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- Herausgeber: John Wiley & Sons
- Kategorie: Wissenschaft und neue Technologien
- Sprache: Englisch
Origin of Life studies have a nearly-impossible goal: understanding nature through the comprehension of its origins and its complexities. As a growing field with poorly-defined borders, Origin of Life studies profit from progress in other disciplines. This book proposes both an overview of this large area and an in-depth look at the opinions and results obtained by some of the active contributors of this fascinating and deeply thought-provoking matter. The topics are presented in a bottom-up order, first touching on the habitability of the universe, then the rationale behind meaningful prebiotic chemistry, the possible or probable prebiotic chemical frames, the problem of chirality, and moving on through the role of minerals in biogenesis, biogenic fertile environments, the in-and-out problem as solved by vesicles physics, the evolution of the codes, the structure of LUCA and its proto metabolisms and the meaning of complex extant biological biomorphs, as exemplified by viroids. These topics and the reasoning within the chapters are provided against the backdrop of the evolution of information and complexity.
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Veröffentlichungsjahr: 2023
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Table of Contents
Cover
Table of Contents
Title Page
Copyright Page
Introduction
1 The Emergence of Life-Nurturing Conditions in the Universe
1.1. Defining properties of life
1.2. Life-supporting conditions and environments
1.3. Setting the stage for chemistry and life in the Universe
1.4. The habitable Universe
1.5. Planetary environments suitable for the origin of life
1.6. The quest for inhabited worlds
1.7. References
2 Chirality and the Origins of Life
2.1. Introduction to chirality
2.2. The asymmetry of life
2.3. The origin of homochirality
2.4. Space missions and the search for life and its origins
2.5. References
3 The Role of Formamide in Prebiotic Chemistry
3.1. Introduction
3.2. Effect of minerals and self-organization in the prebiotic chemistry of formamide
3.3. Continuity and mineral complexity
3.4. Energy-driven selectivity
3.5. References
4 A Praise of Imperfection: Emergence and Evolution of Metabolism
4.1. From Darwin to Jacob: perfection does not exist
4.2. Protometabolic networks
4.3. Enzyme promiscuity and metabolic innovation
4.4. Promiscuity, moonlighting and the essence of life
4.5. Acknowledgments
4.6. References
5 Viruses, Viroids and the Origins of Life
5.1. How were viruses discovered? A brief history
5.2. Viral diversity
5.3. Viral structure and function
5.4. Viruses and mammalian genomes
5.5. Role of viruses in human evolution, health and disease
5.6. Viroids may be a link to ancient evolutionary pathways
5.7. Origin and evolution of viroids
5.8. Conclusion
5.9. References
6 Is the Heterotrophic Theory of the Origin of Life Still Valid?
6.1. Introduction
6.2. The roaring 20s
6.3. Coacervates as models of precellular structures
6.4. Precellular evolution and the emergence of cells
6.5. Final remarks: does Oparin still matter?
6.6. Acknowledgments
6.7. References
7 Making Biochemistry-Free (Generalized) Life in a Test Tube
7.1. Summary
7.2. Introduction and background
7.3. Laboratory implementation of an artificial autonomous, and self-organized functional system
7.4. More physics and chemistry working together: phoenix, self-reproduction via spores, population growth and chemotaxis
7.5. Discussion and conclusions
7.6. Acknowledgments
7.7. Appendices: Some additional emergent features in PISA “powered” synthetic biochemistry free protocells
7.8. References
8 Hydrothermalism for the Chemical Evolution Toward the Simplest Life-Like System on the Hadean Earth
8.1. Introduction
8.2. Hydrothermal environment for the chemical evolution of biomolecules
8.3. Hydrothermal methodologies regarding the origin-of-life study
8.4. RNA world versus hydrothermalism
8.5. Future outlook and conclusions
8.6. Acknowledgments
8.7. References
9 Studies in Mineral-Assisted Protometabolisms
9.1. Metabolism, protometabolism and minerals
9.2. Adsorption on mineral surfaces
9.3. Mineral surfaces and reaction thermodynamics
9.4. Minerals and reaction kinetics: heterogeneous catalysis
9.5. A case study: primordial synthesis of pyrimidines
9.6. Conclusion
9.7. References
10 A Rationale for the Evolution of the Genetic Code in Relation to the Stability of RNA and Protein Structures
10.1. Introduction
10.2. Codon–anticodon recognition
10.3. Concluding remarks
10.4. Acknowledgments
10.5. References
List of Authors
Index
End User License Agreement
List of Tables
Chapter 8
Table 8.1. Different types of flow reactor systems for hydrothermal ...
List of Illustrations
Chapter 1
Figure 1.1. Scheme of the relationship between a living organism and its surroun...
Chapter 2
Figure 2.1. Simplified visualization of the two mirror configurations or enantio...
Figure 2.2. Fischer projection of the enantiomers of the four-carbon sugars: ery...
Figure 2.3. Single frame Rosetta navigation camera image of 67P/Churyumov-Gerasi...
Figure 2.4. Artistic view of the Rosalind Franklin rover on Mars, with the folda...
Figure 2.5. Visualization of an archaeal phospholipid (left) and chlorophyll a (...
Chapter 3
Figure 3.1. Circularity in the prebiotic chemistry of NH2CHO
Figure 3.2. NH2CHO is easily produced from a variety of planetary and space cond...
Figure 3.3. Regioselective and stereoselective synthesis of adenosine from NH2CH...
Figure 3.4. Multi-way regioselective synthesis of amino acid decorated imidazole...
Chapter 5
Figure 5.1. Images of viral diversity.
Figure 5.2. Infection of a bacterial cell by a bacteriophage followed by lysis. ...
Figure 5.3. Diagram of the SARS coronavirus reproduction. The protein capsid is ...
Figure 5.4. Structure of a viroid compared to a viral particle. Viroids are the ...
Figure 5.5. RNA rings can be visualized by atomic force microscopy. The rings fo...
Chapter 7
Figure 7.1. Light mediated polymerization-induced self-assembly.
Figure 7.2. Synthetic autopoiesis: going autonomously from a homogeneous chemica...
Figure 7.3. Time lapse of the phoenix behavior of the polymersomes.
Figure 7.4. (a) With each successive cycle the maximum size of the polymersome d...
Figure 7.5. Schematic representation of a “phoenix” cycle.
Figure 7.6. The noisy blue curve shows the change in the type and number of the ...
Figure 7.7. This idealized and abstract depiction of the cell division cycle for...
Figure 7.8. (a) Trace of the movement of a group of vesicles displaying chemotax...
Figure 7.9. (a) Oscillation profile of the B-Z reaction during amphiphile polyme...
Figure 7.10. SEM (scanning electron microscopy) images of vesicles showing their...
Chapter 8
Figure 8.1. Information flow in modern organism and RNA-based life-like system ...
Figure 8.2. Phase diagram of water.
Figure 8.3. Chemical properties regarding materials to exist as liquid. Left, Pc...
Figure 8.4. Mechanistic diagrams for the two-gene hypothesis. Left, connection b...
Figure 8.5. Mineral surface provides a chemical environment for integrating func...
Figure 8.6. Role of hydrothermal vent system in deep ocean on primitive Earth. ...
Figure 8.7. Chemical evolution of life-like system is dependent of the character...
Figure 8.8. Accumulation of oligonucleotides in an RNA-based life-like system is...
Figure 8.9. General schematic diagram of hydrothermal flow systems including an ...
Figure 8.10. Spectrophotometric detector device with the mineral packed reactor ...
Figure 8.11. Stability of oligonucleotides, dinucleotides, nucleotides, nucleoti...
Figure 8.12. Primitive RNA formation models that were mainly examined under mild...
Figure 8.13. Phosphodiester bond formation between oligonucleotide and monomer o...
Figure 8.14. A possible trajectory between the chemical evolution and the decrea...
Figure 8.15. Future approach for hydrothermalism on the origin-of-life study
Chapter 9
Figure 9.1. Percentage of glycine dimerized at equilibrium as a function of tota...
Figure 9.2. Illustrating de Duve’s paradox for the case of glycine polymerizatio...
Figure 9.3. Illustrating the alternation of dry and wet conditions in WD cycles....
Figure 9.4. The first steps in de novo pyrimidines synthesis through the orotate...
Chapter 10
Figure 10.1.
Guide
Cover Page
Table of Contents
Title Page
Copyright Page
Begin Reading
List of Authors
Index
WILEY END USER LICENSE AGREEMENT
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SCIENCES
Biology, Field Director – Marie-Christine Maurel
Xenobiology, Exobiology, Astrobiology, Origins of Life, Subject Heads – Marie-Christine Maurel and Marc Ollivier
The First Steps of Life
Coordinated by
Ernesto Di Mauro
First published 2024 in Great Britain and the United States by ISTE Ltd and John Wiley & Sons, Inc.
Apart from any fair dealing for the purposes of research or private study, or criticism or review, as permitted under the Copyright, Designs and Patents Act 1988, this publication may only be reproduced, stored or transmitted, in any form or by any means, with the prior permission in writing of the publishers, or in the case of reprographic reproduction in accordance with the terms and licenses issued by the CLA. Enquiries concerning reproduction outside these terms should be sent to the publishers at the undermentioned address:
ISTE Ltd27-37 St George’s RoadLondon SW19 4EUUK
www.iste.co.uk
John Wiley & Sons, Inc.111 River StreetHoboken, NJ 07030USA
www.wiley.com
© ISTE Ltd 2024The rights of Ernesto Di Mauro to be identified as the author of this work have been asserted by him in accordance with the Copyright, Designs and Patents Act 1988.
Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s), contributor(s) or editor(s) and do not necessarily reflect the views of ISTE Group.
Library of Congress Control Number: 2023942095
British Library Cataloguing-in-PublicationData A CIP record for this book is available from the British LibraryISBN 978-1-78945-165-8
ERC code:LS8 Ecology, Evolution and Environmental Biology LS8_5 Evolutionary genetics
Introduction
Ernesto DI MAURO
Institute of Molecular Biology and Pathology, CNR, Rome, Italy
Origin of life studies are an active field whose borders are poorly defined. It allows us to approach the problem with intellectual freedom, out of the limitations imposed by sclerotized disciplines. This book proposes fly-over of this large territory and an in-depth eagle-eyed look of the opinions and the results obtained by some among the active contributors of this fascinating and deeply thought-provoking matter. The topics are presented as usual according to a bottom-up order: the habitability of the Universe, the rationale behind meaningful prebiotic chemistry, the possible and the probable prebiotic chemical frames, the problem of chirality, the role of minerals in biogenesis, the biogenic fertile environments, the in-and-out problem as solved by vesicles physics, the way of the codes, LUCA and protometabolisms, the meaning of complex biological biomorphs (read: viroids). The evolution of information and complexity is the background scenario, which accompanies all of this reasoning.
A single standard-sized book provides a limited space, and in this context 10 chapters are a meagre body. Potential, appropriate and relevant contributors could have been and could be many more. Hence, the effort by each of the authors to widen the field of their descriptions, trying to amend the complexity of this dynamic and multifaceted science.
Connecting cosmology with molecular biology may seem arrogant, but it is not so. The length of the road is the precise indication that we are confronted with an enormous problem that can only be addressed with humility. The daring endeavor is to try to unify under the same perspective topics and discoveries made in very different fields, often told in languages which sometimes are difficult to reconcile. The reader will, in the end, realize that a solid synthesis is for the moment lacking but that, at the same time, the thread connecting the Big Bang to our existence is beginning to become traceable.
Another important message conveyed by the pages of this book is that the approach to the origin of life should be as devoid as possible of anthropocentry. The Universe does not really care for the fact that the leaves will fall from the tree of my garden at due time and “I” will die. But, at the same time, the Universe takes into consideration that life exists, that life is one of its epiphanies. Here, on this planet and as far as we know, life is a continuous uninterrupted and internally interconnected process. Life is a category of phenomena that can be interpreted only if we look at it with the necessary aloofness.
In order to emerge, life requires stability, simplicity and reactivity. It also entails complexity. The recognition of the necessity of these properties is necessarily accompanied by a series of question marks.
Stability
“Something came from nothing because it was more stable than nothing” (Stenger 2006). The uncontroversial truth contained in this aphorism by Victor Stenger applies to the evolution of the organization of matter in the whole Universe which, for what concerns us here, comes out from the Big Bang. In particular, and even more so, this concept applies also to life. A telling example is provided by polymers which, most of the time, are a stabilization form of the monomers that compose it.
As a side product of this forced and directed tendence to stability, internally repetitive structures are produced, which are thus able to elaborate information. They do so by introducing and selecting small variations. This process, in biological terms, is dubbed evolution. Is this an intrinsic property of polymers? It is so only for some of them, and if so which ones? Only for those which undergo repeated cycles of synthesis/degradation? Variations usually and typically occur within the same class of molecules: one amino acid to another amino acid in a peptide chain, and one nucleic base to another nucleic base in RNA or DNA. Evolution is the evolution of information.
A short-term sort of variation is that occurring in the so-called metabolic cycles. Remaining in textbook examples and in a central gear of the machinery (the Krebs cycle), a compound, say citrate, “changes” under the effect of the environment and becomes cis-aconitate, which becomes D-isocitrate, which becomes alfa-ketoglutarate, then succinyl-CoA, and succinatate, fumarate, L-malate, oxaloacetate, which again becomes citrate. But in the meantime, mediated by the interaction with the environment and with ancillary molecules, something “vital” has occurred and, depending on the direction of rotation of the cycle, the transfer of energy or carbon has orderly entered the system. The prebiotic valence, the determination of the whereabouts of these cycles and the possibility of their reconstruction are becoming experimented reality (Muchowska et al. 2019; Isnard and Moran 2020; Preiner et al. 2020; Yadav et al. 2022).
A long-standing debate has dominated the scene of origin of life studies: “genetics-first” or “metabolism-first”? Occasionally, also “membranes-first” accompanied the bias. The answers to these initially reasonable questions found their well-grounded advocates, but it gradually became clear that no real distinction was possible, and that without a system to harness and control energy (a system that is one of the incarnations of the concept of “phenotype”), no replication and transmission of the genotype might have been possible. With no genotype, the phenotype would have succumbed to the laws of disorder and the domination by local conditions. Hence, the necessity of the simultaneous, concurrent and cooperative evolution of both phenotype and genotype, of both nucleic acids and proteins, and of carboxylic acids, all contained in membrane-defined spaces where concentrations and selections could take place. The prebiotic chemistry involved was thus necessarily large-spectrum, and no solitary, selective and fastidious synthesis would have been likely to win the race.
The history of the evolution of the interaction of the RNA world with the protein world goes through appealing and elegantly solved chapters. The structure of the huge ribosome machinery, as determined by the 2009 Nobel Laureates Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath, still conserves in its central RNA core the signs of its initial function of peptide-bond maker. The story of the evolution of ribosomes (Yonath 2010; Belousoff et al. 2010; Petrov et al. 2014; Bose et al. 2022) shows how proteins structurally and functionally gradually replaced RNAs. The extant universal presence of protein enzymes has the same evolutionary history consisting of substitution of the functions initially performed by RNA catalysts. Omnipresent ribo cofactors as NAD are there to remind us. A big part of this story is still unknown. The possibilities of proteins of acquiring independence from nucleic codes are well summarized in Foden et al. (2020) (see also Muchowska and Moran 2020).
I have written above the word “information”. Nothing can be more dangerous. The word information is multisemic, like “richness”, “democracy” or “beauty”. Its meaning depends on the reader and on the context. It does not help much by saying that “information is energy”, nor by saying that information theory is a highly developed science, starting from George Boole going all the way to AI. And it does not help quoting in passing that Claude Shannon obtained his PhD in Cold Spring Harbor Laboratory, the temple of American molecular biology, with a thesis on “An algebra for theoretical genetics”.
In this Universe, everything is information. If our goal is to define life and to find the borders between the living and the nonliving, we need to mitigate this conundrum by focusing on a selected part of the problem. The information of the extant organisms on this planet encompasses, for instance, epigenetics and topology, which are emergent properties embedded in the linear information of our founding polymers. Epigenetics greedily multiplies genetic information and inscribes on DNA the history it goes through; supercoiling (a typically topological property) is a way to multiply and modulate information to regulate and direct genetic expression and replication; some molecules can handle it, some cannot. Are epigenetics and topology only part of thermodynamics, or are they elaborate and highly evolved properties of living entities? The answer by the layman scientist is as follows: both are emergent properties of living entities. Hence, life entails superposition of information levels, which is one of the keys of the evolutionary process.
The question, “how much in life can be considered an emergent property?” is thus justified. If we are trying to retrace the first steps of life, we need to have this question clear in mind.
Keeping the conservative approach of considering life only the ensemble of the structures and interactions of those phenomena that we know based on our terrestrial experience, the classes of molecules that are interesting for us here are the ones that we have under the eyes: DNA, RNA, proteins, carboxylic acids and aliphatic chains. These molecules are each endowed with their own characteristic properties and, at the same time, are functionally interconnnected. Their mutual connections give rise to cycles, conceived in that form of living topology that owns much to Eörs Szathmary (2000). In this perspective, life is the interplay of multiple cycles, whose wheels turn according to the information sedimented by their history and by the environments they have gone through. The rhizome of life is a web of cycles, as intuited by Deleuze and Guattari (1980). Life is a unitary phenomenon, a property which usually escapes our attention. But life is also multiform, and the interest for its particulars often makes us forget the overview.
According to Deleuze and Guattari, a rhizome follows the principles:
1 and 2:
Principles of connection and heterogeneity: every point of a rhizome can be connected to every other and must be.
3:
Principle of multiplicity: only when the multiple is effectively treated as a noun, “multiplicity”, then it ceases to have any relationship with the one.
4:
Principle of no-significant breaking: a rhizome can be interrupted, but it will start again on one of its old lines or on new lines.
5 and 6:
Principles of cartography and decalcomania: a rhizome cannot be traced back to any structural or generative model; it is a map and not a track.
The evocative power of these principles, expressed in a somewhat heterodox way, is interesting. According to these metaphors, the world of the living is a totally connected network in which every single organism is the incarnation of a specific genotype that begins its life at a given moment, determined by the replication/recombination of its parental genetic materials, and ends at the moment of the dissolution of its own specific genome. Each genotype is online with the genotypes from which it derives and with those that could derive from it, it is informationally connected with them. The living network is a unity embedded in space-time and in the genetic space extending, with possible multiple roots, back to the Last Universal Common Ancestor. Before which, by definition, there were only entities immersed in the swamp of combinatorial biochemistry, and only one survivor.
Our body is made up of nucleic bases, amino acids, carboxylic acids and aliphatic chains. The fact that certain classes of molecules (amino alcohols, for instance) do not organize themselves in cycles is particularly interesting and helps to point out the properties which allow other classes of molecules to be dubbed “biogenic”. Why? Because life is interaction among polymers, and the polymers interact according to their own structural and functional properties. The physical–chemical environment in which they occur determines who will stay and who will go, and decides whether their properties allow information to form and be transmitted.
Interaction among macromolecules establishes cycles. These cycles have no purpose but to maintain themselves: a mechanistic property, certainly not a finalistic one. No memory exists of the cycles that do not maintain themselves. It may seem that living entities, “we”, are those coded and transmitted cycles, apparent macro-cycles made of life and death. This is true only superficially and partially: death exists for each individual; it is an intrinsic property of each specific and individual cluster of metabolic cycles. But life has not been interrupted since its beginning, by definition. Life and death do not belong to the same category of phenomena.
Stability is the underlying property of all this. The borders of life are the borders of the stability of its constituents and the stability of the information that organizes them.
Simplicity
The materials life is made of are simple and chip in the market of this Universe. Given the time and energy, atoms combine and, as far as we know, their reactions follow the same rules all over the Universe, up until its poorly defined borders. Hydrogen, carbon and nitrogen combine in hydrogen cyanide (HCN). According to well-established observations of the inter- and circum-stellar space (Millar 2015), this compound is the most abundant molecule among those with three atoms that contain a carbon atom; three-atom molecules are already considered molecules with relevant initial level of information. Other different three-component molecules are possible, but they are there in lower amounts, or are not there at all.
HCN is very reactive. The most abundant three-atom molecule not containing carbon is water (H2O) (note that the fourth most abundant atom oxygen (O) has here entered the combinatorial game) (Millar 2015). Reaction of HCN with H2O affords NH2COH formamide. Formamide is thus one of the possible stabilization forms of the energy initially contained in HCN. Formamide is a highly versatile source of potentially biogenic compounds (Saladino et al. 2001, 2012a, 2012b) and provides an easy way to further levels of chemical complexity.
Parallel chemistries to that of formamide are, among many, those centered on HCN, formaldehyde CH2O, methanol CH3OH, ammonium formiate NH4+ HCOO− and, markedly, on formic acid HCOOH (Mohammadi et al. 2020). Their relevance to plausible prebiotic scenarios depends on the attention dedicated to particular parts of the scene (i.e. the chemistry of sugars, aliphatic compounds and proteins) and on the attention given to particular environments and sets of physical–chemical conditions. The formation of formamide from formic acid and ammonia, for instance, depends on the temperature (Kröcher et al. 2009); these 1C-atom compounds are easily interconverted.
As a matter of fact, formamide seems to be the most versatile and the most adaptive to a large variety of environments, especially the prebiotically plausible ones. In the Urey-Miller experiment, in addition to amino acids and formic acid (Miller 1953), formamide is produced in the boro-silicate glass container (Criado et al. 2021), as expected (Saitta and Saija 2014). The possibility of transformation of each of those compounds into another is facile; it depends, in the endless game of reactions occurring in the sky and on Earth, on where and when we are looking at. The relevant fact remains that our body is made up of H, C, N and O, which are the four most abundant elements.
HCN chemistry is very fertile. From the initial observations of the synthesis of adenine (Oró 1961), to more recent reports (Powner et al. 2009; Sutherland 2016; Sutherland 2017 and references therein), HCN has shown its prebiotic worth, both in the emergence of genetic polymers and proto-metabolism (Yadav et al. 2022).
I personally do not consider HCN chemistry as being alternative to formamide chemistry, nor do I see these two chemistries as mutually exclusive. It depends on the frame of reference in which one considers them. Ultimately, it depends on the prebiotic scenario in which the prebiotic pool formed. Darwin (1871) was, 150 years ago, the first to invoke a warm little pool as the shrine of all biochemistries, but he did not detail its composition, he just had no data for further elaboration of his intuition.
The fact that formamide seems to be the most versatile and the most adapt to a large variety of environments, works as a stabilizing agent of HCN upon its interaction with water, is liquid between 4°C and 210°C, reacts with all sorts of possible catalysts yielding large and complex mixtures of prebiotic compounds under all sorts of energy sources (Saladino et al. 2001, 2012a, 2012b) points to the possible universality of its function and to its presence in the imaginary Darwin pool. The versatility of formamide in accepting as catalyst every mineral tested, from the most common terrestrial oxides to a large variety of meteorites, extends the interest of the function of minerals in prebiotic chemistry. The pivotal role of boric acid (H3BO3) in the prebiotic chemistry of the pentose moiety was shown (Prieur 2001).
About a definition of life
This book does not have the presumption to describe life in all its relevant aspects. Nevertheless, we should at least have a precise idea of what we are talking about. To define life is very difficult, it can be very accurately described, but its formal definition is elusive. The starting point can only be the definition by Schrödinger (1992) who considered life as that which “avoids the decay into equilibrium”.
Edward Trifonov deduced the consensual definition of what life is: “life is reproduction with variations”. This definition does not establish what life is, but provides the consensual definition accepted by contemporary science. The definition was obtained by carrying out a comparative analysis of the 123 existing definitions of the word “life” (Trifonov 2011), starting from the consideration that certain words are more represented than others, thus possibly allowing us to reach a consensus. The structuralistic method employed consists of an initial grammatical analysis, followed by a grouping and by a frequency analysis.
Another good, although less stringently obtained, definition is: life is a self-sustained chemical system capable of undergoing Darwinian evolution (Joyce 1994). This definition has not met, since its 1994 formulation, with major objections, even if a formal analysis reveals some uncertainties. Life does not support itself, as it absorbs and processes energy from the outside; it is not a system, but rather a process; and defining a process not for what it is but for the fact that it can change (i.e. evolve: “Darwinian evolution”) is, in terms of logic, a weakness. Furthermore, we can imagine an environment in which there are no variations well (i.e. in which changes from an optimized status quo can only be harmful); or in which the variations are cyclical and very high frequency, or that they occur in a time scale that does not correspond in a commensurable way to the time scale of the living entities it hosts and supports. In such environments, evolution could not be a categorical property.
A definition worth quoting is that by Emile Cioran: “Life is the kitscht of matter, ..., it is rupture, heresy, derogation from the rules of matter” (Cioran 1960). This is not scientific reasoning, but it highlights by reductio ad absurdum an important aspect of the problem: life is not an emergent property of matter, life is well within its rules. How could we not appreciate these words? A perfect crystal, a diamond for example, does not depart from its elegant rules of symmetry, but it does not live. Life is complexity, an application of intricate and codified rules.
My preference goes to Trifonov’s because it clearly defines the consensus of what science at large thinks that life is. The other formulations aspire to be absolute definitions, but each one is only one among the other 122 alternatives.
Reactivity
For life to emerge, a balance between reactivity and stability is necessary. A clear example of the need for this balance is inside us: RNA. Our >4 billion nucleotides genome is made up of DNA, which is a very complex set of molecules. It has not arisen to its complexity magically and abruptly; it has been derived from the simpler, more reactive and more unstable cognate molecule RNA. Everywhere in the biological world both DNA and RNA are at present made by sets of enzymes codified in RNA or in DNA themselves, which are molecules more complex than their products. But this cannot have always been the case. At one point, the abiotic (life did not exist yet), nonenzymatic (enzymes did not yet exist), spontaneous generation of RNA had to occur. This can be retraced, even though not in detail, at least in principle.
Nonenzymatic polymerization of ribonucleotide monomers is observed when the precursors are activated as phosphorimidazolides or nucleotide triphosphates (as reviewed in Dorr et al. 2012), or are in the 2′, 3′ or 3′, 5′ cyclic form (Costanzo et al. 2009; Costanzo et al. 2021; Wunnava et al. 2021). Phosphorimidazolides and nucleotide triphosphates are not very likely to be abundant prebiotic compounds, due to the complexity of their synthesis and to their high reactivity and subsequent instability. Nevertheless, they have been very useful in the characterization of abiotic polymerization reactions. Nonenzymatic syntheses of RNA have a high-standing record of results, leading to the understanding of the properties of this molecule and its evolutionary capacities. Appropriate points of entry in the vast literature of this topic are mentioned in some previous studies (Mariani et al. 2018; Walton et al. 2019; Kristoffersen et al. 2022).
Focusing our attention to cyclic compounds, 3′, 5′ cyclic nucleotides possess sufficient stability to withstand the extreme conditions most likely present on the early Earth. 3′, 5′ cGMP, in particular, has unique aggregation properties which lead to the formation of oligonucleotide sequences (Costanzo et al. 2009, 2021; Šponer et al. 2021 and references therein), also in acidic (Wunnava et al. 2021) conditions. Nucleotides containing a phosphodiester linkage confined in a strained five-membered ring are stable in certain conditions and are unstable in others; they only require moderate activation energy for undergoing to ring-opening reaction and polymerization. The basic requirement for polymerization is the previous formation of an ordered structure, and these cyclic forms seem to be made on purpose for this. Cyclic CMP affords very short oligonucleotides (Costanzo et al. 2017). The cyclic forms of the other prebiotically potentially relevant nucleotides (especially so for 3′, 5′ cAMP) do so at a lower extent.
The resulting macromolecular RNA is the product of the perfect compromise between stability and reactivity of its precursors. These precursors have the right structure to order themselves (Chwang and Sundaralingam 1974), and the resulting polymer has an effective capacity to establish a balance order/disorder depending on the environment.
The RNA polymer is a trade-off between stability and reactivity. Its O in 2′ is there to allow recombination and sequence evolution, but it is also there to determine a half-life and the hydrolytic susceptibility that puts the molecule at the mercy of the environment. Hence, evolution of RNA sequences by internal and external recombination, hence the evolutionary loss of the 2′ O resulting in the appearance of stabilized genomes made up of (2′-deoxy) DNA.
The stability principle applies well to the polymers we know. Why DNA? Because it is stable. A recent example of stability in which genetic information is inscribed: in the ancient palace built by King Herod the Great in the first century BC date seeds were found. Sarah Sallon at the Louis L. Borick Natural Medicine Research Center in Jerusalem and her colleagues succeeded in growing seven date palm trees (Phoenix dactylifera) from them (Sallon et al. 2020). This would not have been possible if the genetic material was RNA.
The reactive properties of RNA are at the basis of its power to give rise to complex sequence (Guerrier-Takada et al. 1983; Zaug et al. 1983; Cech 1987; Zaug and Cech 1996), as discovered in the ground-breaking observations by Altman and Cech. Interestingly, even simple-sequence spontaneously-generated short ribonucleotides have the property of recombination (Pino et al. 2013; Stadlbauer et al. 2015; Costanzo et al. 2021). We see this intrinsic ability in action in today’s ribozymes (Kaddour et al. 2021 and references therein), indicating potential connections with basic mechanisms at the origin of biogenic information. The reactive properties of RNA allow its nonenzymatic ligation (Usher and McHale 1976; Pino et al. 2008, 2011) and the formation of not-templated complex structures (Wu et al. 2022).
Careful examination of the living systems teaches us that all is relative, even the concepts and the systems that at first sight seem to be a one-way road, as the genetic code was long considered. Thus, the questions must always be asked: “why and how?”. Why and how do we have these codes for the gears that keep the machine running? The answer is that, again, it is a matter of balance between combinatorial chance and thermodynamic necessity.
The genetic code: are alternative codes possible? Yes. A Letter to Nature by Hall (1979) was the first comment to discovered differences to the standard code. Now this seems to be an ascertained and wide-spread reality (Shulgina and Eddy 2022). The code is not universal and unique, alternatives are possible. In the game between chance and necessity, happenstances and their history have an important role. Now we know that the winning code could have been different. And we know that we are here the way we are for both chance and necessity.
It is proposed, and largely agreed upon, that the amino acids composing extant proteins were not 20 since the very beginning (Jukes 1963; Crick 1966, 1968; Trifonov 2000, 2001; Travers 2006). The initial protein world was simpler and initially made of a first generation of amino acids, namely, glycine, alanine, proline and arginine (Travers 2022). The codons of these four amino acids are as follows:
glycine, GGU GGC GGA GGG;
alanine, GCU GCC GCA GCG;
proline, CCU CCC CCA CCG;
arginine: AGA AGG.
In these codons, the first two relevant letters are Gs or Cs. It is presumed that the third letter, the wobbling one, entered later, at the time of expansion of the code into its present form. The amino acids generated upon irradiation of formamide with a beam mimicking the solar wind are exactly glycine, arginine, proline and guanidine (which is a possible component of arginine) (Saladino et al. 2015); as for the amino acids as a class, little quantity is formed in these experimental conditions. It is also worth recalling what was mentioned above: that G-based nucleotides are the ones which oligomerize spontaneously and whose oligos perform terminal swapping with C-based oligos. Even though these reasonings about the origin of the code and these experimental observations are only mere correlations, the possibility that guanine chemistry and its properties played a role in the very beginning of the code is nevertheless suggestive.
The gear toward complexity
Life may be seen as the development of codes and their interactions. The properties of nucleic acids fill up the domains of chemistry, structure, topology and extend them to high refinement and variety. But nucleic acids cannot go beyond their intrinsic limits. The same is true for proteins, aliphatic chains and carboxylic acids. But if one class of molecules, say the nucleic acids, finds the way of programming and controlling the composition of another class of molecules, say of proteins, and learns how to guide them to specific actions, then the limits are bypassed and the properties of each class do not only add each other but, rather, multiply the possibilities. At that point, coevolution starts. We are today witnessing the extreme sophistication that these guided interactions and coevolution have reached. The classes of molecules other than nucleic acids and proteins cannot be considered only as ancillary actors of this evolutionary game, even though they depend on, use, exploit and allow the codes which control the core of the play.
The generation of the genetic code entails the programmation by nucleic acids of defined protein structures. These are made with a purpose whose outcome is worth coding and conserving. The purpose is to reproduce the code and in so doing to generate over again the cycles which orderly harness energy and regenerate themselves and the system.
What interests us here is the multiplication of possibilities, which is the first consequence of the intimate interaction of the coding and the coded. These possibilities are chemical, structural and topological. If we consider that the properties of nucleic acids are largely different from those of proteins, and that by the coding process nucleic acids master to their own purposes the properties of this other class of molecules, the multiplicatory power of this type of double gear becomes clear.
RNA polymerase has evolved in order to better transcribe what it has to transcribe, in the sites, the moment, the amount, the speed and the frequency it has to have. Other examples of the results of the extension-of-properties-through-the-codes fill the textbooks of molecular biology, acting both around the DNA core of the system and in its periphery.
Nucleic acids-to-proteins coding unifies different chemistries resulting, without any finalism, in life. The epigenetic and the neural codes, based on entirely different mechanisms, embody the possibility of connecting the behavior and the flow of life with the genetic code. The complexity of life relies on the coordination capacity of codes.
A long series of events goes from the origin of the universe and from the formation of atoms until us and until the other forms of life that we have not yet encountered. This is a field of study that has its own validity, not determined by what in biogenic space has come before nor from what will come later. The specific aspects of this series of events can be, and must be, studied independently, as single chapters. Attributing particular values to each of them, or to parts of each, considering them only in the perspective of their possible biogenicity would prevent us from evaluating them in their essence, and it risks being an operation, if not devoid of meaning, at least strongly distorted.
A summary, that every reader is anyhow invited to make, is still premature. In this perspective, it would have been appropriate to follow in the presentation of the arguments a top-down direction, not the bottom-up direction that is usually followed in prebiotic compilations, and that is the one that we respect also here. The reason is that no finalism is rationally conceivable, that the choices that have been made among the many possible ones in the domains of complexity can only by understood a posteriori.
The only suitable logic in order to understand these choices and to grasp what life is, is molecular Darwinism.
Time frames
A recent study (Steele et al. 2022) has detected and characterized the products of organic syntheses associated with serpentinization and carbonation on early Mars. The study was performed on the Martian meteorite Allan Hills 84001 (ALH84001) formed during the Noachian period, with an igneous crystallization age of ~4.09 billion years. Complex refractory organic material was found associated with mineral assemblages formed by mineral carbonation and serpentinization reactions. Serpentinization is the aqueous dissolution of olivines (Sleep et al. 2004). That is, the Noachian period (3.9–4.1 billion years ago) was characterized by water–rock interactions and abiotic organic syntheses on Mars. If the single meteorite analyzed for traces of organic syntheses has yielded positive results, the easy bet is that this is not a happenstance, that serpentinization-related organic syntheses were common.
Was planet Earth undergoing the same process of serpentinization and potentially biogenic organic syntheses in the same period? The fact that serpentinization was widespread during the first billion years of this planet is ascertained (as discussed in Garcia-Ruiz et al. 2000), and in fact it still goes on in places as the Cascade Range and the Rift Valley (Saladino et al. 2016). Prebiotic syntheses performed in serpentinization-related conditions, using formamide as precursor, yielded an extremely rich panel of potentially biogenic compounds, amino acids, nucleic bases, aliphatic chains and carboxylic acids included (Saladino et al. 2016, 2019). The implication is that prebiotic organic syntheses were global scale reactions in early planetary ages, both on Mars and, inferentially, Earth.
These results suggest that the conditions required for the synthesis of the molecular bricks from which life self-assembles, rather than being local and bizarre, seem to be universal and geologically conventional. They also lead to the conclusion that the reactions affording potentially biogenic precursors were limited to a first relatively short period. This period is difficult to define precisely but was probably limited on this planet to the first 200–300 million years. After that, the conditions changed and, where they could, complex coded interactions and pre-biology took over.
The other conclusion is that the time of chemistry and the time of biology are different. The time for prebiotic chemistry on this planet was short but sufficient. Chemical reactions are well defined: they are a box of strongly deterministic events that take place if the right conditions are there, they are fast and do not need much time. The time for biology is totally different matter: once started, it has no limits, its combinations are an open system, evolution can go on until the end of time, at its own local and specific pace. Its complex processes adapt, specialize, modify themselves according to the modifications of the environment, develop functional codes and change them when needed. Being different from chemistry, which is intrinsically limited and repetitive, life endlessly invents variants.
This book aims to explore the overlapped borders between the two categories of phenomena.
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1The Emergence of Life-Nurturing Conditions in the Universe
Juan VLADILO
INAF – Trieste Astronomical Observatory, Italy
