From Stars to Brains: Milestones in the Planetary Evolution of Life and Intelligence [1st ed.] 978-3-030-10602-7, 978-3-030-10603-4

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From Stars to Brains: Milestones in the Planetary Evolution of Life and Intelligence [1st ed.]
 978-3-030-10602-7, 978-3-030-10603-4

Table of contents :
Front Matter ....Pages i-xxiv
The Building Blocks of Intelligence (Andrew Y. Glikson)....Pages 1-29
Milestones in Early Evolution (Andrew Y. Glikson)....Pages 31-52
From the Genetic Code to Collective Brains (Andrew Y. Glikson)....Pages 53-88
Intelligent Communities (Andrew Y. Glikson)....Pages 89-114
Directional Thought and Evolution (Andrew Y. Glikson)....Pages 115-141
Epilogue—From Stars to Brains (Andrew Y. Glikson)....Pages 143-152
Back Matter ....Pages 153-160

Citation preview

Andrew Y. Glikson

From Stars to Brains Milestones in the Planetary Evolution of Life and Intelligence

From Stars to Brains: Milestones in the Planetary Evolution of Life and Intelligence

Andrew Y. Glikson

From Stars to Brains: Milestones in the Planetary Evolution of Life and Intelligence

123

Andrew Y. Glikson Research School of Earth Science Australian National University Canberra, ACT, Australia

ISBN 978-3-030-10602-7 ISBN 978-3-030-10603-4 https://doi.org/10.1007/978-3-030-10603-4

(eBook)

Library of Congress Control Number: 2018965880 © Springer Nature Switzerland AG 2019 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Cover illustration: Evolution Panorama mural at NASA Ames Research Center (artist: Robert Bausch, http://www.bauschdesign.com) Disclaimer: The facts and opinions expressed in this work are those of the author(s) and not necessarily those of the publisher. Every effort has been made to contact the copyright holders of the figures and tables which have been reproduced from other sources. Anyone who has not been properly credited is requested to contact the publishers, so that due acknowledgment may be made in subsequent editions. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

The book is dedicated to Arthur Glikson, my late father, an architect, town planner and pioneer of ecological and regional planning

Preface

The whole is greater than the sum of its parts Aristotle Who knows for certain? Who shall here declare it? Whence was it born, whence came creation? The Gods are later than this world’s formation; Who then can know the origins of the world? The Rig Veda, X.129

This treatise aims at exploring individual and swarm behaviour patterns which potentially hint at as yet-unexplained biological principles and laws of complexity. It includes an overview of theories on the evolution of life (Heron and Freeman 2013; Zimmer and Emlen 2015; Futuyma and Kirkpatrick 2017) with perspectives from the earth sciences, commencing with the earliest observed records of life, followed by reviews and discussion of the building blocks of life, the arthropods, deep sea communities associated with hydrothermal springs, the evolution of the eye, the birds and finally of humans and the directionality of evolution. The permutation of basic atoms—carbon, oxygen, hydrogen, nitrogen and sulphur—into the biomolecules Deoxyribonucleic acid (DNA)1 and Ribonucleic acid (RNA)2, which subsequently evolved into cells and the brains, defining the origin or life and of intelligence, remains unexplained by the known laws of physics, nor is the source of the information contained in the basic biomolecules. In so far as it can be expected that life would continue to be formed from inorganic molecules, had this process operated at present it could have been more readily identified. Aristotle’s dictum of “the whole is greater than the sum of the parts”, pertaining to the 1

A molecule composed of two chains (made of nucleotides) which coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. 2 Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes.

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evolution of multicomponent cells, swarm behaviour, Niels Bohr’s theory of holism3 or Ellis’ (2012) theory of top to down causality, remains to be further explored, possibly furnishing essential keys for unknown physical laws that govern the appearance and evolution of life. Inherent in the question of the origin of life is an anthropocentric bias, related to the self-referential Anthropic Principle4 and early views of man’s supposed dominion over all other species5, namely the polarity between animal and human faculties manifested in ancient scripts. In terms of the anthropocentric bias, humans can think but animals act by instinct. However, this bias is contradicted by large bodies of evidence, some of which are considered in this book. A critical exception being that of Homo sapiens, having mastered the ignition of fire and splitting of the atom, leading to the Seventh mass extinction of species. The Anthropic Principle, however should be capable of being circumvented using the scientific falsification method6, applying independently verified constants of physics, including gravity, the speed of light, the universe expansion rate and age since the Big Bang—observations with which inhabitants on other planets may concur? Central to Darwin and Wallace’s theory of evolution is the directionality arising from mutations induced by external environmental events and inter-species competition, such as changes in climate and solar and cosmic radiation, followed by preferential natural selection of adaptable organisms. On the other hand questions inherent in the evolution of intelligence, in particular of purposeful thinking, remain little resolved. As distinct from Darwinian natural selection and survival of the fittest principles, the intelligent probes of humans and animals constitute directional trajectories influenced by both external circumstances and internal pressures. It is far from clear how thought processes, facilitated by neuron networks, leading to purposeful proactive trajectories, arise from natural selection. The narrative of the book focuses on behaviour patterns of life forms, from individual cells to colonial life, from the genetic code to collective brains and swarm intelligence, including that of the termites, bees and Avian birds, the descendants of the Archosauria7 (dinosaurs). It touches on fundamental questions:

3

https://arxiv.org/ftp/arxiv/papers/1608/1608.00205.pdf. The Anthropic principle: A philosophical consideration that observations of the universe must be compatible with the conscious and sapient life that observes it. Some proponents of the anthropic principle reason that it explains why this universe has the age and the fundamental physical constants necessary to accommodate conscious life. As a result, they believe it is unremarkable that this universe has fundamental constants that happen to fall within the narrow range thought to be compatible with life. https://en.wikipedia.org/wiki/Anthropic_principle. 5 As stated: “Then God said, Let us make mankind in our image, in our likeness, so that they may rule over the fish in the sea and the birds in the sky, over the livestock and all the wild animals, and over all the creatures that move along the ground.” (Genesis 1:26). 6 A statement, hypothesis, or theory has falsifiability (or is falsifiable) if it can be proven false by contradicting it with a basic statement or observation. 7 http://www.ucmp.berkeley.edu/diapsids/archosauria.html. 4

Preface

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how have living cells come to contain diverse multi-tasked elements of hardware such as the nucleus, nucleolus, ribosomes, mitochondrion, endoplasmic reticulum, golgi bodies, centrosome, vacuole, lysosome and so on, coordinated for multi-tasked functions by a living software? Fundamental questions arise: how can the cell, a brain and an organism, evolve through a series of accidental genetic mutations, random environmental changes and natural selection, engage in purposeful design of complex technical and social systems, as is the case with colonial arthropods or human civilization? Are unknown laws of self-organization and complexity at work?8 The genius of Darwin himself recognized that the evolution of a complex system, such as the eye, is not readily explained by the theory of evolution, stating “it was absurd to propose that the human eye evolved through spontaneous mutation and natural selection”.9 Kaufmann (1993) suggested that, in order to explain the evolving self-generated architecture of living organisms yet unexplained processes must exist, supplementing Darwinian evolution theory and existence of biological determinism.10 In discussing biological determinism Davies (2000a, b) considers this option, while true, cannot be implied by the known laws of physics and chemistry alone and that additional discoveries or principles may be found in the emerging sciences of complexity and information theory. Such principles appear to govern human civilizations, with the remarkable phenomenon of the human mastery of fire, which allowed the genus Homo to reach major technical and cultural developments. It appears human intellect and science have not reached a stage allowing answers to these fundamental questions. Canberra, Australia

Andrew Y. Glikson

References Davies P (2000a) The fifth miracle: the search for the origin and meaning of life. http://www. simonandschuster.com/books/The-Fifth-Miracle/Paul-Davies/9780684863092 Davies P (2000b) Biological determinism, information theory, and the origin of life. http://www. metanexus.net/essay/biological-determinism-information-theory-and-origin-life Ellis G (2012) Recognizing top-down causation. https://arxiv.org/ftp/arxiv/papers/1212/1212. 2275.pdf Futuyma DJ, Kirkpatrick M (2017) Evolution, 4th edn. Oxford University Press, 594 pp. https:// www.amazon.com/Evolution-Douglas-J-Futuyma/dp/1605356050/ref=sr_1_1?ie=UTF8&qid= 1536619743&sr=8-1&keywords=futuyma+and+kirkpatrick Heron JC, Freeman S (2013) Evolutionary analysis, 5th edn. Pearson, 864 pp. https://www.amazon. com/Evolutionary-Analysis-Jon-C-Herron-ebook/dp/B00E8IW0W6/ref=sr_1_1?ie=UTF8& qid=1536619786&sr=8-1&keywords=herron+evolution 8

https://en.wikipedia.org/wiki/Non-Darwinian_Evolution_(paper). https://www.nature.com/news/2008/081119/full/456304a.html. 10 Biological determinism, also called biologism or biodeterminism, the idea that most human characteristics, physical and mental, are determined at conception by hereditary factors passed from parent to offspring. 9

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Kaufmann SA (1993) The origins of order: self-organization and selection in evolution, 1st edn. https://www.amazon.com/Origins-Order-Self-Organization-Selection-Evolution/dp/ 0195079515 Zimmer C, Emlen DJ (2015) Evolution: making sense of life, 2nd edn. W. H. Freeman, 768 pp. https://www.amazon.com/Evolution-Making-Sense-Carl-Zimmer/dp/1936221551/ref= sr_1_1?ie=UTF8&qid=1536619761&sr=8-1&keywords=zimmer+evolution

Acknowledgements

I am grateful to Brenda McAvoy for consistent support and encouragement, including meticulous proofs checking. The study greatly benefited from the support of and discussions with the late Professor Colin Peter Groves, distinguished anthropologist and primatologist. I like to thank the following people for comments and discussion: Mark Bonta, Stephen Boyden, John Carter, Hugh Davies, Victor Gostin, Arthur Hickman, Debbie Jennings, Gerta Keller, Alan Landford, Robert Pidgeon, Juanita Rodriguez, Stephen Stearns, Alastair Stewart, Will Steffen and Malcolm Whyte.

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Contents

1 The Building Blocks of Intelligence . . . . . . . . . . . . 1.1 From a Singularity to a Bio-friendly Universe . 1.2 The Second Law of Thermodynamics . . . . . . . 1.3 The Living Enigma . . . . . . . . . . . . . . . . . . . . . 1.4 Panspermia and Transpermia . . . . . . . . . . . . . . 1.5 Evolution: Charles Darwin and Alfred Wallace References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .

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2 Milestones in Early Evolution . . . . . . . 2.1 Early Atmospheres and Oceans . . . 2.1.1 Early Records of Life . . . . 2.1.2 Mass Extinction of Species References . . . . . . . . . . . . . . . . . . . . . .

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3 From the Genetic Code to Collective Brains . 3.1 From Amino Acids to Nucleic Acids . . . . 3.2 The Intelligent Cell . . . . . . . . . . . . . . . . . 3.3 The Phylogenetic Scheme . . . . . . . . . . . . 3.4 Marine and Hydrothermal Communities . . 3.5 Multicellular and Colonial Life . . . . . . . . 3.6 Evolution of the Eye . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . .

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4 Intelligent Communities . . . . . 4.1 Arthropod Civilizations . . . 4.2 The World of Birds . . . . . 4.3 Fire and the Human Mind . References . . . . . . . . . . . . . . . .

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5 Directional Thought and Evolution . . . . . . . . 5.1 The Anthropic Principle . . . . . . . . . . . . . 5.2 Swarm Intelligence and Collective Minds 5.3 Evolution of the Brain . . . . . . . . . . . . . . 5.4 The Directional Thought Process . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . .

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6 Epilogue—From Stars to Brains . . . . . . . . . . . . . . . . . . . . . . . . . . . . 143 References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 151 Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153

About the Author

Andrew Y. Glikson an Earth and paleo-climate scientist, studied geology at the University of Jerusalem and graduated at the University of Western Australia in 1968. He conducted geological and geochemical surveys of the oldest geological formations in western and central Australia, South Africa, India and Canada; studied large asteroid impacts, including effects on the atmosphere, oceans and mass extinction of species. Since 2005 he studied the relations between climate and human evolution. He was active in communicating nuclear and climate change evidence to the public and parliament through papers, lectures, conferences and presentations.

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Contributed Books List

The Archaean: Geological and Geochemical Windows into the Early Earth http://www.springer.com/gp/book/9783319079073. The Asteroid Impact Connection of Planetary Evolution http://www.springer.com/gp/book/9789400763272. Asteroids Impacts, Crustal Evolution and Related Mineral Systems with Special Reference to Australia http://www.springer.com/us/book/9783319745442. Climate, Fire and Human Evolution: The Deep Time Dimensions of the Anthropocene http://www.springer.com/gp/book/9783319225111. The Plutocene: Blueprints for a Post-Anthropocene Greenhouse Earth http://www.springer.com/gp/book/9783319572369. Evolution of the Atmosphere, Fire and the Anthropocene Climate Event Horizon http://www.springer.com/gp/book/9789400773318.

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Introduction: The Origin of Intelligence

My suspicion is that the universe is not only queerer than we suppose, but queerer than we can suppose. J. B. S. Haldane

Life, synonymous with natural intelligence11, is everywhere, from primary DNA-RNA molecules all the way to the brain, on every scale from microns to mega-cities, including individual intelligence (Fig. 1) and collective swarm intelligence of species. Advanced life, representing transient reversal of entropy inherent in the second law of thermodynamics (Malley et al. 2016), is believed to have emerged on Earth at least *500.106 years, following planetary accretion about 4.54  109 ± 1% years-ago.12 No one knows where intelligence comes from nor, along with Darwinian evolution, is it clear how intelligence has evolved. The origin and evolution of living forms are closely related to and reflect the milieu in which they have emerged, rendering studies of the physical and chemical nature of their surrounds closely relevant to the question. According to Davies (2000a, b) and (Rees 2017) the universe appears to be hospitable to life, or bio-friendly, a possibly unique condition among cosmic realms in a multiverse13, an ensemble of universes most of which may be sterile. On Earth, the initial condition for life almost certainly required a presence of water, allowing microbes a source of energy by breaking down H2O molecules and combining oxygen and hydrogen ions with metals as a source of energy.14 The initial conditions that allowed synthesis of the early bio-molecules are not known, nor whether such biogenetic conditions persisted. The likelihood that the laws which govern life are written into nature, allowing life to emerge under suitable conditions, remains undefined. The question is whether life sprang by Intelligence, the subject of a cultural and philosophical bias, is defined by the “The ability to learn or understand or to deal with new or trying situations or the ability to apply knowledge to manipulate one’s environment”. 12 Age of the Earth (2007) USGS https://pubs.usgs.gov/gip/geotime/age.html. 13 The Multiverse. Last edited 20 July 2018 https://en.wikipedia.org/wiki/Multiverse. 14 Solar fuels as generated by nature https://www.mpg.de/8373743/photosynthetic-water-splitting. 11

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Fig. 1 Intelligence is everywhere. The human-like face of a fruit fly. Nature Picture Library. Fruit flies (Drosophila melanogaster) have a kind of mind’s eye (© Solvin Zankl/naturepl.com, reprinted with permission). http://www.bbc.com/earth/story/20170123-how-insects-like-bumblebees-do-somuch-with-tiny-brains

chance or, alternatively, as a function of unknown laws of physics. The synthesis and growth of bio-molecules on the surfaces of planets face formidable hazards, from a lack of water, cosmic radiation, meteorite and asteroid impacts, and volcanic activity. Sources of energy for life processes vary from photosynthesis15 at surface or near-surface levels, to microbial-facilitated oxidation/reduction reactions16 around deep sea hydrothermal vents. The question is whether life has originated at one point in time or, alternatively, repeatedly emerged through multiple geneses (Davies 2000a, b). Following in the steps of Darwinian evolution the growth of integrated complex systems, from individual cells to the brain to swarm intelligence, pose yet-unanswered questions. Concepts such as emergent properties, intelligent design, fractal theory or algorithms of life, relevant to the principles of animation and structural patterns, regularities and proliferation, are not readily integrated with Darwinian evolution theory. Questions remain hardly answered regarding the origin of highly complex

15 Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organisms’ activities (energy transformation). This chemical energy is stored in carbohydrate molecules, such as sugars, which are synthesized from carbon dioxide and water. 16 Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom, or ion. Reduction is the gain of electrons or a decrease in oxidation state by a molecule, atom, or ion.

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information storage and multiplication systems facilitated by the DNA, RNA, ribosome17 and other biomolecules. How has the complex multi-component and multi-tasked machinery of the living cell, containing diverse elements such as nucleus, nucleolus18, ribosomes, mitochondrion19, endoplasmic reticulum20, golgi bodies21, centrosome22, vacuole23, lysosome24 and so on, evolved through random processes? What roles are played by genes25 and what by learnt behaviour? Does human cultural evolution represent the successor of biological evolution? How can the cell or an organism, evolved through a series of accidental genetic mutations, random environmental events and natural selection engage in purposeful or directional design of complex technical and social systems? What are the origins of directional purposeful thinking processes? How can computer-like biological systems be constructed without an intelligent plan? The answers may evade the human mind. Is it possible that intellect and science have not developed to a stage allowing answers to these questions? Directionality of evolution may be accounted for by natural selection of relatively adaptable collective behaviour of organisms, however a fundamental enigma pertains to the possible existence of a vector of purpose, intention or directionality in the behaviour of individual organisms and cooperative colonies. The development of the hardware and software26 of multi-component systems, such as cell, the 17

A minute particle consisting of RNA and associated proteins found in large numbers in the cytoplasm of living cells. They bind messenger RNA and transfer RNA to synthesize polypeptides and proteins. 18 A small dense spherical structure in the nucleus of a cell during interphase. 19 Membrane-bound organelle found in the cytoplasm of almost all eukaryotic cells (cells with clearly defined nuclei), the primary function of which is to generate large quantities of energy in the form of adenosine triphosphate (ATP). Mitochondria are typically round to oval in shape and range in size from 0.5 to 10 lm. In addition to producing energy, mitochondria store calcium for cell signalling activities, generate heat, and mediate cell growth and deat. 20 A network of membranous tubules within the cytoplasm of a eukaryotic cell, continuous with the nuclear membrane. It usually has ribosomes attached and is involved in protein and lipid synthesis. 21 A complex of vesicles and folded membranes within the cytoplasm of most eukaryotic cells, involved in secretion and intracellular transport. 22 An organelle that is the main place where cell microtubules are organized. Also, it regulates the cell division cycle, the stages which lead up to one cell dividing in two. 23 A membrane-bound organelle which is present in all plant and fungal cells and some protist, animal [1] and bacterial cells. [2] Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules including enzymes in solution, though in certain cases they may contain solids which have been engulfed. Vacuoles are formed by the fusion of multiple membrane vesicles and are effectively just larger forms of these. 24 An organelle in the cytoplasm of eukaryotic cells containing degradative enzymes enclosed in a membrane. 25 A basic physical and functional unit of heredity. Genes, which are made up of DNA, act as instructions to make molecules called proteins. In humans, genes vary in size from a few hundred DNA bases to more than 2 million bases. 26 Hardware: the physical machinery and devices that make up a computer system. Software: the programs and instructions used to run the system.

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eye, insect colonies and human civilization, may be facilitated by factors further than natural selection? In terms of the whole being greater than the sum of the parts, the selfish gene theory Dawkins (2006) can hardly be reconciled with evidence for whole-cell synergy and intra-cell and inter-cell intelligence of complex life forms. In terms of the principle of the survival of the fittest, there are difficulties in reconciling mathematical modelling with perceived vectors of evolutionary purpose or directionality, for example the evolution of centrally controlled intelligent communities such as bee hives, termite nests and human civilizations. Through geological time gradual evolution has been interrupted by episodes of mass extinction of species triggered by impact of large asteroids, volcanic eruptions, methane release, extreme glaciations and other factors, disrupting long-term evolutionary cycles (Keller 2005).27 It is not clear how the molecular clock, namely the regular mutation rate of nucleotide sequences used to deduce time, can be reconciled with the biological effects of random external events.28 The concept of panspermia, namely interstellar transport of biomolecules associated with cometary dust and vapor, or within meteorites (Hoyle and Wickramasinghe 1977), remains unconfirmed, although possible evidence by Callahan et al. (2011) for nucleobases, including adenine, guanine, xanthine, hypoxanthine and purine in carbonaceous chondrites, could suggest synthesis of biomolecules in asteroids parent bodies? Transpermia, the transport of microbes between planets, is supported by the discovery of Martian meteorites on Earth.29 While this may defer the question of the origin of life one step further in time and space, it does not contradict terrestrial biogenesis, nor does it explain biogenesis. Fundamental questions remain. Can intelligence emerge through a series of mutations, natural selection and coincidences? How can the rapid appearance of high intelligence, represented for example by the advent of human cave painting and ornamentation since about 35,600 years ago30 (Fig. 2)—a blip in the evolutionary record—be explained in terms of Darwinian principles.

27

https://www.tandfonline.com/doi/abs/10.1080/08120090500170393. https://www.sciencedirect.com/science/article/pii/S0960982216303165. In the 1960s, several groups of scientists, noted that proteins experience amino acid replacements at a surprisingly consistent rate across very different species. This presumed single, uniform rate of genetic evolution was subsequently described using the term ‘molecular clock’. Biologists quickly realized that such a universal pacemaker could be used as a yardstick for measuring the timescale of evolutionary divergences: estimating the rate of amino acid exchanges per unit of time and applying it to protein differences across a range of organisms would allow deduction of the divergence times of their respective lineages. 29 Mars Meteorites. 1996-2006. NASA Jet Propulsion Laboratory, California Institute of Technology. https://www2.jpl.nasa.gov/snc/index.html. 30 Oldest cave painting in the world http://www.oldest.org/artliterature/cave-paintings/. 28

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Fig. 2 Detail of a bison in the cave at Altamira, 35,600 years-old, in northern Spain, discovered within the 19th century. By Museo de Altamira y D. Rodríguez, https://commons.wikimedia.org/ w/index.php?curid=24512679 licensed under CC BY-SA 3.0

A plethora of studies exist concerned with the origin of life31, including theories of an “RNA world”32, “metabolism first”33 and others.34 Experimental studies with implications for the origin of life, such as by Sutherland (2017)35, have not to-date resolved the source of information leading to formation of biomolecules, as stated: “To proceed from simple feedstock molecules and energy sources to a living system requires extensive synthesis and coordinated assembly to occur over numerous steps, which are governed only by environmental factors and inherent chemical reactivity. Demonstrating such a process in the laboratory would show how life can start from the inanimate. If the starting materials were irrefutably primordial and the end result happened to bear an uncanny resemblance to extant biology—for what turned out to be purely chemical reasons, albeit elegantly subtle ones—then it could be a recapitulation of the way that natural life originated. We are not yet close to achieving this end, but recent results suggest that we may have nearly finished the first phase: the beginning”.

31

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683543/. https://www.ncbi.nlm.nih.gov/books/NBK26876/. 33 http://sciencecases.lib.buffalo.edu/cs/files/origins_debate_intro.pdf. 34 https://gabrielledallman.wordpress.com/2016/10/15/metabolism-first-vs-replication-first. 35 https://www.nature.com/articles/s41570-016-0012. 32

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Introduction: The Origin of Intelligence

References Callahan MP et al (2011) Carbonaceous meteorites contain a wide range of extraterrestrial nucleobases. Proc Natl Acad Sci USA. http://www.pnas.org/content/early/2011/08/10/1106493108 Davies P (2000a) The fifth miracle: the search for the origin and meaning of life. http://www. simonandschuster.com/books/The-Fifth-Miracle/Paul-Davies/9780684863092 Davies P (2000b) Biological determinism, information theory, and the origin of life. http://www. metanexus.net/essay/biological-determinism-information-theory-and-origin-life Dawkins R (2006) The selfish gene: 30th anniversary edition. Oxford University Press, 384 pp. https://www.bookdepository.com/Selfish-Gene-Richard-Dawkins/9780199291151 Hoyle F, Wickramasinghe NC (1977) Polysaccharides and infrared spectra of galactic sources. http://adsabs.harvard.edu/abs/1977Natur.268..610H Keller G (2005) Impacts volcanism and mass extinction: random coincidence or cause and effect? Aust J Earth Sci 52:725–757. https://www.tandfonline.com/doi/abs/10.1080/0812009050017 0393 Malley K et al (2016) 2nd law of thermodynamics. Libretexts, California State University. https:// chem.libretexts.org/Core/Physical_and_Theoretical_Chemistry/Thermodynamics/The_Four_ Laws_of_Thermodynamics/Second_Law_of_Thermodynamics Rees M(2017) Our cosmic habitat. Princeton University Press, New Jersey. https://press.princeton. edu/titles/11154.html Sutherland JD (2017) Opinion: studies on the origin of life—the end of the beginning. Nat Rev Chem 1, Article number: 0012. https://www.nature.com/articles/s41570-016-0012

Chapter 1

The Building Blocks of Intelligence

Veins of the cosmos surging with poetry Verses recited since creation and not completed Fabric of song holding the sky together A vast curtain of frail trembling beauty A play of shadow and light A slow dance between the celestial and the demonic (Peter Huta)

Abstract The ancient Greek philosopher Anaximander postulated the development of life from non-life and the evolutionary descent of man from animal. Ever since the development of the theory of evolution by Darwin (1859) and Wallace in 1858, the theory stands up as the landmark of fundamental knowledge in life sciences, with a common ancestor, genetic selection and biological diversity as the cornerstone of biological science, yet essential questions remain. Charles Darwin and Alfred Wallace’s theory of evolution by natural selection, which dominates biological science, explains the most part of biological evolution, yet leaves many questions unanswered regarding the origin of complex living systems and observations of directionality and sense of purpose. The fundamental question is how can an assemblage of atoms—carbon, oxygen, hydrogen, nitrogen and sulfur—evolving over time through mutations and natural selection, culminate in the brain and in consciousness—a consciousness capable of resolving the basic laws of physics, the atomic and subatomic structure of matter and astronomy. The likelihood of an emergence of life is intimately related to initial cosmological conditions and the laws and constants of physics, indicating whether life has sprang by chance or is destined to emerge due to unknown and possibly unknowable principles. In terms of the second law of thermodynamics the phenomenon of life depends on differential trajectories among atoms, where entropy increase in closed systems but can decrease in open systems that absorb energy. Inherent in these questions is the contrast between the Selfish Gene hypothesis of Dawkins and theories that emphasize the interconnectedness and the emergent properties of the complex cells, where Aristotle’s dictum the whole is greater than the sum of the parts assumes key significance. Inherent in the question is inherent in the contrast between the “Selfish Gene” hypothesis of Dawkins (2006) and theories that emphasize the interconnectedness and the emergent properties of the complex cells, © Springer Nature Switzerland AG 2019 A. Y. Glikson, From Stars to Brains: Milestones in the Planetary Evolution of Life and Intelligence, https://doi.org/10.1007/978-3-030-10603-4_1

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where the whole is greater than the sum of the parts. Since organisms reflect and respond to the environment in which they have evolved, the study of early habitats is closely relevant to life’s origin. Keywords Evolution · Directional · Brain · Consciousness · Living systems

1.1 From a Singularity to a Bio-friendly Universe The ancient Greek philosopher Anaximander postulated the development of life from non-life and the evolutionary descent of man from animal.1 Ever since the development of the theory of evolution by Darwin (1859) and Wallace in 1858, the theory stands up as the landmark of fundamental knowledge in life sciences (MartinDelgado 2012), with a common ancestor, genetic selection and biological diversity as the cornerstone of biological science, yet essential questions remain. Related to these questions is the enigma regarding the nature of the Universe. According to Rees (2017), the universe, possibly unique among other realms within a multiverse2 (Fig. 1.1), constitutes an entity within an ensemble of universes most of which may be lifeless. In this model the laws of nature would form local bylaws, imposed in the aftermath of the Big Bang. The likelihood of an emergence of life in some of these universes is intimately related to initial cosmological conditions and the laws and constants of physics, indicating whether life has emerged by chance or is destined to emerge due to unknown and possibly unknowable principles. That the physical constants governing the Big Bang3 and its aftermath appear to have been favorable to the subsequent appearance of life is suggested by a number of considerations (Davies 2000a, b): A. Had the dispersive energy of the Big Bang been too strong, particles and waves would have scattered too rapidly, precluding the subsequent accretion of galaxies4 and stars. By contrast, had the explosion been less intense the early universe would have collapsed back on itself before galaxies and stars could coalesce.

1 https://www.britannica.com/biography/Anaximander. 2 A hypothetical set of various possible universes including the universe which we live in. Together,

these universes comprise the entirety of space, time, matter, energy and the physical laws and constants that describe them. 3 The prevailing cosmological model for the universe from the earliest known high density and high temperature state through its subsequent large-scale evolution. The model describes how the universe expanded from a very high-density and high-temperature state. 4 A gravitationally bound system of stars, stellar remnants, interstellar gas, dust, and dark matter.

1.1 From a Singularity to a Bio-friendly Universe

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Fig. 1.1 A detailed all-sky picture of the infant universe created from seven years of WMAP (Wilkinson Microwave Anisotropy Probe) data. The image reveals 13.7 billion year old temperature fluctuations, shown as differences in color that correspond to the seeds that grew to become galaxies. Credit NASA/WMAP, https://www.nasa.gov/topics/universe/features/wmap-complete.html

The inflationary universe theory5 postulates expansion was propelled by antigravity,6 where at 10−35 s from the Big Bang event at a density of 1035 kg/m3 and temperature of 1027 K, the unified strong, weak and electromagnetic forces shifted to a state of thermal equilibrium (Table 1.1). B. The subsequent uniform distribution of matter across the universe avoided chaotic expansion and thereby random collisions between galaxies. However, a completely uniform dispersal would have prevented matter from aggregating into galaxies and stars, a process allowed by minor irregularities on the scale of 1 part in 105 parts, echoed by the thermal satellite WMAP (Wilkinson Microwave Anisotropy Probe)7 (Fig. 1.1). The image represents a snapshot of the distribution of temperature and density in the young universe some 380,000 years following the Big Bang,8 some 13.7 × 109 years ago. The denser clusters displayed by the WMAP image represent seeds of subsequent clusters of galaxies created by gravitational instabilities and quantum fluctuations dating from the inflationary era.

5 The

Inflation Theory proposes a period of extremely rapid exponential expansion of the universe during its first few moments. The Origins of the Universe: Inflation http://www.ctc.cam.ac.uk/ outreach/origins/inflation_zero.php. 6 The antithesis of gravity; a hypothetical force by which a body of positive mass would repel a body of negative mass or a controllable force that can be made to act against the force of gravity. 7 The Wilkinson Microwave Anisotropy Probe (WMAP) is a NASA Explorer mission that launched June 2001 to make fundamental measurements of cosmology. 8 NASA—Five Year Results on the Oldest Light in the Universe https://map.gsfc.nasa.gov/news/ 5yr_release.html.

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Table 1.1 Major Epochs in the evolution of the universe. Timeline of the Big Bang. Creative commons. https://en.wikipedia.org/wiki/Graphical_timeline_of_the_Big_Bang

Since carbon forms the cores of biological molecules, the abundance of carbon in the universe is of key significance in connection with the appearance of life. As a result of the proton–proton chain reaction and the carbon–nitrogen–oxygen cycle Helium accumulates in the core of stars, with further nuclear fusion reactions of helium with hydrogen or another alpha particle producing lithium-5 and beryllium-8 respectively (Fig. 1.2). When a large star runs out of hydrogen to fuse in its core, it begins to collapse until the central temperature rises to 108 K, six times hotter than the sun’s core (Zimmer and Emlen 2015). At this temperature and density, alpha particles can fuse fast enough to produce significant amounts of carbon and restore thermodynamic equilibrium in the core. Formed by nuclear fusion of three molecules of helium (Hoyle et al. 19539 ) this process depends on the magnitude of the strong nuclear force and the nuclear resonance in the neighborhood of 7.7 MeV.10 Had the strong nuclear force been just a few per cent stronger or weaker, carbon would

9 Triple

Alpha Process http://hyperphysics.phy-astr.gsu.edu/hbase/Astro/helfus.html#c1. million electron volts.

10 MeV—1

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Fig. 1.2 The triple-alpha process: Nucleosynthesis of carbon in massive stars from Helium and Beryllium atoms. By Borb (assumed—based on copyright claims), https:// commons.wikimedia.org/w/ index.php?curid=697609, licensed under CC BY-SA 3.0

not have formed in abundance in the universe. Similar considerations pertain to the dissemination of carbon in supernova explosions.11 The possibility that the laws which govern life are written into nature, and that life can arise spontaneously where physical conditions are suitable, remains enigmatic (Kaufmann 1995). While cosmological constants appear to favor biogenesis, biomolecules on the surface of planets face formidable hazards, from cosmic,12 alpha,13 beta14 and gamma15 ray radiation, meteorite and asteroid impacts and volcanic activity. Life emerged on Earth at least ~500 × 106 years following accretion about 4.56 Ga (Badro and Walter 2015), although it is not known whether life originated only once or has it repeatedly emerged through multiple genesis?

1.2 The Second Law of Thermodynamics16 In the monograph titled What Is Life Schrödinger (1944) (Fig. 1.3) suggested that, according to the second law of thermodynamics, entropy must increase in isolated or closed system over time, whereas in an open system energy can be divided among

11 A supernova is a transient astronomical event that occurs during the last stellar evolutionary stages of a massive star’s life. 12 Almost 90% of the cosmic rays which strike the Earth’s atmosphere are protons (hydrogen nuclei) and about 9% are alpha particles. Electrons amount to about 1%. 13 Alpha particles are energetic nuclei of helium. The production of alpha particles is termed alpha decay. Alpha particles consist of two protons and two neutrons bound together into a particle identical to a helium nucleus. 14 Electron or positron emitted in the radioactive decay of an atomic nucleus. 15 Ionizing atoms or photons in the highest observed range of photon energy. 16 The 2nd law of thermodynamics states that the state of entropy of the entire universe, as an isolated system, will always increase over time. The second law also states that the changes in the entropy in the universe can never be negative.

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its atoms toward an increase as well as a decrease in entropy.17 An essential physical property of living entities is the capture of chemical or solar energy from the environment and its use for reactions producing complex biological systems, which then undergo reactions involving oxidation and dissipation of heat (England 2013).18 Photo-synthetizing plants absorb high energy sunlight, produce sugars and develop complex high energy-potential living systems. At the same time the overall entropy of surrounding open systems increases as the sunlight and heat dissipate. Features characteristic of life include a reproductive directional vector capable of thermodynamic expression according to an extension of the second Law of Thermodynamics. According to England (2013), using a novel extension of the 2nd Law of Thermodynamics, the growth rate and durability of self-replicators set constraints on the minimum amount of chemical fuel required for growth. This includes proof of principle for a previously predicted ‘self-organization’ of a primitive metabolism, whereby a randomly-wired chemical network spontaneously discovers a finely-tuned, stable way of extracting a rich source of chemical energy from its environment. According to the physicist Prigogine (1977a, b), the introduction and dissipation of energy into chemical systems could reverse the maximization of entropy rule imposed by the second law of thermodynamics, which leads to self-organizing living systems. In this concept, based on quantum physics, deterministic notions by Newton, Einstein and Schrödinger lose their explanatory power: According to Ilya Prigogine19 “The more we know about our universe, the more difficult it becomes to believe in determinism”. Instability resists standard deterministic explanation and due to their sensitivity to initial conditions unstable systems can only be explained statistically, namely in terms of probability. Accordingly determinism is contrasted to the arrow of time20 and, like weather systems, organisms constitute unstable systems existing far from thermodynamic equilibrium (Malley et al 2016). According to England (2013), systems driven by an external energy source such as electromagnetic waves release heat to the environment,21 as in photosynthesis, stating: “We can show very simply from the formula that the more likely evolutionary outcomes are going to be the ones that absorbed and dissipated more energy from the environment’s external drives”. In this model energy dissipation and adaptive organization occur during self-replication of RNA molecules and bacterial cells (Wolchover 2014). Such self-replication is reported from inorganic systems (Marcus 2013) as well as applied by computer simulations to inanimate matter. In ‘Statistical physics of self -replication’ England (2013) states: “Self -replication is a capacity common 17 A simplified definition of entropy refers to the idea that everything in the universe eventually moves from order to disorder, and entropy is the measurement of that change. https://www.vocabulary.com/ dictionary/entropy. 18 England lab @ MIT Physics. https://www.englandlab.com/. 19 https://www.azquotes.com/quote/820379. 20 https://en.wikipedia.org/wiki/Ilya_Prigogine. 21 Photosynthesis itself is an endothermic reaction. Plant uses the energy of the light to form chemical bonds, so it requires energy, but and it’s a big but, there’s heat being released during photosynthesis. Released heat doesn’t come from photosynthesis itself but a mechanism called non photochemical quenching (NPQ).

1.2 The Second Law of Thermodynamics

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Fig. 1.3 Erwin Schrodinger, University of Vienna, Austria. By Daderot at the English Wikipedia, https:// commons.wikimedia.org/w/ index.php?curid=318491 licensed under CC BY-SA 3.0

to every species of living things, and simple physical intuition indicates that such a process must invariably be fueled by the production of entropy. Here, we undertake to make this intuition rigorous and quantitative by deriving a lower bound for the amount of heat that is produced during a process of self -replication in a system coupled to a thermal bath. We find that the minimum value for the physically allowed rate of heat production is determined by the growth rate, internal entropy, and durability of the replicator, and we discuss the implications of this finding for bacterial cell division, as well as for the pre-biotic emergence of self -replicating nucleic acids”. The theory of self-replication of colloidal aggregates has been further advanced by Zeravcic and Brenner (2014), who present theoretical models and simulations of microstructures that self-replicate and construct schemes for self-replication of small clusters of isotropic particles. By manipulating the energy landscape of the process, replication can be achieved by exponential self-replication of an octahedral cluster using finite-temperature computer simulations. According to England (2013) “You start with a random clump of atoms, and if you shine light on it for long enough, it should not be so surprising that you get a plant”, an idea remaining as perplexing as it is controversial.

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1.3 The Living Enigma Beginnings Where the dunes merge with the sea In space-time rhythms flowing free Water lick the budding land Islands born out of sand. Air-strokes gently ripple waves Sparks of light each other crave Wind-swept spores that seed a grove Sprout all over an alcove. What rhyme or reason springing birth Upon the ancient face of Earth Where for a moment you and me Savour a fleeting eternity. (Andrew Glikson) As stated by Francis Drake, who jointly with James Watson discovered the structure of the DNA: “An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going. But this should not be taken to imply that there are good reasons to believe that it could not have started on the earth by a perfectly reasonable sequence of fairly ordinary chemical reactions. The plain fact is that the time available was too long, the many microenvironments on the earth’s surface too diverse, the various chemical possibilities too numerous and our own knowledge and imagination too feeble to allow us to be able to unravel exactly how it might or might not have happened such a long time ago, especially as we have no experimental evidence from that era to check our ideas against”. Early terrestrial beginnings are interpreted in terms of a cosmic collision between an embryonic semi-molten Earth and a Mars-scale body, Theia, determined from Pb isotopes as ~4.56 billion years-ago (Stevenson 1987). The consequent formation of a metallic core, inducing a magnetic field which protects the Earth from cosmic radiation, and a strong gravity field which constrains the escape of atmospheric gases from the gravity field of Earth, created a haven for life at the Earth surface (Gould 1990). Relic ~4.4 Ga and younger zircons, representing a pre-4.0 Ga Hadean era (Cloud 1973), signify vestiges of granitic and felsic volcanic crustal nuclei and therefore the presence of a water component in the granite magma and thereby relatively low-temperature surface conditions (Wilde et al. 2001; Mojzsis et al. 2001; Knauth 2004; Valley et al. 2000). However Pidgeon et al. (2013) and Pidgeon (2014) attributed the δ18 O values of zircon to secondary radiation damage associated with hydrous alteration. Precambrian terrains contain high-grade metamorphosed relicts

1.3 The Living Enigma

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of ~4.1–3.8 Ga-old rocks, including volcanic and sedimentary rocks, exposed in Greenland, Labrador, Slave Province, Minnesota, Siberia, northeast China, southern Africa, India, Western Australia and Antarctica (Van Kranendonk et al. 2018). Some of these formations formed contemporaneously with, as well as prior to, the Late Heavy Bombardment (LHB) on the Moon (~3.95–3.85 Ga) (Ryder 1991), but are metamorphosed to an extent complicating recognition of signatures of the LHB on Earth. The question of the origin of life is inherent in the search for early biological signatures in the geological record (Darwin 1859; Cloud 1968; Davies 2000a, b; Schopf et al. 2007; Awramik 1992) such as microbialites. Since organisms reflect and respond to the environment in which they have evolved, the study of early habitats is closely relevant to life’s origin. According to the Miller–Urey and other experiments22 life has arisen by synthesis of abiogenic precursors to organic amino acids,23 the building blocks of life, triggered by lightning and radiation affecting a “primordial soup” rich in organic matter. Oparin (1924) regarded atmospheric oxygen as a constraint on synthesis of biomolecules, restricting original synthesis of biomolecules to the preoxygenation era, which would constrain continuous generation of biomolecules once oxygen levels in the atmosphere and ocean have risen. Oparin thought “colonies” of proteins clustered together are capable of carrying out metabolism. Haldane (1929) suggested that macromolecules needed to become enclosed in membranes to make cell-like structures. In some theories life developed from inanimate matter through complex reactions on the surfaces of silicate minerals, in particular clay minerals (Cairns-Smith 1987) (Fig. 1.4). Experimental tests of the Oparin-Haldane hypothesis conducted by Miller and Urey (1953)24 (Fig. 1.5) demonstrated formation of amino-acids, sugars,25 lipids and other organic molecules from inorganic components (H2 O, NH4 , CH4 , N2 ) under reducing high-temperature conditions, thought to be analogous to the early atmosphere. Application of electrical sparks simulating lightning resulted in production of amino acids (Fig. 1.5), followed by polymerization of amino acids leading to formation of polypeptides.26 However, whereas only the large complex nucleic-acid

22 Windows

into the universe: The Miller Urey Experiment. https://www.windows2universe.org/ earth/Life/miller_urey.html. 23 Amino acids are organic compounds containing amine (–NH ) and carboxyl (–COOH) functional 2 groups, along with a side chain (R group) specific to each amino acid. 24 https://www.windows2universe.org/earth/Life/miller_urey.html. 25 Lactose, maltose, and sucrose are all compound sugars, disaccharides, with the general formula C12 H22 O11 . 26 Any of a group of natural or synthetic polymers made up of amino acids chemically linked together; this class includes the proteins.

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Fig. 1.4 2.3 billion years old microbialites Eastern Andes, South of Cochabamba, District of Cochabamba, Bolivia. Creative commons. https://upload.wikimedia.org/wikipedia/commons/f/fd/ Stromatolites_Cochabamba.jpg

bio-molecules are capable of controlled directed replication, DNA,27 RNA28 and protein29 were missing from the products of the Miller-Urey experiment. 27 Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base. The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The order of these bases is what determines DNA‘s instructions, or genetic code. Human DNA has around 3 billion bases, and more than 99% of those bases are the same in all people. 28 Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation, and expression of genes. 29 Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including cat-

1.3 The Living Enigma

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Fig. 1.5 A sketch of the apparatus used by Miller and Urey (1953) to simulate conditions on early Earth. By the original uploader Carny at Hebrew Wikipedia. Transferred from he.wikipedia to Common., https://commons.wikimedia. org/w/index.php?curid= 2173230, licensed under CC BY 2.5

Based on experiments similar to those of the Miller-Urey experiments (Fig. 1.5) Fox and Dose (1972) suggested life can emerge from abiogenic reactions under conditions similar to those on the early Earth, where amino acids synthesize to form polymers called proteinoids30 able to act as enzymes31 and catalyze organic reactions to form microsphere globules, or protocells. Harada and Fox (1964) performed an experiment yielding similar results, where methane flows through a concentrated solution of ammonium hydroxide and then into a hot tube containing silica sand at about 1000 °C. Fox indicated that silica gel, volcanic lava, and alumina could be used in place of silica sand. The gas was then absorbed in cold, aqueous ammonia. The results included twelve protein-like amino acids: aspartic acid, glutamic acid, glycine, alanine, valine, leucine, isoleucine, serine, threonine, proline, tyrosine, and phenylalanine.32 A principal question related to the origin of life is whether metabolism occurred prior to replication, or the other way around, leading to a view of life as an extreme expression of kinetic control and an emergence of metabolic pathways manifesting replicative chemistry (Pross 2004). According to Davies (2000a, b) the probability of an accidental formation of primordial DNA and RNA biomolecules is about 1–1022 . This renders it of equal probability the natural intelligence underlying these characteristics resides in undecoded laws of complexity. According to Russell and Hall (2006) viruses, forming parasitic entities on life forms, acted as mobile RNA worlds alyzing metabolic reactions, DNA replication, responding to stimuli, and transporting molecules from one location to another. 30 A polypeptide or mixture of polypeptides obtained by heating a mixture of amino acids. 31 Macromolecular biological catalysts. Enzymes accelerate chemical reactions. The molecules upon which enzymes may act are called substrates and the enzyme converts the substrates into different molecules known as products. 32 http://www.cryst.bbk.ac.uk/education/AminoAcid/the_twenty.html.

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injecting genetic elements into proto-cells capable of replicating themselves around submarine alkaline hydrothermal vents. There, chemical reactions created biosynthetic pathways leading to emergence of sparse metabolic network and the assembly of pre-genetic information by primordial cells. In this concept, life and evolution of prokaryotes constituted a deterministic process governed by bio-energetic principles likely to apply on planets, which means life could be everywhere. Theories suggesting seeding of life on Earth by comets have been lacking in evidence since, while comets and meteorites (Fig. 1.7) may contain amino acids, they were not known to contain biomolecules. However Callahan et al. (2011) reported nucleobases, including adenine, guanine, xanthine, hypoxanthine, purine from carbonaceous chondrites,33 stating: “Here, we investigated the abundance and distribution of nucleobases and nucleobase analogs in formic acid extracts of 12 different meteorites by liquid chromatography–mass spectrometry. The Murchison and Lonewolf Nunataks 94,102 meteorites contained a diverse suite of nucleobases, which included three unusual and terrestrially rare nucleobase analogs: purine, 2.6diaminopurine, and 6.8-diaminopurine … Our results demonstrate that the purines detected in meteorites are consistent with products of ammonium cyanide chemistry, which provides a plausible mechanism for their synthesis in the asteroid parent bodies, and strongly supports an extraterrestrial origin. The discovery of new nucleobase34 analogues in meteorites also expands the prebiotic molecular inventory available for constructing the first genetic molecules”. The possibility that these biomolecules represent contaminants with terrestrial materials is not clear. Exobiogenic theories, and possible evidence, which invoke introduction of biomolecules to Earth from other planets do not contradict indigenous terrestrial biogenesis. According to Russell and Hall (2006) chemical reactions involving dissolved H2 , HCOO− , CH3 S− and CO2 associated with reactions with ferrous iron in the early oceans constituted triggers for development of inorganic membranes and subsequently chemosynthetic life in hydrothermal environments. In this model these reactions produce metal-enzymes such as greigite (Fe5 NiS8 ) which catalyzes synthesis of acetate (H3 C.COO− ), leading to synthesis of more complex organic molecules such as glycine (+H3 N.CH2 .COO− ) and other amino acids and to RNA, generated within cavities of FeS. The process includes polymerizing glycine and other amino acids

33 https://en.wikipedia.org/wiki/Category:Nucleobases. 34 Nucleobases are parts of RNA and DNA that may be involved in pairing. They include cytosine, guanine, adenine, thymine in (DNA), uracil in (RNA) and xanthine and hypoxanthine (mutated forms of guanine and adenine). These are abbreviated as C, G, A, T, U, X and HX respectively. They are usually simply called bases in genetics. Because A, G, C and T appear in the DNA, these molecules are called DNA-bases; A, G, C and U are called RNA-bases. Nucleobases, also known as nitrogenous bases or often simply bases, are nitrogen-containing biological compounds that form nucleosides which in turn are components of nucleotides, with all of these monomers constituting the basic building blocks of nucleic acids. A nucleoside consists simply of a nucleobase (also termed a nitrogenous base) and a five-carbon sugar (either ribose or deoxyribose), whereas a nucleotide is composed of a nucleobase, a five-carbon sugar, and one or more phosphate groups.

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into short peptides35 on phosphorylated36 mineral surface where the peptides are protected. RNA acts as a polymerizing agent for amino acids, regulating metabolism and providing genetic information. Considerations of original life forms commonly refer to extremophile microbial communities, such as around submarine hydrothermal vents (“black chimneys”) (Martin et al. 2008). These authors compare the chemistry of the H2 –CO2 redox couple in hydrothermal systems and core energy metabolic biochemical reactions of modern prokaryotic autotrophs. The high greenhouse gas levels (CO2 , CO, CH4 ) of the early atmosphere, which allowed the presence of water at the Earth surface despite low solar luminosity, implies high partial CO2 pressure and thereby low pH of the Archaean oceans (Fig. 2.3). Dissociation of H2 O associated with microbial-mediated oxidation of FeO to Fe2 O3 under these conditions would have released hydrogen (Russell and Hall 2006). According to these authors life emerged around hydrothermal vents in connection with reactions involving H2 , HCOO− , CH3 S− and CO2, catalyzed by sulphide, analogous to the synthesis of acetate (H3 C.COO− ). In this model glycine (+H3 N; CH2 .COO− ) and other amino acids, as well as tiny quantities of RNA, were trapped within tiny iron sulphide cavities. The released energy from these reactions resulted in introduction of polymerizing glycine and other amino acids into short peptides upon phosphorylated mineral surface. RNA acted as a polymerizing agent for amino acids in a process regulating metabolism and transferring genetic information. Such biosynthetic pathways probably evolved before 3.7 Ga before the build-up of free atmospheric oxygen. Inherent in Charles Darwin’s and Alfred Russel Wallace’s theory of evolution is the descent from a single common ancestor by small-scale gradual changes through an unguided process of natural selection acting upon random mutation as the primary mechanism driving the evolution of life. Darwin’s evolution theory indicates plants, animals and other life forms originate from pre-existing types modified in successive generations, leading to more than 2 million species named and described, with some 10–30 million remaining to be identified. The original idea of gradual evolution has been replaced by evidence for gradual evolution disrupted by catastrophic mass extinctions of species, as forecasted by Patrick Matthew (Weale 2015). About a quarter century prior to the advent of uniformitarian evolution, the theory of catastrophism prevailed (Cuvier 1812). Whereas Darwin regarded hiatuses in the paleontological record as due to lack of evidence, modern documentation of mass extinction events indicates some of them were triggered by environmental catastrophes such as volcanic and asteroid events (Alvarez et al. 1980), justifying the concept of environmentally disrupted evolution. Darwin’s evolution theory consists of several basic premises (Mayr 1982), including (A) Population may increases exponentially if all agents reproduce; (B) Populations are stable except for occasional fluctuations; (C) Resources are limited and relatively constant; (D) There is a fierce competition for survival with only a small fraction of the progeny of each generation making it to the next; (E) No two agents 35 Short

chains of amino acid monomers linked by peptide (amide) bonds. a phosphate group into (a molecule or compound).

36 Introduce

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are exactly the same; (F) Much of this variation is heritable; (G) Survival depends in part on the heredity of the agent; (H) Over generations this produces continual gradual change. Kaufmann (1993) wonders whether evolution can be explained strictly on the basis of the Darwinian principles of random mutations and natural selection, or whether laws of self-organization and complexity are at work. He concludes that in order to explain the evolving self-generated architecture of living organisms yet little-formulated unexplained processes must exist, supplementing Darwinian evolution theory, namely an existence of “biological determinism”. In discussing this concept Davies (2000a, b) suggests that, while true, biological determinism cannot be implied by the known physics and chemistry alone and additional discoveries or principles may be found in the emerging sciences of complexity and information theory. According to Eigen and Schuster (1979a, b) life can be treated as a molecular phenomenon whose essential factors include specific physical and physicochemical states of matter characterized by long range order, coherent domains and active and diffused organized information. These characteristics pertain to nano-and microvesicular systems including nano-bacteria, such as Nanobes (Uwins et al. 1998) representing an actual passage from non-living forms to primitive organisms.37 The “RNA world”38 theory (Gilbert 1986) suggests self-replicating RNA constituted initial life forms whereas the metabolism-first hypothesis39 places metabolic networks before DNA or RNA. RNA can catalyze chemical reactions, including the polymerization of nucleotides40 and is thus uniquely capable to serve as a template to catalyze its own replication (Cooper 2000). Consequently RNA is generally believed to have been the initial genetic system, and an early stage of chemical evolution is thought to have been based on catalyzing self-replicating RNA molecules (Altman and Cech 1989), a period of evolution known as the “RNA world”. In this model ordered interactions between RNA and amino acids then evolved into the present-day genetic code, and DNA eventually replaced RNA as the genetic material. In one model monomers41 such as amino-acids can be synthesized under anhydrous high temperature conditions into polymers, such as proteins. For example ocean water carrying amino acids could have splashed onto a hot lava flow, boiling away 37 A proposed class of living micro-organisms of a size much smaller than the generally accepted lower limit for life (about 200 nm for bacteria). The status of nano-bacteria has been controversial, with some researchers suggesting they are a new class of living organism and others attributing to them a simpler abiotic nature. Research tends to agree that these structures exist and appear to replicate in some way but the idea they are living entities has largely been discarded, and the particles are instead thought to be nonliving crystallizations of minerals and organic molecules. 38 A hypothetical stage in the evolutionary history of life on Earth, in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. 39 In this model the first reactions involve spontaneous formation of simple molecules such as acetate, a two-carbon compound formed from carbon dioxide and water. 40 Nucleotides form the basic structural unit of nucleic acids such as DNA. Composed of a phosphate group, the bases include adenine, cytosine, guanine, and thymine, and a pentose sugar. In RNA the thymine base being replaced by uracil, a compound consisting of a nucleoside linked to a phosphate group. 41 A molecule that can be bonded to other identical molecules to form a polymer.

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the water and leaving behind a protein (Fox and Dose 1972). The surface of clay minerals such as montmorillonite42 can act to catalyze the formation of RNA polymers and facilitate assembly of cell-like lipid vesicles. Crick (1958), co-discoverer of the double helix structure of DNA, called the DNA-RNA-Proteins system the Central Dogma of molecular biology,43 which states that once information has passed into protein it cannot get out again. Thus, whereas the transfer of information between nucleic acids or from nucleic acid to protein is possible, information transfer from protein to protein or from protein to nucleic acid is not possible. Information means the precise determination of sequence, either of bases in the nucleic acid or of aminoacid residues in the protein. A different model was developed by Carter and Wills (2017), suggesting molecular biology emerged simultaneously from simple origins in a peptide-RNA partnership, an idea based on experimental study of peptide enzymes called aminoacyl-tRNA synthetases44 which convert genetic information into proteins. In this view RNA molecules were preceded by nucleotides,45 organic molecules that serve as monomer units for forming nucleic acid polymers.46 Nucleotides, consisting of sugar attached to a phosphate and a nitrogen-containing base molecule, serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Two types of Nucleotides, the building blocks of RNA, have been synthetized in the laboratory. Yet another model has been advanced suggesting the building blocks of DNA can form spontaneously from chemicals thought to be present on the primordial Earth. Chaitin (1966, 2009) originated the field of ‘meta-biology’, a mathematical computation approach to evolution proving Darwin’s theory, elucidating a scheme that can explain life itself with reference to the mathematical studies of John von Neumann and Alan Turing. Algorithmic information theory allows an elucidation of the structure of objects, examines probability, statistics and information through the algorithmic lens, later developed a central part of theoretical computer science (Fig. 1.6). In this theory genes constitute software transformed into forms controlled by the physics of the organisms’ environment. Evolution can be mathematically formalized by the genetic code, where the physical form of organisms is a translation of genes into form. A result is delineation of three potential types of design: blind search, evolution, intelligent design. In Chaitin’s approach there is no reproduction, there is only one organism mutating through time, which Chaitin terms algorithmic muta42 (Na,Ca) 0.33 (Al,Mg)2 (Si4 O10 )(OH)2 ·nH2 O. 43 The central dogma of molecular biology is an explanation of the flow of genetic information within

a biological system. It is often stated as “DNA makes RNA and RNA makes protein,” although this is an oversimplification. 44 https://en.wikipedia.org/wiki/Aminoacyl_tRNA_synthetase. 45 A nucleotide is one of the structural components, or building blocks, of DNA and RNA. A nucleotide consists of a base (one of four chemicals: adenine, thymine, guanine, and cytosine) plus a molecule of sugar and one of phosphoric acid. 46 Is a large mol Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid and ribonucleic acidecule, or macromolecule, composed of many repeated subunits.

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Fig. 1.6 Pioneers of molecular biology and theoretical and mathematical studies of the origin of life: Fred Hoyle. By vla22 (https://commons.wikimedia.org/wiki/File:Institute_of_Astronomy,_ statue_of_Sir_Fred_Hoyle.jpg), licensed under CC BY 4.0

tions. Algorithmic mutation combines the act of mutating and selection in one step, it is an n-bit program that takes the current organism A and outputs a new organism B of higher fitness. Stanislaw Ulam and John von Neumann (Fig. 1.6) developed the field of stochastic cellular automaton and asynchronous cellular automaton (Von Neumann 1966). A cellular automaton consists of a regular grid of cells, each in one of a finite number of states, such as on and off. The grid can be in any finite number of dimensions. For each cell, a set of cells called its neighborhood is defined relative to the specified cell. An initial state (time t  0) is selected by assigning a state for each cell. A new generation is created (advancing t by 1), according to some fixed rule (generally a mathematical function) that determines the new state of each cell in terms of the current state of the cell and the states of the cells in its neighborhood. Typically, the rule for updating the state of cells is the same for each cell and does not change over time, and is applied to the whole grid simultaneously. Cellular automata can

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simulate a variety of real-world systems, including biological and chemical ones. Von Neumann developed a mathematical analysis of self-reproducing automata in a twodimensional grid, preceding the discovery of the structure of DNA by Watson and Crick (1953). A cellular automaton consists of cells each of which has a value or state and is connected to neighboring cells forming a one- or multidimensional lattice (Von Neumann 2010) (Fig. 1.6). The states of the cells change at discrete time-steps—the new state of a cell is computed from the previous states of the connected neighboring cells using pre-defined rules. Von Neumann described a cellular automaton with twenty-nine possible states for each cell and in which every cell is connected to the cell above, below, left, and right, indicating the dynamics exhibited by such a cellular automaton are similar to the biological processes involved in self-reproduction and evolution of DNA. An analogy with swarm intelligence (Section E-2) is tempting but far from certain. According to Darwinian evolution theory repetitive hierarchical designs in nature ensue mainly from two factors (1) random genetic mutation, and (2) Natural Selection. In contrast, the French mathematician Mandelbrot (1982), modelled a fractal geometry of nature on the basis of a number of suppositions—including curved space, multidimensional space, shapes defined by iteration in feedback loops—leading to the development of fractal (fractional) geometry and mathematics (Norman 2018). Fractal meant self-similar or multiscale symmetry involving pattern repetition, suggesting the physical world is structured by fractal geometry (BBM 1995). An example is cited as coast lines that display repetitive contours over long distances. However such regularities occur only where the initial conditions are similar, where the coast line reflects the wave action, but do not apply where the geological and morphological attributes and sea current directions vary. Similar reservations apply to other examples purporting to observe a purely mathematical control of biological evolution.

1.4 Panspermia and Transpermia Davies (2000a, b) proposed a test of possible multiple re-emergence of life using the exclusive left-handed chirality47 of terrestrial amino acids,48 assuming spontaneous re-emergence or introduction of life could possess right-hand chirality. According to Davies and Lineweaver (2005) “If life emerges readily under earth-like conditions, the possibility arises of multiple terrestrial genesis events. We seek to quantify the probability of this scenario using estimates of the Archaean bombardment rate and the fact that known life established itself fairly rapidly on Earth once conditions 47 A chiral molecule/ion is non-superimposable on its mirror image. The presence of an asymmetric

carbon center is one of several structural features that induce chirality in organic and inorganic molecules. 48 Organic compounds containing amine (–NH ) and carboxyl (–COOH) functional groups, along 2 with a side chain (R group) specific to each amino acid.

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became favorable. We find a significant likelihood that at least one more sample of life may have emerged on Earth, and could have co-existed with known life. Indeed, it is difficult to rule out the possibility of extant ‘alien’ life. We offer some suggestions for how an alternative sample of life might be detected”. The possibility that life began on Earth more than once but traces of secondary life were destroyed or have not been identified, or that secondary life forms intermingled with primary life forms, may be impossible to determine. While amino-acids have been detected in cometary dust (McKee 2009) and in meteorites, the premise that the presence of organic molecules such as amino acids in an aqueous medium, under a favorable range of chemical composition, acidity, oxygen fugacity, temperature, pressure, radiation or lightning, is sufficient for the emergence of life, as tested in the Miller-Urey experiment,49 has not been confirmed. Hoyle (1983) (Fig. 1.6) estimated the probability of formation of a simple living organism through random rearrangements of organic matter over the duration of the universe (t), as less than 3700-Ma sea-floor sedimentary rocks from West Greenland. Science 283:674–6. https://www.ncbi.nlm.nih.gov/pubmed/9924024

References

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Rosing MT (2010) No climate paradox under the faint early Sun. Nature 464:744–747. https:// www.nature.com/articles/nature08955 Royer, DL et al (2001) Paleobotanical evidence for near present-day levels of atmospheric CO2 during part of the Tertiary. Science 292:2310–2313. http://science.sciencemag.org/content/292/ 5525/2310.full Royer DL et al (2004) CO2 as a primary driver of phanerozoic climate. GSA Today 14(3):4–10. https://www.geosociety.org/gsatoday/archive/14/3/pdf/i1052-5173-14-3-4.pdf Royer DL, Berner RA, Park J (2007) Climate sensitivity constrained by CO2 concentrations over the past 420 million years. Nature, 446:530–532. https://www.nature.com/articles/nature05699 Ruddiman WF (ed) (1997) Tectonic uplift and climate change. Springer https://www.springer.com/ us/book/9780306456428 Sagan C, Mullen G (1972) Earth and Mars: evolution of atmospheres and surface temperatures. Sci New Series 177(4043):52–56. https://courses.washington.edu/bangblue/Sagan-Faint_ Young_Sun_Paradox-Sci72.pdf Schidlowski MA (1988) 3800-million-year Isotopic record of life from carbon sedimentary rocks. Nature 333:313–315. https://www.nature.com/articles/333313a0 Schidlowski M et al (1979) Carbon isotope geochemistry of the 3.7×109-yr-old Isua sediments, West Greenland: implications for the Archaean carbon and oxygen cycles. Geochim Cosmochim Acta 43(2):189–199. https://www.sciencedirect.com/science/article/pii/0016703779902382 Schopf JW (2001) Cradle of life: the discovery of Earth’s earliest fossils. Princeton UP, 367 pp. https://books.google.com.au/books?id=YJHBAolcIk8C&dq=&redir_esc=y Sepkoski JJ (1996) Patterns of Phanerozoic extinction: a perspective from global data bases. In: Walliser OH (ed) Global events and event stratigraphy. Springer, Berlin, pp 35–52. https://link. springer.com/chapter/10.1007/978-3-642-79634-0_4 Shukolyukov A et al (2000) The oldest impact deposits on earth—first confirmation of an extraterrestrial component. In: Impacts and the Early Earth. Lecture Notes in Earth Sciences, vol 91. https://link.springer.com/chapter/10.1007/BFb0027758 Simonson BM et al (2000) Geochemical evidence for an impact origin for a late Archean Spherule Layer, Transvaal Supergroup, South Africa. Geology 28 (12):1103–1106. J Geodynamics 32:205–229. https://pubs.geoscienceworld.org/gsa/geology/article-abstract/28/12/1103/ 207170 Simonson BM, Davies D, Hassler SW (2001) Discovery of a layer of probable impact melt spherules in the late Archaean Jeerinah Formation, Fortescue Group, Western Australia. Aust J Earth Sci 47:315–325. https://onlinelibrary.wiley.com/doi/full/10.1046/j.1440-0952.2000.00784.x Simonson BM, Glass, BP (2004) Spherule layers—records of ancient impacts. Annu Rev Earth Planet Sci 32:329–361. https://www.annualreviews.org/doi/abs/10.1146/annurev.earth.32. 101802.120458 Simonson BM, Hassler SW (1997) Revised correlations in the early Precambrian Hamersley Basin based on a horizon of re-sedimented impact spherules. Aust J Earth Sci 44:37–48 Sloan D, Batista RA, Loeb A (2017) The resilience of life to astrophysical events. Nat Sci Rep 7(5417). https://www.nature.com/articles/s41598-017-05796-x Solanki SK (2002) Solar variability and climate change: is there a link? Astronomy Geophysics 43(5):509–513. https://onlinelibrary.wiley.com/doi/full/10.1046/j.1468-4004.2002.43509.x Thiemens MH (1999) Mass-independent isotope effects in planetary atmospheres and the early solar system. Science 283:341–345. https://www.ncbi.nlm.nih.gov/pubmed/9888843 Tice MM, Lowe DR (2004) Photosynthetic microbial mats in the 3416-Myr-old Ocean. Nature: 431:549–52. https://www.ncbi.nlm.nih.gov/pubmed/15457255 Trainer MG et al (2006) Organic haze on titan and the early Earth. PNAS, 103(48):18035–18042. http://www.pnas.org/content/103/48/18035.short Valley JW et al (2000) A cool early Earth. Geology 30:351–354. https://pdfs.semanticscholar.org/ f5ef/422d4abc265a5283ba4d3eab2795baa8c573.pdf

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Valley JW (2008) The origin of habitats. Geology 36(11):911–912. (https://pubs.geoscienceworld. org/gsa/geology/article/36/11/911/29767/the-origin-of-habitats; http://www.learner.org/courses/ envsci/unit/text.php?unit=1&secNum=4) Van Zuilen MA et al (2003). Graphite and carbonates in the 3.8 Ga old Isua Supracrustal Belt, Southern West Greenland. Precambrian Res 126:331–348. http://www.whoi.edu/science/GG/ geodynamics/2005/images2005/van%20Zuilen%20et%20al%202003.pdf Vasconcelos C, Bernasconi S (1995) Microbial mediation as a possible mechanism for natural dolomite formation at low-temperatures. Nature 377(6546):220–222. https://www.researchgate. net/publication/224962213_Microbial_Mediation_as_a_Possible_Mechanism_for_Natural_ Dolomite_Formation_at_Low-Temperatures Walker JCG et al (1983) Possible limits on the composition of the Archaean ocean. Nature 302. https://www.nature.com/articles/302518a0 Ward PD (2007) Under a green sky: global warming, the mass extinctions of the past, and what they can tell us about our future. Harper Collins, New York, 242 pp. https://www.amazon.com/ Under-Green-Sky-Warming-Extinctions/dp/0061137928 Whiteside JH et al (2010) Compound-specific carbon isotopes from earth’s largest flood basalt eruptions directly linked to the end-Triassic mass extinction. Proc Natl Acad Sci USA 107(15):6721–6725, pnas.1001706107. http://www.pnas.org/content/107/15/6721 Zahnle KJ (1986) Photochemistry of methane and the formation of hydrocyanic acid (HCN) in the Earth’s early atmosphere. J Geophysical Res 91(D2):2819–2834. https://agupubs.onlinelibrary. wiley.com/doi/abs/10.1029/JD091iD02p02819 Zahnle K, Sleep NA (2006) Impacts and the early evolution of life. In: Thomas PJ et al (eds), Comets and the origin and evolution of life. Springer Berlin pp 207–251. https://link.springer. com/chapter/10.1007/3-540-33088-7_7

Chapter 3

From the Genetic Code to Collective Brains

Superstrings Tiny wispy strings Cryptic little things Shape universes, sing Oh take me on your wings. X-apparitions chase Light speed - a cosmic race Appears from quantum space Oblivious to my race. DNA chains extend RNA healers bend Repair a link, append life’s wonder: self -amend. RNA chains collapse A lover’s final gasp Queen Cleo’s sacrifice While gods are playing dice. Unseen hands strum guitar Bells’ echoes reach afar No strings attached, no bar Can bind a young blue star. My thought waves rise and ebb Brains weave a spider’s web Probe truths or make believe Loft crests I can’t achieve. Web sites each other find A net’s collective mind Tripwire humankind A cyclops stumbling blind. (Andrew Glikson)

Abstract In physical terms life constitutes a complex carbon-based system which replicates information, departs from thermodynamic equilibrium through the use of chemical metabolism, and undergoes variation and selection. Living things tend to © Springer Nature Switzerland AG 2019 A. Y. Glikson, From Stars to Brains: Milestones in the Planetary Evolution of Life and Intelligence, https://doi.org/10.1007/978-3-030-10603-4_3

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be complex and highly organized, have an ability to acquire energy from the environment and transform it for growth and reproduction, tending toward homeostasis, response, stimulation, reaction, recoiling, learning, reproduction, growth and development. A phylogenetic scheme is based upon ribosomal RNA sequence which shows living systems belong to one of three classes: (A) the eubacteria, comprising all typical bacteria; (B) the archaebacteria, containing methanogenic bacteria; and (C) the Eukaryotes, comprising cytoplasmic components within eukaryotic cells from which species and kingdoms evolved. Evolving cell network emerge as output of a cellular computing network, inducing changes in structure of the network itself through changes in the DNA activity patterns. In an “RNA world” self-replication is reached by combination of the nucleotides adenine, uracil, guanine and cytosine, forming templates for synthesis of new strands of RNA. Early cells formed by enclosure of self-replicating RNA in membrane composed of phospholipids, the basic components of biological membranes of prokaryotic and eukaryotic cells. The DNA of Eukaryote cells may contain 0.6–5.0 × 106 base pairs, capable of encoding about 5000 different proteins. Given the distinct structure and composition of the cell and computer chips, both possessing high processing power and natural and artificial intelligence, respectively, the design of artificial intelligence offers insights into some of the processes taking place in natural systems. The exploration of the deep hot biosphere located in oceanic hydrothermal energy sources, or within fractures in deep seated rocks, isolated from the influence of the sun and photosynthesis, has opened new windows in the search for early evolution of life. The development of colonies consisting of specialized cells signifies emergence of inter-cellular communications and coordination, implying each cell possess information regarding what the other cells are doing—a quantum leap toward evolution of complex multi-task organisms. Keywords DNA · RNA · Phylogenetic · Prokaryotes · Eukaryotes Attempts at a definition of life, as distinct from non-biotic systems,1 reflect its complexity, ranging in scale from nanometers to many meters (Fig. 3.1), a question dominating whole branches of biology, biochemistry, genetics, and the search for life elsewhere in the universe (Gayon et al. 2010; Gabbatiss 2017). Living things tend to be complex and highly organized, have an ability to acquire energy from the environment and transform it for growth and reproduction, tending toward homeostasis, response, stimulation, reaction, recoiling, learning, reproduction, growth and development. By contrast inorganic crystals lack what commonly is thought of as a biological nervous system.2

1 http://www.bbc.com/earth/story/20170101-there-are-over-100-definitions-for-life-and-all-are-

wrong. 2 https://www.nasa.gov/vision/universe/starsgalaxies/life’s_working_definition.html.

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Fig. 3.1 The scale of life. The relative sizes from microbes to humans on a logarithmic scale. By OpenStax College, Biology, https://www.khanacademy.org/science/biology/structure-of-a-cell/ prokaryotic-and-eukaryotic-cells/a/prokaryotic-cells, licensed under CC BY 3.0

3.1 From Amino Acids to Nucleic Acids In physical terms Life constitutes a complex carbon-based system which replicates information, departs from thermodynamic equilibrium through the use of chemical metabolism, and undergoes variation and selection. In one definition “Life, living matter and as such matter that shows certain attributes that include responsiveness, growth, metabolism, energy transformation, and reproduction. Although a noun, as with other defined entities, the word life might be better cast as a verb to reflect its essential status as a process”, or “an organismic state characterized by capacity for metabolism, growth, reaction to stimuli, and reproduction”.3 The fundamental architecture of life, DNA-RNA nucleotid sequences pairs embedded within the cell nucleus (Fig. 3.2) (Rettner 2017), chromosomes and cells is analogous to a computer hardware and software systems. The interaction between individual genes and the genome4 manifests synergy where the whole is greater than the sum of the parts.5 Evolving cell networks emerge as output of a cellular computing network, inducing changes in structure of the network itself through changes in the DNA activity patterns. As suggested by Davies (1999) biogenic processes depend on both the formation of a chemical substrate analogous to the hardware, and on an information processing system analogous to software. Davies suggests that, whereas the hardware can be formed by modifications of non-biological substances such as clay minerals, the information system or the software may reflect quantum systems, 3 Life—definition.

Merriam-Webster Dictionary. Last updated July 2018 https://www.merriamwebster.com/dictionary/life. 4 Genes are made from DNA. A gene that is formed from DNA codes for a specific protein. A genome is the collection of a lot of strands of DNA, where thousands of genes are included. 5 https://en.wikipedia.org/wiki/Synergy#Descriptions_and_usages.

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Fig. 3.2 a Comparison of RNA (left) with DNA (right), showing the helices and nucleobases. RNA World. Wikipedia. Last edited June 2018. By File:Difference DNA RNA-DE.svg: Sponk/*translation: Sponk—Chemical structures of nucleobases by Roland 1952, CC BY-SA 3.0, https://commons.wikimedia.org/w/index.php?curid=9810855; b The structure of the DNA double helix. The atoms in the structure are color-coded by element and the detailed structures of two base pairs are shown in the bottom right. DNA, Wikipedia. Last edited July 2018. By Zephyris, https:// commons.wikimedia.org/w/index.php?curid=15027555, licensed under CC BY-SA 3.0

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including ‘quantum replication, copied qubits’ and related quantum theories (Pati 2004; Wigner 1961; Davies 2004). Davies (1999) discussed the likelihood of molecular evolution according to the known laws of physics, the chemistry and the principles of natural selection, and environmental variations consistent with the principles of Darwinian evolution. However a problem arises regarding the origin of the information processing system itself, namely the operating system. Thus Davies states: “the genetic information stored on a genome is of no use on its own; it must be both interpreted and processed. Interpretation requires the operation of the genetic code, while data processing requires a suite of proteins and other specialized molecules to implement the instructions in life’s “program”. It is far from clear that molecular evolution proceeding by purely Darwinian means of random variation and selection can create these essential operating system features from scratch.” Dawkins (2006) focuses on a gene-centered theory whereby the basic life forms consisted of the replicating nucleic acids DNA and RNA, containing genes which constitute regions of DNA encoding specific functions and instructions directing the RNA how to make proteins. A combination of genes constitutes a chromosome,6 the human chromosome having up to 500 million base pairs of DNA with thousands of genes. The RNA molecules are considered a fundamental primary unit as it acts as a catalyst (ribozymes7 ), in distinction from the DNA, in addition to self-replicating and bearing information, passing information from generation to generation. The basic system is superposed by metabolic networks.8 An emergent properties theory9 suggests networks of metabolic processes have predated the formation of complex nucleic acids, involving spontaneous formation of simple molecules such as acetate, a two-carbon compound formed from carbon dioxide and water. A Metabolism-first theory10 suggests the origin of life stems from a system of self-catalytic molecules capable of experiencing Darwinian-type evolution without the need of RNA or DNA and their replication. The essence of the Metabolism First 6 A chromosome is a DNA molecule with part or all of the genetic material (genome) of an organism.

Chromosomes, which carry the hereditary material, or DNA, are contained in the nucleus of each cell. Chromosomes come in pairs, with one member of each pair inherited from each parent. The two members of a pair are called homologous chromosomes. Each cell of an organism and all individuals of the same species have, as a rule, the same number of chromosomes. The reproductive cells (gametes) are an exception; they have only half as many chromosomes as the body (somatic) cells. But the number, size, and organization of chromosomes varies between species. 7 Ribozymes (ribonucleic acid enzymes) are RNA molecules that are capable of catalyzing specific biochemical reactions, similar to the action of protein enzymes. 8 CK-12 (2018) First Organic Molecules—Advanced. https://www.ck12.org/book/CK-12-BiologyAdvanced-Concepts/section/10.8/. 9 An emergent property is a property which a collection or complex system has, but which the individual members do not have. A failure to realize that a property is emergent, or supervenient, leads to the fallacy of division. An emergent behavior or emergent property can appear when a number of simple entities (agents) operate in an environment, forming more complex behaviors as a collective. If emergence happens over disparate size scales, then the reason is usually a causal relation across different scales. 10 https://www.sciencedaily.com/releases/2010/01/100108101433.htm.

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Fig. 3.3 Differences between Prokaryotic and Eukaryotic cells. The cells of eukaryotes (left) and prokaryotes (right). By Science Primer (National Center for Biotechnology Information), vectorized by Mortadelo 2005, https://en.wikipedia.org/wiki/File:Celltypes.svg, public domain

theory is that the complex molecules of life came after the spontaneous formation of very simple molecules, formed for example in the vicinity of submarine thermal vents (Moran 2009). The evolution of complex molecules was assisted by various catalysts some of biological nature. The chromosome and self-replicating ribozyme are enveloped by phospholipid bilayer, forming the cell. In this model life does not depend strictly on the DNA genes but on the entire cell system, including the DNA, RNA and the produced proteins. This is indicated by the complex multi-component structure of the cell, including a nucleus, nucleolus, ribosomes, centrosome, vacuole, mitochondrion, lysosome, endoplasmic reticulum, golgi bodies and other components (Figs. 3.2, 3.3 and 3.4). In multicellular organisms cells may be grouped together to form tissues. Organs are then formed from the functional grouping of multiple tissues. Organs that interact may form organ systems capable of carrying out specific body functions. Organ systems collectively carry out the life functions of the complete organism. It follows that within the cells and between cells emergent properties lead to a hierarchy of levels, culminating in complex biological systems where the total is greater than the sum of the parts.11 In an “RNA world” (Cheriyedath 2017), self-replication of RNA is reached by combination of the nucleotides adenine, uracil, guanine and cytosine, formed templates for synthesis of new strands of RNA. Early cells formed by enclosure of self-replicating RNA in membrane composed of phospholipids,12 the basic components of biological membranes of prokaryotic and eukaryotic cells. Phospholipids 11 At its most basic level, the concept of emergent properties states that with rising levels of complexity in living things, new patterns will emerge. This is the case whether you move up the chain from simple single-celled organisms to much more complex multi-celled organisms, or whether you move from a single organism to an entire population of that organism. http://education.seattlepi. com/emergent-properties-living-things-biology-6131.html. 12 A lipid containing a phosphate group in its molecule, e.g. phosphatidylcholine.

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Fig. 3.4 Major Cell Organelles in a typical animal cell. Within the cytoplasm, the major organelles and cellular structures include: (1) nucleolus (2) nucleus (3) ribosome (4) vesicle (5) rough endoplasmic reticulum (6) Golgi apparatus (7) cytoskeleton (8) smooth endoplasmic reticulum (9) mitochondria (10) vacuole (11) cytosol (12) lysosome (13) centriole. By Messer Woland and Szczepan 1990, https://simple.wikipedia.org/wiki/Organelle, licensed under CC-BY-SA-3.0

have long, water-insoluble hydrocarbon chains joined to water-soluble head groups that contain phosphate, forming membranes that separate the interior of the cell from the external environment.

3.2 The Intelligent Cell Cells include two main classes: (1) Prokaryotic cells (bacteria), which lack a nuclear envelope, and (2) eukaryotic cells13 containing a nucleus in which the genetic material is separated from the cytoplasm. Prokaryotic cells are generally smaller and simpler than eukaryotic cells and their genomes are less complex and do not contain cytoplasmic organelles or a cytoskeleton. However the same basic molecular mechanisms govern both prokaryotes and eukaryotes, indicating that all present-day cells are descended from a single primordial ancestor. By contrast to prokaryotic cells Eukaryotes can be single-celled or multi-celled, have membrane-bound organelles, including the nucleus, containing the genetic material enclosed by the nuclear membrane (Fig. 3.4). 13 Khan

Academy. Intro to Eukaryotic Cells. https://www.khanacademy.org/science/biology/ structure-of-a-cell/prokaryotic-and-eukaryotic-cells/a/intro-to-eukaryotic-cells.

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The origin of a cell requires an enclosing membrane to contain the organic materials of the cytoplasm. To combine as cell organic molecules must join as complex polymers, such as polysaccharides and proteins. RNA molecules are able to direct the synthesis of new RNA and DNA molecules, suggesting a possible ancestry of RNA molecules.14 Prokaryote and Eubacteria15 cells consist of nucleus-free unicellular bacteria, including Archaeobacteria.16 The earliest primitive forms of life are the Prokaryotes, nucleus-free single cells dating back to at least 3.7 billion years ago. Eukaryote nucleus-bearing cells are known from about 2.7 billion years ago. Prokaryotes form clones by splitting whereas in Eukaryotes DNA replaced RNA, allowing replication which involves fusion of cells, namely sexual reproduction. Prokaryote cells have no nucleus and their organelles17 are free from membrane coatings. Prokaryotes can live in extreme environments, including within fractures in rocks, sulphur-rich springs, hot springs, under ice sheets and hypersaline environments, where they constitute extremophiles.18 An example is furnished by thermosacidophiles which live in hot sulfur springs with temperatures as high as 80 °C and pH values as low as 2. Eubacteria possess cell walls made of peptidoglycan.19 Prokaryote cell walls are composed of polysaccharides and peptides and are internally coated by plasma membrane. Nutrition is conducted mainly by absorption (heterotrophic) including some photosynthesis or autotrophic chemosynthesis. Archaea and Eubacteria reproduce asexually through binary fission. The largest Prokaryote are represented by cyanobacteria20 capable of photosynthesis. The DNA forms a circular molecule surrounded by but not separated by a membrane from cytoplasm.21 The cytoplasm contains approximately 30,000 ribosomes (RNA molecules) where proteins are produced. A mammalian cell can contain as many as 10 million ribosomes. Eukaryote Cells are two to three orders of magnitude larger than Prokaryote cells and are considered to have evolved from the fusion of two prokaryote cells. No conclusive evidence exists for the age of the earliest Eukaryotes, which could have 14 CliffsNotes (2016) Origin of Cells. Houghton Mifflin Harcourt. https://www.cliffsnotes.com/ study-guides/biology/biology/the-origin-and-evolution-of-life/origin-of-cells. 15 Prokaryotic nucleus-free cells that are very common in the environment. 16 Archaea are prokaryotes, meaning they have no cell nucleus or any other membrane-bound organelles in their cells. They have unique properties separating them from the other two domains of life, Bacteria and Eukaryota. 17 An organelle is a tiny cellular structure that performs specific functions within a cell. Organelles are embedded within the cytoplasm of eukaryotic and prokaryotic cells. In the more complex eukaryotic cells, organelles are often enclosed by their own membrane. 18 Extremophiles are organisms that survive in environments that were once thought not to be able to sustain life, including intense heat, highly acidic environments, extreme pressure and extreme cold. 19 A substance forming the cell walls of many bacteria, consisting of glycosaminoglycan chains interlinked with short peptides. 20 Cyanobacteria are Prokaryotes, which are known to be the earliest forms of life, throughout time they have adapted to the changing earth, and in turn help it. 21 Cytoplasm: the material or protoplasm within a living cell, excluding the nucleus.

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emerged about the same time as the Prokaryotes or later (Woese et al. 1966). They contain a nucleus and membrane-bound organelles and include the presence of mitochondria,22 chloroplasts,23 cytoskeleton,24 a variety of cytoplasmic organelles, and chromosomal25 DNA of different structure than that of Prokaryotes. Eukaryotes such as protists26 and unicellular fungi may reproduce by mitosis; most of these are also capable of sexual reproduction. The organelles facilitate different metabolic activities. The DNA of Eukaryote cells may contain 0.6–5.0 × 106 base pairs, capable of encoding about 5000 different proteins. The nucleus contains linear DNA molecules and is the site of DNA replication and RNA synthesis. The translation of RNA into proteins takes place on ribosomes in the cytoplasm. Mitochondria constitute sites of oxidative metabolism, responsible for generating ATP27 from the breakdown of organic molecules. The organelles mitochondria and chloroplasts contain their own genetic systems, distinct from the nuclear genome of the cell. In plants photosynthesis takes place in chloroplasts that contain the chlorophyll. The Chloroplasts are surrounded by a double membrane and contain an thylakoid membrane. Lysosomes28 and peroxisomes29 provide specialized metabolic compartments for the digestion of macromolecules and for oxidative reactions, respectively. Other organelles facilitate movement and capture of other organisms for food. Plant cells also contain vacuoles30 for digestion of macromolecules and the storage of waste products and nutrients. Symbiogenesis or endosymbiotic theory suggests an origin of eukaryotic cells from prokaryotic organisms (Margulis et al. 2018).

22 Mitochondria are organelles, or parts of a eukaryote cell, located in the cytoplasm rather than the nucleus. They make most of the cell‘s supply of adenosine triphosphate (ATP), a molecule that cells use as a source of energy. Their main job is this energy conversion. 23 A plastid in green plant cells which contains chlorophyll and in which photosynthesis takes place. 24 Cytoskeleton: a microscopic network of protein filaments and tubules in the cytoplasm of many living cells, giving them shape and coherence. The cytoskeleton cytoskeleton is responsible for the movements of entire cells, intracellular transport and positioning of organelles. 25 Chromosome: a thread-like structure of nucleic acids and protein found in the nucleus of most living cells, carrying genetic information in the form of genes. 26 A protist is any eukaryotic organism that is not an animal, plant or fungus. The protists do not form a natural group. 27 ATP: Adenosine triphosphate. Adenosine triphosphate. An energy-carrying molecule found in the cells of all living things. It captures chemical energy obtained from the breakdown of food molecules and releases it to fuel other cellular processes. The phosphate tail of ATP is the actual power source taps y the cell. 28 An organelle in the cytoplasm of eukaryotic cells containing degradative enzymes enclosed in a membrane. 29 A small organelle present in the cytoplasm of many cells, which contains the reducing enzyme catalase and usually some oxidases. 30 A vacuole (/ vækju o*l/) is a membrane-bound organelle which is present in all plant and fungal cells and some protist, animal and bacterial cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules.  

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Fig. 3.5 a Mitochondria. Two mitochondria from mammalian lung tissue displaying their matrix and membranes as shown by electron microscopy. By Louisa Howard—http://remf. dartmouth.edu/images/ mammalianLungTEM/ source/8.html, public domain; b Mitochondrion. By Kelvinsong, https:// commons.wikimedia.org/w/ index.php?curid=27715320, licensed under CC0

Large Eukaryotes such as Amoeba proteus (Fig. 3.5) can exceed 1 mm, more than 100,000 times the size E. coli, and are highly mobile through extension of their cytoplasm, capable of capturing other organisms such as bacteria and yeasts, as food. Amoebas are found in every major lineage of eukaryotic organisms and occur in fungi, algae, and animals. Elements of the cell include: • Cell membrane: a thin layer that surrounds a cell; this layer separates and protects the inside of the cell from harmful agents around the cell and controls what moves in and out of the cell. • Lysosome: breaks down waste materials in an animal cell. • Nucleus: the information center of a cell that controls the chemical reactions that happen in cytoplasm; also stores DNA.

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• Nucleolus: a round structure that is inside the nucleus of a cell; this structure makes ribosomes.31 • Nuclear membrane: separates the nucleus from the rest of the cell; regulates substances that move in and out of the nucleus. • Vacuole: stores food, water, and wastes. • Mitochondrion: converts food into usable energy. • Golgi body: processes, packs, and transports proteins to be sent outside a cell. • Ribosomes: produce proteins for a cell. • Endoplasmic reticulum: processes and transports proteins from place to place inside a cell. • Cytoplasm: a jellylike substance that fills up the inside of a cell. • Centrosome: the region of a cell that is located next to the nucleus and contains the centrioles. Central to the operation of the cell are mitochondria (Fig. 3.5), membrane-bound organelle found in the cytoplasm of almost all eukaryotic cells, the primary function of which is to generate large quantities of energy in the form of adenosine triphosphate (ATP).32 Mitochondria are typically round to oval in shape and range in size from 0.5 to 10 μm. In addition to producing energy, mitochondria store calcium for cell signalling activities, generate heat, and mediate cell growth and death. The number of mitochondria per cell varies widely; for example, in humans, erythrocytes (red blood cells) do not contain any mitochondria, whereas liver cells and muscle cells may contain hundreds or even thousands. Mitochondria are unlike other cellular organelles in that they have two distinct membranes and a unique genome and reproduce by binary fission; these features indicate that mitochondria share an evolutionary past with prokaryotes. Mitochondria and chloroplasts are the powerhouses of the cell. Mitochondria appear in both plant and animal cells as elongated cylindrical bodies, roughly one micrometer in length and closely packed in regions actively using metabolic energy. Mitochondria oxidize the products of cytoplasmic metabolism to generate adenosine triphosphate (ATP), the energy currency of the cell.33 Chloroplasts are the photosynthetic organelles in plants and some algae. They trap light energy and convert it partly into ATP but mainly into certain chemically reduced molecules that, together with ATP, are used in the first steps of carbohydrate production. Mitochondria and chloroplasts share a certain structural resemblance, and both have a somewhat independent existence within the cell, synthesizing some proteins from instructions supplied by their own DNA. The internal membrane of a mitochondrion is elaborately folded into 31 A

ribosome is a cell organelle. It functions as a micro-machine for making proteins. Ribosomes are composed of special proteins and nucleic acids. The translation of information and the Linking of amino acids are at the heart of the protein production process. Ribosomes consist of two major components: the small ribosomal subunit, which reads the RNA, and the large subunit, which joins amino acids to form a polypeptide chain. Each subunit is composed of one or more ribosomal RNA (rRNA) molecules and a variety of ribosomal proteins (r-protein). 32 Mitochondrion. Encyclopedia Britannica. https://www.britannica.com/science/mitochondrion. 33 Mitochondrion, Britannica. https://www.britannica.com/science/mitochondrion.

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structures known as cristae. Cristae increase the surface area of the inner membrane, which houses the components of the electron-transport chain. Proteins known as F1F0ATPases that produce the majority of ATP used by cells are found throughout the cristae. Internal structures of the chloroplast contains flattened sacs of photosynthetic membranes (thylakoids) formed by the invagination and fusion of the inner membrane. Thylakoids34 are usually arranged in stacks (grana) and contain the photosynthetic pigment (chlorophyll). The grana are connected to other stacks by simple membranes (lamellae) within the stroma, the fluid proteinaceous portion containing the enzymes essential for the photosynthetic dark reaction.35 Cells use adenosine 5-triphosphate (Rathmacher 2012) (ATP) as their source of metabolic energy to drive the synthesis of cell constituents and carry out other energyrequiring activities, such as movement, evolved in stages along with the evolution of glycolysis,36 photosynthesis,37 and oxidative metabolism. The anaerobic breakdown of glucose leads to net energy gain of two molecules of ATP. The development of photosynthesis allowed the cell to harness energy from sunlight, breakdown water molecules and use CO2 molecules to produce sugar molecules and oxygen and synthesize energy-rich carrier molecules such as ATP. Microbial breakdown of water38 could have triggered the evolution of life around volcanic gas vents, or ‘black chimneys’, at an early stage. The release of oxygen by photosynthesis leads to oxidative metabolism,39 a process producing more energy carrying ATP molecules than anaerobic glycolysis.40 At a later stage the accumulation of oxygen through photosynthesis has changed the composition of the atmosphere, allowing emergence of advanced life forms (Fig. 3.6). Given the distinct structure and composition of the cell and computer chips, both possessing high processing power and natural and artificial intelligence respectively, the design of artificial intelligence offers some insights into some of the processes taking place in natural systems (Box 3.1) (Minkel 2007).

34 Each of a number of flattened sacs inside a chloroplast, bounded by pigmented membranes on which the light reactions of photosynthesis take place, and arranged in stacks or grana. 35 Mitochondrion, Britannica https://www.britannica.com/science/mitochondrion. 36 The breakdown of glucose by enzymes, releasing energy and pyruvic and lactic acid. 37 Photosynthesis CO + 2H O + photons → [CH O] + O + H O. Plants, some bacteria and some 2 2 2 2 2 one-cell organisms use the energy from sunlight to produce glucose from carbon dioxide and water, a reaction which releases oxygen. 38 Hydrogen Production: Photobiological https://energy.gov/eere/fuelcells/hydrogen-productionphotobiological. 39 Chemical process in which oxygen is used to make energy from carbohydrates (sugars). 40 The metabolic pathway that converts glucose C H O , into pyruvate, CH COCOO− + H+ . 6 12 6 3 The free energy released in this process is used to form the high-energy molecules ATP (adenosine triphosphate) and NADH (reduced nicotinamide adenine dinucleotide).

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Fig. 3.6 (a) Animal cell structure (https://commons.wikimedia.org/w/index.php?curid=4266142); (b) animal cell and components. (https://commons.wikimedia.org/wiki/File:0312_Animal_Cell_ and_Components.jpg)

Box 3.1 “Life-like” microchip” Scientists create ‘brain-like’ photonic computer microchips http://www.ox.ac.uk/news/2017-09-28-scientists-create-brain-photoniccomputer-microchips

Scientists have made a crucial step towards unlocking the ‘holy grail’ of computing—microchips that mimic the way the human brain works to store and process information. The research team has made the pioneering breakthrough

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of the development of photonic computer chips that imitate the way the brain’s synapses operate. The work, conducted by researchers from Oxford, Münster and Exeter universities, combined phase-change materials, commonly found in household items such as re-writable optical discs, with specially designed integrated photonic circuits to deliver a biological-like synaptic response. Crucially, their photonic synapses can operate at speeds a thousand times faster than those of the human brain. The team believes that the research could pave the way for a new age of computing, where machines work and think in a similar way to the human brain, while at the same time exploiting the speed and power efficiency of photonic systems … Via a network of neurons and synapses the brain can process and store vast amounts of information simultaneously, using only a few tens of watts of power.

3.3 The Phylogenetic Scheme A phylogenetic tree a branching diagram or “tree” showing the evolutionary relationships among various biological species or other entities developed by Woese and Fox (1977) (Fig. 3.7) and others is based upon ribosomal RNA sequence which shows living systems belong to one of three classes: (A) the eubacteria, comprising all typical bacteria; (B) the archaebacteria, containing methanogenic bacteria; and (C) the Eukaryotes, comprising cytoplasmic components within eukaryotic cells from which species and kingdoms evolved (Fig. 3.7). While the early stromatolites may represent Prokaryotes, Eukaryotes possibly appeared about ~2.1–1.6 Ga (Knoll et al. 2006), or earlier (Sugitani et al. 2009). Eukaryote colonial green algae consist of hollow balls of hundreds or thousands of cells embedded in a gelatinous matrix and organized into three main tissue systems: ground tissue, dermal tissue, and vascular tissue (Cooper 2000a, b). The ground tissue41 contains parenchyma cells42 that carry out most metabolic reactions of the plant, including photosynthesis. Ground tissue also contains two specialized cell types that are characterized by thick cell walls and provide structural support to the plant. Dermal tissue covers the surface of the plant and is composed of epidermal43 cells which allow absorption of nutrients. Several types of elongated cells form the vascular system which is responsible for the transport of water and nutrients throughout the plant.

41 All

tissues that are neither dermal nor vascular. specifically, parenchyma cells are thin-walled cells that make up the inside of many nonwoody plant structures including stems, roots, and leaves. 43 The epidermis is the outer layer of the three layers that make up the skin, the inner layers being the dermis and hypodermis. 42 Plants

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Fig. 3.7 A phylogenetic tree based on RNA data, emphasizing the separation of bacteria, archaea, and eukaryotes as proposed by Woese and Fox (1977). By NASA Astrobiology Institute, https:// en.wikipedia.org/wiki/Phylogenetic_tree, public domain

Cells in animals are considerably more diverse, and in the human body for example consist of more than 200 different kinds of cells in five main types of tissues: epithelial tissue, connective tissue, blood, nervous tissue, and muscle (Cooper 2000a, b). While stromatolites represent some of the oldest photosynthesizing colonies, some of the most primitive animals are represented by sponges (phylum Porifera, Metazoa), known from at least 580 Ma, branching off the evolutionary tree from the common ancestor of all animals. The evolution of multicellular animals depended on cells being able to sense and respond to other cells—to work together. Cells can migrate and transform from one type to another. Sponges do not have nervous, digestive or circulatory systems and rely on constant water flow to obtain food and oxygen and to remove wastes (Cooper 2000a, b). Sponges form multicellular organisms with pore and channel-rich bodies that allow circulation of water consisting of jelly-like gelatinous matrix (mesohyl) located between two thin layers of cells (Fig. 3.8). The sponges filter food from the water pumped through the channels in their bodies and can slowly inflate and constrict these channels to expel any sediment and prevent them clogging up. These movements are triggered when cells detect chemical messengers like glutamate pumped out by other cells in the sponge. These chemicals play a similar role in our brains today and the view that sponges lack tissue level organization, epithelia, sensory cells and coordinated behavior is challenged by recent molecular studies showing the existence in Porifera44 of molecules and proteins that define cell signalling systems in higher order metazoans. This suggests sponges coordinate behavior using chemical messenger systems common to other animals (Elliott and Leys 2010). 44 Poriferans

are commonly referred to as sponges.

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Fig. 3.8 Callyspongia sp. (Tube sponge) attracting cardinal fishes, golden sweepers and wrasses. By Nick Hobgood, https:// commons.wikimedia.org/w/ index.php?curid=5741176, licensed under CC BY-SA 3.0

3.4 Marine and Hydrothermal Communities The exploration of the deep hot biosphere (Gold 1992) located in deep ocean hydrothermal energy sources, or within fractures in deep seated rocks, isolated from the influence of the sun and photosynthesis, has opened new windows in the search for early evolution of life (Shock 2007). For life to obtain chemical energy independently from the sun has profound implications for its occurrence on other planets, albeit with an essential caveat—the need for the presence of water molecules. Observations of microbial communities around submarine hydrothermal vents relevant to early habitats include distinct environments, comprising (1) high temperature (~350 °C) black smokers underlain by magma chambers below ocean floors spreading zones and (2) moderate temperature (50–90 °C) related to serpentinization45 of basalts on the ocean floor, a process releasing H2 and subsequently methane (CH4 ) from sea floor basaltic 45 Serpentinization involves the hydrolysis and transformation of primary ferromagnesian minerals such as olivine ((Mg,Fe)2 SiO4 ) and pyroxenes ((Mg,Fe)SiO3 ) to produce H2 -rich fluids and a variety of secondary minerals over a wide range of environmental conditions. The continual and elevated production of H2 is capable of reducing carbon, thus initiating an inorganic pathway to produce organic compounds.

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rocks during hydrothermal processes (Martin et al. 2008; Holm et al. 2018; Mügler et al. 2016; Butterfield et al. 1997). 2Mg2 SiO4 (Ol) + 3H2 O ⇔ Mg3 Si2 O5 (OH)4 (Srp) + Mg(OH)2 (Brc)

(1)

3Fe2+ + 4H2 O ⇔ Fe3 O4 + H2 + 6H+

(2)

The mixing of hot mantle-derived hydrothermal fluids and cold oxygen-rich hydrospheric water at ocean ridge environments (Fig. 3.9a) as well as in land settings (Fig. 3.9b) results in a redox and temperature gradient at the seafloor where microbially-mediated and inorganic chemical reactions take place. Here electron donors generated from the underlying magma (H, HS, Fe) mix and react with electron acceptors (O, SO, NO) in circulating seawater create zones where fluid-microbe interactions dominate. The chemical composition of fluids during post-eruption periods is an important factor influencing microbial growth and colonization (Holden et al. 1998) (Fig. 3.9). In this study thermophilic and hyperthermophilic microorganisms were cultured from diffuse hydrothermal fluids at 18 °C at a deep-sea hydrothermal vent site 3 months after an eruption resulting from an intrusion of magma into shallow crust (Holden 2018; Jannasch and Mottl 1985). The abundances of these organisms decreased over a 3-year period as the shallow magma cooled. The presence of these organisms at the site suggests that they grew in response to nutrient input from hydrothermal fluid circulation and were transported to the surface following the eruption. Thermophiles and hyperthermophiles were also found in low-temperature (3–30 °C) fluids. The origin of these organisms is not known but may include the overlying seawater or a shallow to deep sub-seafloor habitat. The H2 –CO2 redox couple in hydrothermal systems and metabolic reactions in prokaryotic autotrophs display analogies, hinting at processes associated with early biogenesis. Methanogenic microbes46 and acetogenic micro-organism47 obtain energy through an acetyl-coenzyme pathway of CO2 fixation. The process operating through Chemiosmosis processes48 is considered an abiogenic precursor of modern microbial methane (CH4 ) and acetate (C2 H3 O2 − ) production. Chemo-lithotrophic bacteria use these reduced chemical species as sources of energy for the reduction of CO2 to organic carbon. Electron donors for aerobic microbial metabolism include mainly reduced sulfur-bearing molecules, methane, hydrogen, iron and manganese. Geochemical and isotopic composition of hydrothermal fluids of the Central Indian Ridge display a heterogeneity of carbon isotopic compositions of methane between the main hydrothermal vent and adjacent divergent vent site, representing potential 46 Methanogens are prokaryotic Archaea microorganisms that produce methane (CH ) as a metabolic 4

byproduct in anoxic conditions. 47 Acetogenic microbes generate acetate (CH COO− ) as an end product of anaerobic respiration or 3

fermentation. 48 Chemiosmosis

is the movement of ions across a semipermeable membrane, down their electrochemical gradient. An example of this would be the generation of adenosine triphosphate (ATP) by the movement of hydrogen ions across a membrane during cellular respiration or photosynthesis.

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Fig. 3.9 a A diagram portraying a hydrothermal submarine black chimney system. Seawater percolates through the sea floor and is modified by chemical exchange with the surrounding rocks and rising magmatic fluid. The altered seawater is released back into the ocean at the vent site and forms a hydrothermal plume. The rising plume mixes rapidly with ambient seawater, lowering the temperature and diluting the particle concentration. The plume will continue to rise through seawater as long as it is less dense than the surrounding seawater. Once the density of the hydrothermal plume matches the density of the seawater, it stops rising and begins to disperse laterally. Public Domain Basics of a hydrothermal vent—a Black Smoker. By NOAA, https://en.wikipedia.org/ wiki/File:Deep_Sea_Vent_Chemistry_Diagram_workaround.svg, public domain. b Thermophiles, a type of extremophile, produce some of the bright colors of Grand Prismatic Spring, Yellowstone National Park. By Jim Peaco, National Park Service—http://www.nps.gov/features/yell/slidefile/ thermalfeatures/hotspringsterraces/midwaylower/Images/17708.jpg, transferred from the English Wikipedia, original upload 1 April 2004 by ChrisO, https://commons.wikimedia.org/w/index.php? curid=326389, public domain

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subsurface microbial methanogenesis, where 13 C-depleted methane is emitted from the divergent vents. High magmatic energy sources such as hydrogen in the fluids enhance hydrogen-based microbial activity. Recycling of seawater through mid-ocean ridge systems involves transfer of geothermal energy to chemical energy in the form of reduced inorganic compounds derived from high-temperature reactions at depths of 2000–3000 m. Bacteria thrive in the shallow crust where upwelling hot reducing hydrothermal fluid mixes with downwelling cold, oxygenated seawater. Methanogenic, sulfur respiring, and extremely thermophilic microbes carry out anaerobic chemosynthesis. Forming the base of the food chain, the chemo-bacteria support large populations of hyperthermophilic and extremophile invertebrates, including grazers such as shrimp swarming around microbial colonies, crabs predators, lobsters scavengers, giant tube worms (Riftia pachyptila), anemones collecting organic debris and other organisms (Fig. 3.10). A predominance of methanogens and fermenters including methanococcale microbes in superheated hydrothermal emissions, along with the other major microbial thermococcales, represents hydrogen-driven subsurface microbial communities. Symbiotic relations between animals and plants dominated marine reef life since the Palaeozoic, including stromatoporoids49 and coral reefs forming including hermatypic50 fauna, tabulate and rugose and bryozoans with microbial structures. Shallow-water fringe-continent reefs were common during the Middle and Late Devonian, such as the 350 Ma Fitzroy reef in the Kimberley, northwestern Australia (Fig. 3.11), forming “springboards” for further introduction of fauna to the land. Dominated by cyanobacteria, stromatoporoids and corals, along with ammonoids,51 fish, and conodonts,52 the reefs are compared to atolls, fringing reefs, and barrier reefs. Minute algae belonging to the genera Renalcis and Chabakovia occur in great abundance in many of the fore-reef and back-reef facies. Other reef-building organisms include corals, brachiopods, and sponges (Playford et al. 2009). Coral reefs (Fig. 3.11) depend on the relations between the corals invertebrate phylum Cnidaria (Coelenterate) and the unicellular dinoflagellate53 algae, called zooxanthellae,54 the most well-known relationship is between zooxanthellae and hermatypic or reefforming, corals. Coral polyps resemble sea anemones but are mostly colonial. Initial

49 Stromatoporoids are layered sponges, filter feeders, that collected particulate organic debris floating in the water. 50 Hermatypic corals are those corals in the order Scleractinia which build reefs by depositing hard calcareous material for their skeletons, forming the stony framework of the reef. 51 Ammonoid or Ammonites are an extinct group of marine animals of the subclass Ammonoidea in the class Cephalopoda, phylum Mollusca. 52 Minute toothlike fossil composed of the mineral apatite (calcium phosphate); conodonts are among the most frequently occurring fossils in marine sedimentary rocks of Paleozoic age. 53 A large group of flagellate eukaryotes that constitute the phylum Dinoflagellata. Most are marine plankton, but they also are common in freshwater habitats. 54 A yellowish-brown symbiotic dinoflagellate present in large numbers in the cytoplasm of many marine invertebrates.

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polyps divide themselves into daughter polyps and divide in turn into colonies up to several meters large, joined by rigid calcareous skeleton attached to the seafloor. Mostly in shallow sunlit water up to 40 m deep at temperatures in the range 15–28 °C. Calcareous algae, mollusks, echinoderms, and protozoans also contribute to the reefs. Different organisms have different reef-building roles. Other organisms, especially algae and protozoans, bind and cement the reefs. Studies of Archaean fossil microbial relics in the Pilbara and Kaapvaal cratons reveal a wide range of morphotypes (Fig. 3.12). Detailed morphological, microchemical, organic petrology and isotopic investigations (Schopf and Barghoorn 1967; Schopf 2006; Sugitani et al. 2009; Golding and Glikson 2011; Glikson et al. 2008, 2011) superposed by extensive hydrothermal alteration (Marshall et al. 2013). Carbon isotopes display low 13/12 C (Morag et al. 2016). The carbon isotopic analysis of ∼3.5 Ga organic matter and coexisting carbonate δ13 C values in organic microstructures range between −33.6 and −25.7‰, supporting a biotic origin and variable

Fig. 3.10 Deep sea fauna around black smoker hydrothermal vents. a Concentration of Riftia pachyptila worm tubes surrounded by anemones and by mussels. From the 2011 NOAA Galapagos Rift Expedition. By NOAA Okeanos Explorer Program, Galapagos Rift Expedition 2011—Flickr NOAA Photo Library, https://commons.wikimedia.org/w/index.php?curid= 35246911, public domain; b A multitude of tubeworms and mussels. By NOAA—NeMO 2007 Cruise Report, https://commons.wikimedia.org/w/index.php?curid=15667839, public domain; c Alvinocarididae shrimps. By NOAA Vents Program—http://www.photolib.noaa.gov/htmls/ expl1283.htm, public domain; d Deep sea Shrimp. By Etrusko25, https://commons.wikimedia. org/w/index.php?curid=8045392, public domain

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Fig. 3.11 a Devonian reef, Fitzroy River, Kimberley, Northwestern Australia. By Brian W. Schaller, FAL, https://commons.wikimedia.org/w/index.php?curid=30810932; b The Great Barrier Reef from space (by NASA, https://www.nasa.gov/centers/goddard/images/content/143896main_ heron_island_lg.jpg, public domain; c The Great Barrier Reef. By Toby Hudson, https://en. wikipedia.org/wiki/File:Coral_Outcrop_Flynn_Reef.jpg, licensed under CC BY-SA 3.0

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Fig. 3.12 Comparison between modern and ancient microfossils. a Electron micrographs of ultra-thin sections displaying a highly diverse assemblage of microorganisms containing anaerobic low-organic including morphologies suggestive of possibly a methane- or ammonia-oxidizing bacterium and sulfur-oxidizing bacterium, East Pacific Rise (Holden et al. 1998). https://academic.oup.com/femsec/article/25/1/33/621595, reprinted with permission from Oxford University Press; b Photomicrographs of key specimens of spheroidal microstructures, Mount Goldsworthy–Mount Grant area in the northeastern Pilbara Craton, Western Australia. https://www.aca.unsw.edu.au/sites/default/files/publications/Sugitani%2C%20Grey%2C% 20Nagaoka%2C%20Mimura%20and%20Walter%202009.pdf, reprinted with permission from Elsevier

carbon fixation paths (Morag et al. 2016) Sulphur isotopes of early Archaean sediments of the Pilbara Craton include both positive and negative δ33 S values, suggesting mixing of mass independently fractionated sulphur, providing evidence for microbial sulphate reduction. Pyrite occuring in barite is depleted in 34 S relative to the host, suggesting microbial sulphate reduction (Golding and Glikson 2011).

3.5 Multicellular and Colonial Life The oldest known colonial bioherms are found in the Isua greenstone belt, southwestern Greenland (Nutman et al. 2016) (Fig. 3.13) in a shallow marine environment, indicated by seawater-like rare-earth element plus yttrium trace element signatures of the meta-carbonates, including interlayered detrital sedimentary rocks with cross-

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lamination and storm-wave generated breccia. 3.48 Ga stromatolites occur in the Dresser Formation of the Pilbara Craton, Western Australia (Fig. 3.14) (Buick et al. 1980) and 3.43 Ga stromatolite reef from the Strelley Formation (Allwood et al. 2006, 2007) (Fig. 3.14). Vertical and lateral variations occur within the reef in an isolated, partially restricted, peritidal marine carbonate platform where no trace occurs of hydrothermal or terrigenous clastic input. By contrast stromatolites are absent in correlated deeper marine settings. Some stromatolite types occur across different palaeo-environments, highlighting the combined influence of biological and environmental processes on stromatolite formation (Webb 2002). The regional distribution of stromatolites in the palaeo-environment suggests a biological response to variations in water depth, sediment influx and hydrothermal activity with stromatolite formation. A close association is observed between stromatolites and evaporite crystal pseudomorphs. Stromatolite colonies consist of two or more identical clones evolved by repeated iteration of genetically identical cells. The energy saved for any individual cell allows the colony to invest more energy or response to environmental conditions. At an advanced stage individual cells may develop specific functions within the colony, including feeding, reproduction, and defense. The transformation of colonial aggregates to multicellular organisms was later accompanied with specialization of cells and increased complexity and diversity. The aggregation of cells in clusters has many survival advantages for individual cells in terms of defense from damaging environ-

Fig. 3.13 Microbialites at 3.42 Ga Strelley Pool Chert, Pilbara Craton, Western Australia. By Didier Descouens, https://commons.wikimedia.org/w/index.php?curid=15944367, licensed under CC BY-SA 4.0

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Fig. 3.14 Pilbara stromatolites. a Stromatolite in chert, ~3.49 Ga Dresser Formation, North Pole dome; b ~3.42 Ga, Strelley Formation, Kelly belt’; c ~2.75 Ga, Fortescue Group, Eastern Pilbara; d A ~2.63 Ga, A giant stromatolite, Carawine Dolomite, Carawine Pool, DeGrey River. Photographs by the author

mental effects, such as the disruptive effects of currents, exposure to the atmosphere at low tide and protection from predator cells. In the case of the photothropic55 stromatolites, constituting bioherm assemblages of Eukaryote cells, the formation of colonial reef allows adjustment of the colony to tidal fluctuations. This ensures parts of the colony persist under shallow water thus avoiding desiccation of the upper parts of the bioherm exposed to the atmosphere. The development of colonies consisting of specialized cells signifies emergence of inter-cellular communications and coordination, implying each cell possess information regarding what the other cells are doing—a quantum leap toward evolution of complex multi-task organisms. Such intercellular synergy56 represents a step beyond the coordinated interactions among the genes and the genome57 or the intra-cellular relations between organelles. The principle of self-Organized Criticality58 was firstly introduced on statistical basis by Bak et al. (1987), where a simple cellular automaton was shown to produce several characteristic features observed in natural complexity 55 An

organism obtaining energy from sunlight to synthesize organic compounds for nutrition. The creation of a whole that is greater than the simple sum of its parts. 57 A genome is an organism’s complete set of DNA, including all of its genes. Each genome contains all of the information needed to build and maintain that organism. In humans, a copy of the entire genome—more than 3 billion DNA base pairs—is contained in all cells that have a nucleus. 58 Self-organized criticality, Wikipedia. https://en.wikipedia.org/wiki/Self-organized_criticality. 56 Synergy:

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generated as an emergent feature of extended systems with simple local interactions. These authors demonstrate numerically that dynamical systems with extended spatial degrees of freedom naturally evolve into self-organized critical structures of states which are barely stable and that this self-organized criticality is the common under-lying mechanism for natural phenomena. According to Corning (1995) synergy explains the biological evolution of complexity with time, where synergetic effects drive cooperative relationships in living systems, providing functional advantages for natural selection in terms of survival and reproduction. Mathematical modelling of biological processes, utilizing a new generation of non-linear dynamical systems models, gives rise to a hypothesis where spontaneous autocatalytic processes may be responsible for much of the order found in nature. According to this model naturally emerging natural laws of organization are responsible for driving evolutionary processes and truncating the role of natural selection. Studies of fractals59 by Mandelbrot (1982) related complexity and repetitiveness in nature to mathematical laws. However, the specialization of intra-cellular entities, including genes, nucleus, nucleolus, vacuoles, mitochondrion, ribosomes and other organelles, does not appear to be resolved by the mathematical model of fractals. Prokaryotes60 —unicellular organisms that lack a membrane-bound nucleus, mitochondria61 or any other membrane-bound organelle—have a single chromosome, a circular, double-stranded DNA chain located in an area of the cell called the nucleoid. Prokaryotes are divided into two domains, Archaea and Bacteria. There exists an uncertainty regarding whether life appeared on Earth prior to, or after, the termination of the late heavy bombardment (LHB) about 3.85 Ga, with an increased ratio of 12 C to 13 C, indicating photosynthesis (Schidlowski 1988), and stromatolite fossils (Nutman et al. 2016, Fig. 3.13; Dunlop 2015, Fig. 3.14a) both pointing to the onset of life a time prior to 3.7 Ga. Several stages can be recognized regarding levels of oxygen in the atmosphere: Stage 1 (3.85–2.45 Ga): Practically no O2 in the atmosphere. Stage 2 (2.45–1.85 Ga): O2 produced, but absorbed in oceans and seabed rock. Stage 3 (1.85–0.85 Ga): O2 starts to gas out of the oceans, but is absorbed by land surfaces and formation of ozone layer. Stages 4 and 5 (0.85 Ga–present): O2 sinks filled, the gas accumulates. The oldest hints of life known to date are ~3.7 Ga-old 13 C isotopic carbon signatures in sediments of the Isua greenstone belt in southwestern Greenland (Schidlowski 59 A

fractal is a never-ending pattern. Fractals are infinitely complex patterns that are self-similar across different scales. They are created by repeating a simple process over and over in an ongoing feedback loop. 60 Prokaryotic cells. https://www.khanacademy.org/science/biology/structure-of-a-cell/ prokaryotic-and-eukaryotic-cells/a/prokaryotic-cells. 61 Mitochondria are organelles that are virtually cells within a cell. The most prominent roles of mitochondria are to produce the energy currency of the cell, ATP (i.e., phosphorylation of ADP), through respiration, and to regulate cellular metabolism.

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et al. 1979; Rosing 1999). Stromatolites, sedimentary structures produced by the sediment trapping, binding, and precipitating activity of phototrophic microbes, can be traced back 3.7 billion years (Nutman et al. 2016). These phototrophic microbes include cyanobacteria/blue-green algae. The marine stromatolite communities occur mostly in hypersaline subtidal to supertidal settings (Awramik and Sprinkle 1999). Nonmairine stromatolites have been found in streams, lakes, thermal springs, and even frozen lakes. Recently, stromatolites, the oldest known colonial life forms, were identified in south west Greenland. Nutman et al. (2016) reported 1–4-cmhigh stromatolites62 in 3700-Myr-old meta-carbonate rocks in this greenstone belt (Fig. 3.13). The stromatolites grew in a shallow marine environment, indicated by seawater-like rare-earth element plus yttrium trace element signatures of the metacarbonates, including interlayered detrital sedimentary rocks with cross-lamination and storm-wave generated breccia. Prior to this discovery the oldest known were 3.48 Ga (Buick et al. 1980) (Fig. 3.14a) and 3.46 Ga stromatolites (Allwood et al. 2007) (Fig. 3.14b) the Pilbara Craton, Western Australia. Phototrophic oxygen-releasing cyanobacteria prokaryotes lacking a nucleus and other membrane bound cell organelles form microbial mats and stromatolite colonies forming domal structures and located mostly in hypersaline subtidal to super-tidal settings. The mats are produced by the sediment trapping, binding, and precipitating activity subsequently cemented by carbonate precipitation (Awramik and Sprinkle 1999), indicating an origin of photosynthesis63 processes as early as 3.70 Ga (Nutman et al. 2016). Colonial green algae consist of balls in which hundreds of thousands of cells are embedded in a gelatinous matrix. Photosynthesizing bacteria are mobile and capable of motion toward light, with consequent development of domal structures through precipitation of calcium carbonate. The rise in atmospheric oxygen from the Archaean to the Proterozoic led to increased diversification of stromatolites to 176 known species and in the upper Proterozoic to 340 species in the middle Riphean ~1100 Ma-ago, a period when Eukaryotes proliferated as well. From that stage stromatolites became less common, a decline attributed to an increase in grazing metazoans,64 multicellular animals, and sediment disturbance by metazoans, with further decline during the Ordovician parallel to the rise in eukaryotes. The observation of stromatolite-like forms in chert-carbonate-barite sequence of the ~3.49 Ga Dresser Formation, North Pole dome, central Pilbara Craton (Dunlop 2015; Buick et al. 1980) gave rise to a major controversy regarding the biogenic origin of these structures. Noffke et al. (2006) documented microbially induced sedimentary structures from the Dresser Formation and interpreted the relations between micro62 Layered mounds, columns, and sheet-like sedimentary rocks. They were originally formed by the growth of layer upon layer of cyanobacteria, a single-celled photosynthesizing microbe that lives today in a wide range of environments ranging from the shallow shelf to lakes, rivers, and even soils. 63 Process by which plants and bacteria use energy from sunlight to produce glucose from carbon dioxide and water, releasing oxygen in the process. 64 Any group of animals with a body composed of cells differentiated into tissues and organs and usually a digestive cavity lined w The growth or movement of a fixed organism, especially a plant, toward or away from sunlight. ith specialized cells.

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bial mats and the physical sedimentary environment. Detailed mapping on the scale of meter to millimeter indicates five sub-environments typical of coastal sabkha which contain distinct macroscopic and microscopic associations of microbially- induced sedimentary structures. Outcrop-scale microbial mats include polygonal oscillation cracks and gas domes, erosional remnants and pockets, and mat chips. Microscopic microbial laminae comprise tufts, sinoidal structures, and lamina fabrics and consist of primary carbonaceous matter, pyrite, and hematite, plus trapped grains. Greater confidence exists regarding the nature of ~3.43 Ga Strelley Pool Chert (Lowe 1983). Despite reservations (Brasier 2006) the heliotropic65 reef-forming structure of the microbialites supports a biological origin (Hofmann et al. 1999; Van Kranendonk et al. 2003). Allwood et al. (2007) documented evidence for palaeoenvironmental extensive stromatolite-like reefs, including seven stromatolite morphotypes in different parts of a peritidal carbonate platform. The diversity, complexity and environmental associations of the stromatolites display marked analogies to similar stromatolite reef settings in younger geological systems. Late Archaean ~2.73 Ga stromatolites, containing inter-bioherm debris are widespread in the Fortescue Basin, Pilbara Craton, reaching dimensions of tens of meters and yet younger ~2. 63 Ga stromatolites have flourished in the central and East Fortescue Basin, displaying similarities with modern Shark Bay stromatolites. Some of the oldest possible micro-fossils occur in black chert of the Dresser Formation, (Duck et al. 2007; Golding and Glikson 2011) and in brecciated chert of the ~3465 Ma Apex Basalt, Warrawoona Group, Pilbara Craton (Schopf 2007). The paleo-environment, carbonaceous composition, mode of preservation, and morphology of these microbe-like filaments, backed by new evidence of their cellular structure provided by two- and three-dimensional Raman imagery, support a biogenic interpretation. Evidence for hydrothermal and methanogenic microbial activity (Schopf and Packer 1987; Schopf 2007; Hofmann et al. 1999; Duck et al. 2007) and intermittent appearance of shallow water stromatolites in ~3.49 Ga sediments (Buick et al. 1980) and ~3.42 Ga sediments (Allwood et al. 2007) (Fig. 3.14b) testify to a diverse microbial habitat. This included heliotropic and by implication photosynthesizing stromatolites effecting release of oxygen. Problems in identifying early Archaean stromatolites were expressed by Lowe (1994) and by Brasier (2006). Some of the earliest manifestations of biological activity may be represented by banded iron formations (BIF) from the ~3.7 Ga Isua supracrustal belt (southwest Greenland). Banded iron formations are commonly intercalated with volcanic tuff and carbonaceous shale whose low δ13 C indices are indicative of biological activity. The carbon isotopic compositions of Archaean black shale, chert and BIF provide vital clues to the proliferation of autotrophs66 in the shallow and deep marine environment. Peak biogenic productive periods about 2.7–2.6 Ga are represented by low δ13 C of chert and black shale intercalated with banded iron formations in the Superior Province, Canada (Goodwin et al. 1976 ), and in the Hamersley Basin, Western 65 The

growth or movement of a fixed organism toward or away from sunlight. autotroph is an organism that can produce its own food using light, water, carbon dioxide, or other chemicals. 66 An

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Australia (Eigenbrode and Freeman 2006). This peak, which coincides with intense volcanic activity in greenstone belts world-wide, suggests enhanced biological activity related to volcanic emanations and enriched nutrient supply. The enhancement of biological processes include oxygen-releasing photosynthesizing colonial prokaryotes (stromatolites) and algae, oxygen capture by iron-oxidizing microbes, microbial methanogenesis67 producing atmospheric CH4 , microbial sulphur metabolism producing H2 S, ammonia-releasing microbes, culminating in production of O2 -rich atmosphere and the O3 ozone layer. Earliest manifestations of biological forcing may be represented by banded iron formations, widely held to represent ferrous to ferric iron oxidation by microbial reactions (Cloud 1968, 1973; Morris 1993; Konhauser et al. 2002; Glikson and Hickman 2014). The origin of BIFs has been interpreted in terms of transportation of ferrous iron in ocean water under oxygen-poor atmospheric and hydrospheric conditions of the Archaean (Cloud 1968; Morris 1993). Oxidation of ferrous to ferric iron could occur through chemotrophic or phototrophic bacterial processes (Konhauser et al. 2002) and/or by UV-triggered photo-chemical reactions. The near-disappearance of banded iron formations (BIF) about ~2.4 Ga, with transient re-appearance about 1.85 Ga and in the Vendian (650–543 Ma), likely reflect increase in oxidation, where ferrous iron became unstable in water and the deposition of BIF was replaced by that of detrital hematite and goethite. Archaean impact ejecta units in the Pilbara and Kaapvaal Cratons are commonly overlain by ferruginous shale and BIF (Glikson 2006; Glikson and Vickers 2007), hinting at potential relations between Archaean impact clusters, impact-injected sulfate, consequent ozone depletion, enhanced UV radiation and formation of BIFs (Glikson 2010), possibly by photolysis through the reaction: 2H2 O < > 2H+ + 2e− + O2 followed by 2FeO + O < > Fe2 O3 . A study of 3.47–3.30 Ga carbonaceous chert layers and veins in the Onverwacht Group of the Barberton Greenstone Belt suggests an origin of the bulk of the carbonaceous matter in the chert by biogenic processes, accompanied by modification through hydrothermal alteration (Walsh and Lowe 1985; Walsh 1992). The above studies identified textural evidence in cherts for microbial activity represented by carbonaceous laminations in intercalations within the Hoogenoeg and Kromberg Formations, with affinity to modern mat-dwelling cyanobacteria68 or bacteria. These include a range of spheroidal and ellipsoidal structures analogous to modern coccoidal bacteria and bacterial structures, including spores. The Pilbara Craton in Western Australia contains evidence of >3.0 Ga microfossils, trace fossils, stromatolites, biofilms, microbial and microscopic sulfide minerals with distinctive biogenic sulphur isotope signatures (Wacey 2012). Schopf and Packer (1987) identified 11 taxa, including eight new species of cellularly preserved filamentous Prokaryote microbes in a shallow chert sheet of the ~3.459 Ga Apex Basalt. This assemblage indicates morphologically diverse extant trichomic cyanobacterium-like microorganisms, suggesting presence of oxygen-producing photoautotrophs. However, a possibility remains these microbes represent contamination by ground water. 67 The 68 A

production of methane by bacteria or other living organisms. phylum of bacteria that obtain their energy through photosynthesis.

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Studies of microbial remains from the ~3.49 Ga Dresser Formation, North Pole Dome, central Pilbara Craton (Glikson et al. 2008) and of filamentous microbial remains and carbonaceous matter (CM) from Archaean black cherts (Duck et al. 2007) have used the following methods: (1) organic petrology; (2) Transmission Electron Microscopy (TEM); (3) Electron Dispersive Spectral Analysis (EDS); (4) high resolution TEM (HRTEM); (5) elemental and carbon isotope geochemistry studies (6) reflectance measurements determining thermal stress. The analyses resolve images of microbial relics and cell walls analogous to the modern hyperthermophilic Methano-caldococcus jannaschii residing in hydrothermal sea floor environments. Analogies include the wall structure and thermal degradation mode about 100 °C considered as the upper limit of life, whereas complete disintegration takes place at 132 °C. The δ13 C values of CM from the ~3.49 Ga Dresser Formation (−36.5 to − 32.1‰) show negative correlation with total organic carbon (TOC  0.13–0.75%) and positive correlation with Carbon/Nitrogen ratios (C/N  134–569). These values are interpreted in terms of oxidation and recycling of the CM and loss of light 12 C and N during thermal maturation. The TEM and carbon isotopic compositions are consistent with activity of chemosynthetic microbes in a seafloor hydrothermal system accompanied by rapid silicification at relatively low temperature. Transmission Electron Microscopy (TEM) studies of filamentous and tubular structured isotopically light (δ13 C −26.8 to −34.0‰ V-PDB) carbonaceous material associated with ~3.24 Ga epiclastic and silicified sediments overlying sulphide indicate close analogies with sea floor hydrothermal environments (Duck et al. 2007). The total organic carbon (