- (Popa 2014). This definition, however, is not very useful in
terrestrial life (Dick and Lupisella 2009; Dick 2015), astrobi- search for extraterrestrial life, since it would require observa-
ology may use a transdisciplinary approach. This approach is tion of evolution (Catling 2013). What is desired is a definition
useful in studies of complex and mega problems, which are at of life that will also be applicable to life in general and thus to
once between the disciplines, across different disciplines, and the putative extraterrestrial life. A universal definition of life
beyond all disciplines (Repko 2012). in which living beings are considered autonomous systems
Interdisciplinary and transdisciplinary nature of astrobi- with open-ended evolutionary capacities has been proposed
ology is especially needed for the study of cosmic evolution. (Ruiz-Mirazo et al. 2004). A generalized and universal-
Progress in understanding of the individual steps of this evo- ized definition of life has been proposed for the identifica-
lution has been made based mostly on the multidisciplinary tion of extraterrestrial and artificial life forms (Clark 2004).
approach. However, a full integration of the insights from An examination of the proposal that prebiotic evolution that
the individual disciplines that are involved in these evolu- leads to life is Darwinian continues, with no definitive conclu-
tionary steps has not yet been achieved. This is notably the sion (Perry and Kolb 2004). One area of progress is a better
case for the cosmic evolutionary step of the origin of life on understanding of viruses, which are in the twilight zone of
Earth. life (Villarreal 2004). The question if viruses are alive is also
Astrobiology may also be considered an evolutionary sci- discussed from the philosophical point of view of dialethe-
ence. The multi-/interdisciplinary nature of astrobiology ism, which allows for viruses to be considered both alive and
evolves to include more disciplines and subdisciplines and not alive (Kolb 2010a). The problem of defining life is further
to achieve a better integration of the disciplinary insights. discussed in Section 2 of this handbook.
Astrobiology research tools, which are typically initially
borrowed from its contributing disciplines, become more 1.1.4.2 ChemiCaLs in the Universe and their
advanced and specialized for astrobiology use, which allows
deLivery to the earLy earth
for new research programs to emerge. Technological advances
enable space missions that search for extraterrestrial life and The formation of chemicals in the universe and their deliv-
habitable places within our solar system. Based on these and ery to the early Earth (Shaw 2006; Longstaff 2015; Kwok
many more new developments, critical issues, goals, and 2016, 2017) were necessary for life to evolve. Many inter-
objectives of astrobiology evolve accordingly. An evolution- stellar molecules are prebiotically relevant. Complex organic
ary approach to astrobiology is presented in a recent book molecules were formed in space and delivered to the solar
(Kolb 2014a). system and early Earth. The delivery occurred mostly by the
In the next section, selected key developments in astrobiol- comets (e.g., Chyba et al. 1990) and meteorites. The origin
ogy are overviewed. of terrestrial water, which is critical to life, is from comets
but also from other sources (O’Brien et al. 2018). Meteorites
1.1.4 A BRIEF OVERVIEW OF SELECTED KEY of the carbonaceous chondrite type (McSween 1999) deliv-
ered complex chemical compounds, many of which were
DEVELOPMENTS IN ASTROBIOLOGY
important for the emerging life. They include amino acids
As shown in the previous section, astrobiology research themes and nucleobases (Sephton 2004; Schmitt-Kopplin et al.
are numerous and constantly expanding. There are “astro” and 2010, 2014; Burton et al. 2012). This is further discussed in
“bio” themes, and the organization of their coverage presents Section 4 of the handbook.
6 Handbook of Astrobiology
1.1.4.3 prebiotiC Chemistry and the that might have facilitated polynucleotide replication (James
ribonUCLeiC aCid WorLd and Ellington 2000; Orgel 2004).
Key discoveries in prebiotic chemistry and the origin
In 1953, Stanley Miller published the results of a seminal of the RNA world up to the early 2000s were reviewed by
experiment that showed that the amino acids, which are the Orgel (2004). This review includes work on template-
building blocks of proteins, can be synthesized in the labora- directed synthesis of nucleotides by Orgel and his coworkers.
tory under the reaction conditions that simulate those on the Eschenmoser’s work is also highlighted. With his cowork-
early Earth (Miller 1953; Mesler and Cleaves 2016). Miller ers, he synthesized and studied close chemical alternatives to
built a glass apparatus consisting of a series of connected RNA and DNA in a systematic manner to gain an insight into
flasks and tubing to simulate the primitive Earth’s environ- the selection of the naturally occurring forms. They synthe-
ment. One flask was filled with water, representing the early sized RNA and DNA analogs in which the sugar component,
ocean. Water could be heated to simulate evaporation. Another ribose for RNA and deoxyribose for deoxyribonucleic acid
flask simulated the early atmosphere. It contained gases meth- (DNA), were substituted with a different sugar type or a dif-
ane, hydrogen, ammonia, and water vapor, which reflected the ferent sugar form (in both RNA and DNA, the sugar form is
belief at that time that the early Earth’s atmospheric condi- a five-membered ring). For example, they synthesized homo-
tions were reducing. The source of energy in the experiments DNA, in which the five-membered ring was expanded to a
was electrical spark generated by Tesla coil. Various amino six-membered ring, an analog of glucose. They also prepared
acids were formed, including glycine and alanine. Miller’s pyranosyl-RNA, based on a six-membered sugar form rather
experiment showed that organic compounds that are impor- than the five-membered form found in RNA. In addition,
tant for life can indeed be formed under prebiotic conditions. they varied a sugar type and prepared threose nucleic acid
Many more prebiotic experiments by different investiga- (TNA), which is based on the sugar threose rather than ribose.
tors followed. Much progress has been made by the early Eschenmoser put together all the experimental results to
1970s, as shown in the book “The origins of life on earth” determine “chemical etiology” of nucleic acids (Eschenmoser
(Miller and Orgel 1974). Prebiotic syntheses of amino acids, 1999). The latter explains how changes in chemical structures
urea, fatty acids, porphyrins, vitamins, purines, pyrimidines, influence hydrogen bonding, folding, and other properties of
sugars, and nucleosides have been attempted, and some gave nucleic acids. For example, while homo-DNA can make a
excellent yields. stable double helix via hydrogen bonds, the type of its helix is
Further progress in prebiotic syntheses has been achieved incompatible with the RNA helix. This prevents formation of
in the next three decades (Brack 2000; Bilgen 2004; Orgel a double helix between a strand of homo-DNA and a strand of
2004; Herdewijn and Kisakürek 2008; Peretó 2012). Some of RNA, which makes homo-DNA unsuitable for the transcrip-
these syntheses facilitated new proposals on the origins of life. tion process. This etiology of nucleic acids provided an insight
Selected examples are presented here. Miller performed syn- into the selection of the present-day type and form of nucleic
theses of amino acids under mildly reducing or non-reducing acids (Eschenmoser 1999). Benner expanded the genetic
conditions, which reflected an updated view on the atmo- alphabet from standard AGCT/U (adenine, guanine, cytosine,
spheric conditions on the early Earth. The results were less thymine/uracil) with synthetic unnatural nucleobases. He
favorable than those in the reducing atmosphere, but, in com- also synthesized sulfone-linked RNAs (Benner 2004). The
bination with other prebiotic factors, these results were judged sulfone-based RNA backbone is not charged, as opposed to
adequate (Miller 2000). Wächtershäuser proposed that the the natural phosphate backbone. Like Eschenmoser, Benner
original source of prebiotic organic material under deep-sea used the experimental results to gain insight into the structure
vents conditions may have been a reduction of carbon diox- and function of nucleic acids by considering their hydrogen
ide with hydrogen sulfide over ferrous sulfide as the reducing bonding and folding properties and the reasons why some nat-
agent. He believed that life originated in an iron–sulfur world ural structures are superior to the analogous unnatural ones.
(Wächtershäuser 2000, 2008; Orgel 2004). Based on the clues As one example, sulfone-linked RNAs are unsuitable, since
from the present-day biology, De Duve (2000) proposed an they fold and aggregate in water. This shows the importance
early thioester world, in which thioesters had a role in primi- of charged backbones in nucleic acids, since charges prevent
tive (proto) metabolism. Progress in non-enzymatic autoca- undesired folding and aggregation in water. Charged back-
talysis and self-replication, notably by von Kiedrowski and bones are thus selected in nature.
coauthors, has been made (Burmeister 2000). Prebiotic synthesis of biological compounds (Cleaves 2013,
The proposal of ribonucleic acid (RNA) world emerged as 2014) as well as the work on biochemical pathways as evidence
a leading hypothesis for the origins of life (Joyce and Orgel for prebiotic synthesis (McDonald 2014) have advanced. The
1993; Orgel 2004). This hypothesis postulates that the RNA progress in prebiotic synthesis continued with a new, innova-
is the original self-replicator that has a capability to carry the tive prebiotic synthesis of nucleotides (Powner et al. 2011;
genetic information and act as a catalyst. Within this hypoth- Islam and Powner 2017; Sutherland 2017), which has previ-
esis, various aspects of RNA were studied. Examples include ously been only marginally successful. Significant new work
non-enzymatic polymerization of RNA monomers to RNA, on the RNA world and its connection to the origins of life
with montmorillonite clay as a catalyst (Ferris 2000), and the has been recently reported (e.g., Robertson and Joyce 2012;
enzymatic ribozyme (RNA that acts as an enzyme) catalysis Higgs and Lehman 2015; Pressman et al. 2015; Mathis et al.
Astrobiology 7
2017). The advances in prebiotic chemical pathways to RNA 1.1.4.6 phosphorUs in prebiotiC Chemistry
and the properties of RNA that enable its self-replication and
enzymatic activity are further covered in Sections 5 and 6 of Life on Earth requires phosphorus in DNA/RNA and in the
this handbook. chemical energy sources. Thus, the study of the role of phos-
phorus in prebiotic chemistry is important. A convincing sce-
nario for the incorporation of phosphorus from geologically
1.1.4.4 prebiotiC reaCtions in hydrothermaL vents plausible sources into chemical systems on the early Earth
Prebiotic reactions under the conditions of hydrothermal was not initially conceived, leading to the so-called “phos-
vents gained importance, since such vents on Earth are rich phorus problem.” Progress has been made on this front, as
with life. These vents provide both chemicals and energy a result of several approaches (Fernández-García et al. 2017;
sources, making them feasible as a niche for the emergence Pasek et al. 2017), as well as the discovery of a meteoritic
of life. Thus, other bodies in the solar system that possess source of reactive phosphorus, which may have been deliv-
hydrothermal vents could also be habitable. Chemistry under ered to the early Earth (Maciá 2005; Pasek and Lauretta 2005;
the conditions of the hydrothermal vents has a substantial Schwartz 2006; Pasek 2014). This subject is further discussed
prebiotic potential (Holm and Andersson 2000; Orgel 2004; in Section 5 of this handbook.
Padgett 2012; Sojo et al. 2016). As one example, components
of the citric acid cycle, which are important for development
1.1.4.7 prebiotiC evoLUtion of homoChiraLity
of protometabolism, have been synthesized under these con-
ditions (Orgel 2004). Prebiotic chemistry in hydrothermal The origin of biological homochirality is one of the central
vents is further discussed and updated in Section 5 of this problems in understanding chemistry of life. Chiral mol-
handbook. ecules (or other objects) are not superimposable with their
mirror images (such as the left hand and the right hand).
1.1.4.5 prebiotiC reaCtions in Water Each of the pair of such molecules is termed an enantiomer.
Homochirality occurs when all the constituent units are mol-
and in the soLid state
ecules of the same chiral form (enantiomer).
Progress has been made in prebiotic organic reactions in water Many key biochemical compounds are chiral. Chiral
as a reaction medium, a model for the prebiotic soup. While properties provide an extra dimension in the specificity of
most organic compounds are not water-soluble, prebiotic reac- molecular recognition, such as between the enzymes and
tions are supposed to happen in water, which is the ubiquitous their substrates. Homochirality is common in biology. Thus,
solvent on Earth and is also the medium for life. Recent find- nature uses almost exclusively l-amino acids and d-sugars,
ings show how prebiotic reactions of water-insoluble organic thus only one out of the two possible forms. A question is
compounds can occur in water, by a special mechanism called posed about the origin of homochirality, if it occurred pre-
“on-water” reactions. According to this mechanism, insolu- biotically or during the biotic evolution. Prebiotic evolu-
ble organic materials are driven toward each other in water tion of homochirality is envisaged to occur in three steps:
by the hydrophobic interactions. The proximity between the mirror-symmetry breaking, chiral amplification, and chiral
molecules then facilitates the reaction. Furthermore, selectiv- transmission. The mirror-symmetry breaking occurs under
ity and specificity of the reactions are often improved (Kolb the influence of circularly polarized light or other physi-
2014b). This type of reaction is an exception from the usual cal causes. It results in a minute enantiomeric imbalance.
formation of intractable mixtures in the prebiotic experiments A slight enantiomeric excess observed in the meteoritic
(Benner et al. 2012; Benner 2014). amino acids indicates an asymmetric influence on organic
Many classical organic reactions, which are a bread and chemical syntheses under abiotic conditions (Cronin and
butter of prebiotic chemistry, are possible in superheated Pizarrello 1997; Pizzarello 2008). The second step, chiral
water and thus under hydrothermal conditions. They have amplification, leads to enantiomeric enrichment. The third
been studied in context of green chemistry (environmentally step, chiral transmission, enables the transfer of chiral-
friendly) (e.g., Kolb 2016). This is covered in more detail in ity between molecules. Studies on the origin of a single
Section 5 of this handbook. chirality of amino acids and sugars indicate that a partial
Prebiotic chemistry in water–ice matrix occurs readily enantioenrichment in prebiotic world may have been suf-
(Menor-Salván and Marín-Yaseli 2012). Organic materials ficient to trigger chemical and physical processes to enable
and salts concentrate in the liquid phase of the crystalline ice further amplification of the enantiomeric excess (Hein and
matrix and form eutectic solutions. The concentration effect Blackmond 2012). Enantioselective automultiplication of
generally increases the reaction rates. Thus, prebiotic chemis- chiral molecules can occur via asymmetric catalysis, in
try in the ice world is feasible. which a chiral compound acts as a chiral catalyst for its
Prebiotic reactions can also occur quite successfully in own production (Soai et al. 2000). Reviews of the prebi-
the solid state. Surprisingly, the reactions are often very fast otic origins of homochirality are available (Coveney et al.
and specific. This has a direct application to the chemistry on 2012; Ruiz-Mirazo et al. 2014). Origin and chemical evo-
asteroids and meteorites (Kolb 2010b, 2012). These reactions lution of biological homochirality are further discussed in
are also covered in Section 5 of this handbook. Section 5 of this handbook.
8 Handbook of Astrobiology
1.1.4.8 approaChes to reConstrUCting zone is not known. Progress has been made in the under-
the origin of Life standing of the nature of life as an organized complexity. Life
represents order, which imposes thermodynamic require-
The emergence of life is a historical process, which scientists ments between the life entity (typically a compartmentalized
try to reconstruct. Different approaches exist to this problem. system) and its environment. However, both thermodynamic
The “metabolism first” approach envisions that the process and kinetic factors constitute driving force for the emergence
starts with the development of a primitive metabolism. Others of life (Pross 2003, 2012). Emergence of order out of chaos
believe that compartmentalization is the essential first step has been invoked as a way for an organized system to emerge
(Deamer 2000, 2007). The “genetics first” proponents believe from chaotic mixtures of components (Kauffman 1993, 1995,
that the formation of self-replicating polymers, such as RNA, 2000). Properties attributed to chemical systems that are
is critical. Peretó discusses problems and controversies of these transitioning to life are complex chemical behaviors, such
approaches (Peretó 2005). Most believe that the origin of life is as self-organization and self-assembly; formation of auto-
linked to the RNA world, in which RNA has both genetic and catalytic networks and protometabolic cycles; and establish-
enzymatic properties and is capable of self-replication. ment of self-replicating systems (Padgett 2012; Peretó 2012;
The research approaches that are employed for reconstruc- Ruiz-Mirazo et al. 2014). Possible scenarios of protobiological
tion of the origin of life are bottom-to-top and top-to-bottom events prior to the emergence of the last universal common
approaches. In the former, prebiotic chemistry is studied ancestor (LUCA) have been proposed (Mann 2013). The idea
experimentally under simulated prebiotic conditions, start- of an alternative living world that existed prior to the LUCA
ing from the simple compounds and moving toward molecu- of the organisms, as we know them, is introduced. Peretó dis-
lar complexity that is characteristic of life (Lahav 1999). This cusses proposed stages in the origin of life, which comprise
research pathway benefited greatly from new developments in prebiotic, protobiological, and biological stages. Each stage
prebiotic synthetic methods and an increased knowledge of consists of the additional sub-stages, such as the pre-RNA
the environmental conditions on the early Earth under which world (Peretó 2005). Joyce (2012) also discusses pathways to
these syntheses occurred. Lahav considered different ways of life and considers the pre-RNA life, which was based on dif-
bottom-up reconstruction of early stages of chemical evolution. ferent types of RNA. Krishnamurthy (2017) took a chemical
The reconstruction could be without or with specific biogeo- approach to the transition from prebiotic chemistry to proto-
chemical constraints. The latter included minerals that acted biology and analyzed how a diverse pool of prebiotic building
as catalysts or were involved in energy production and transfer, blocks could lead to a self-assembling system that is capable
among other roles (Lahav 1999). The bottom-to-top approach of chemical evolution. His analysis encompassed different
needs to be looked at in conjunction with the conditions on the classes of biomolecules that built the thioester world, protein
Early Earth (Burton et al. 2012; Scharf et al. 2015; Domagal- world, metabolism world, lipid world, and RNA world.
Goldman et al. 2016). Also, the chemistry on meteorites, which Theoretical and computational approaches have been used
are the prebiotic laboratory, needs to be considered. to examine if there is an algorithm for abiotic-to-biotic tran-
In the top-to-bottom approach, a reconstruction of the sition (Walker 2014). The nature of biological information,
origin of life is attempted, going from its most primitive life informational limits of evolution, Shannon information con-
forms to the putative RNA world (Lahav 1999; Sephton 2004) tent of biopolymers, molecular quasispecies, and replicator
and the pre-RNA world (Hazen 2005). Development of new equations were addressed. While no definitive conclusion
research tools, notably those in molecular biology, facilitated was reached, it appears that the answer to how life emerged
this approach. These tools are responsible for rapid recent from non-life will probably come from some combination
advances in the understanding of RNA and the RNA world of chemistry and information-based formalism. Since life is
(Ruiz-Mirazo et al. 2014). Progress has been made in modeling an organized complexity, studies of complexity and in rela-
the RNA world by the RNA viral quasispecies (Padgett 2012; tion to life are relevant to the understanding of the nature of
Eigen 2013). The newest research on this topic is covered in transition zone to life and to the emergence of life (Waldrop
Sections 5 and 6 of this handbook. It includes various aspects 1992; Holland 1995; Mitchell 2009; Lineweaver et al. 2013).
of prebiotic pathways to RNA, coevolution of RNA and pep- The topics of transition from prebiotic toward biotic world
tides, and the role of RNA and ribozymes in the development and life are updated and further discussed in Section 6 of this
of life, among others. This is the most significant and most rap- handbook.
idly developing area of research into the origins of life, which
thus justifies its extensive coverage in this handbook.
1.1.4.10 earLy CompartmentaLization and
deveLopment of protoCeLLs
1.1.4.9 abiotiC-to-biotiC transition
Since his original proposal in 1924, Oparin made experimental
Both bottom-to-top and top-to-bottom approaches to the ori- progress in study of coacervates. Coacervates are feasible
gins of life lead to a putative transition zone between life and as prebiotic compartmentalized systems and can serve as
non-life. The nature of this zone is not elucidated, but it is prebiotic chemical reactors. In addition, they are capable
assumed to contain a complex mixture of organic compounds. of undergoing a primitive “reproduction” by splitting into
The mechanism by which life emerged from the transition smaller units (Oparin 1968).
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Language: Finnish
Kirj.
Stanley J. Weyman
Mary Hämeen-Anttila
SISÄLLYS:
I. Zatonin majatalo
II. »Vihreässä pilarissa»
III. Linna metsässä
IV. Madame ja mademoiselle
V. Hyvitys
VI. Pic du Midin kupeella
VII. Kunnon kepponen
VIII. Eräs kysymys
IX. Clon
X. Vangitseminen
XI. Matkalla Pariisiin
XII. Tienristeyksessä
XIII. Martinpäivän aatto
XIV. Jälkikesä
I luku
Zatonin majatalo
»Merkityt kortit!»
Se pisti markiisia.
»Vettä pyysin teiltä eilen, mutta sitä ette suonut minulle», murisin
minä. »No niin, parempi myöhään kuin ei milloinkaan. Menkää
hakemaan. Jos minut hirtetään, niin tahdon tulla hirtetyksi kuten
ritari. Mutta siitä saatte olla varma, että kardinaali ei tee sellaista
kurjaa kepposta vanhalle ystävälle.»
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