Evolution of the coenzymes

Theories of the origin of the genetic code: Strong corroboration for the coevolution theory

I analyzed all the theories and models of the origin of the genetic code, and over the years, I have considered the main suggestions that could explain this origin. The conclusion of this analysis is that the coevolution theory of the origin of the genetic code is the theory that best captures the majority of observations concerning the organization of the genetic code. In other words, the biosynthetic relationships between amino acids would have heavily influenced the origin of the organization of the genetic code, as supported by the coevolution theory. Instead, the presence in the genetic code of physicochemical properties of amino acids, which have also been linked to the physicochemical properties of anticodons or codons or bases by stereochemical and physicochemical theories, would simply be the result of natural selection. More explicitly, I maintain that these correlations between codons, anticodons or bases and amino acids are in fact the result not of a real correlation between amino acids and codons, for example, but are only the effect of the intervention of natural selection. Specifically, in the genetic code table we expect, for example, that the most similar codons - that is, those that differ by only one base - will have more similar physicochemical properties. Therefore, the 64 codons of the genetic code table ordered in a certain way would also represent an ordering of some of their physicochemical properties. Now, a study aimed at clarifying which physicochemical property of amino acids has influenced the allocation of amino acids in the genetic code has established that the partition energy of amino acids has played a role decisive in this. Indeed, under some conditions, the genetic code was found to be approximately 98% optimized on its columns. In this same work, it was shown that this was most likely the result of the action of natural selection. If natural selection had truly allocated the amino acids in the genetic code in such a way that similar amino acids also have similar codons - this, not through a mechanism of physicochemical interaction between, for example, codons and amino acids - then it might turn out that even different physicochemical properties of codons (or anticodons or bases) show some correlation with the physicochemical properties of amino acids, simply because the partition energy of amino acids is correlated with other physicochemical properties of amino acids. It is very likely that this would inevitably lead to a correlation between codons (or anticodons or bases) and amino acids. In other words, since the codons (anticodons or bases) are ordered in the genetic code, that is to say, some of their physicochemical properties should also be ordered by a similar order, and given that the amino acids would also appear to have been ordered in the genetic code by selection natural, then it should inevitably turn out that there is a correlation between, for example, the hydrophobicity of anticodons and that of amino acids. Instead, the intervention of natural selection in organizing the genetic code would appear to be highly compatible with the main mechanism of structuring the genetic code as supported by the coevolution theory. This would make the coevolution theory the only plausible explanation for the origin of the genetic code.

Self-catalytic mechanism of prebiotic reactions: from formamide to pterins and guanine

Reaction pathway of prebiotic reactions for formation of the pteridines: pterin, xanthopterine, isoxanthopterine and leucopterine, as well as the purine nucleobase guanine from pure formamide are presented. In these reactions, formamide or its tautomer, formimidic acid, play the role of proton-carrying catalyst. All required raw materials, such as hydrogen cyanide, ammonia, water, formic acid, urea, 2-aminomalononitrile, glyoxal, glyoxylic acid and oxalic acid needed in the self-catalyzed reactions are obtained by partial decomposition of formamide. We show that the prebiotic formation of nucleobases and pterins is closely linked and they probably coexisted at the beginning of chemical evolution.

The Grayness of the Origin of Life

In the search for life beyond Earth, distinguishing the living from the non-living is paramount. However, this distinction is often elusive, as the origin of life is likely a stepwise evolutionary process, not a singular event. Regardless of the favored origin of life model, an inherent "grayness" blurs the theorized threshold defining life. Here, we explore the ambiguities between the biotic and the abiotic at the origin of life. The role of grayness extends into later transitions as well. By recognizing the limitations posed by grayness, life detection researchers will be better able to develop methods sensitive to prebiotic chemical systems and life with alternative biochemistries.

Coenzymes and Their Role in the Evolution of Life

The evolution of coenzymes, or their impact on the origin of life, is fundamental for understanding our own existence. Having established reasonable hypotheses about the emergence of prebiotic chemical building blocks, which were probably created under palaeogeochemical conditions, and surmising that these smaller compounds must have become integrated to afford complex macromolecules such as RNA, the question of coenzyme origin and its relation to the evolution of functional biochemistry should gain new impetus. Many coenzymes have a simple chemical structure and are often nucleotide-derived, which suggests that they may have coexisted with the emergence of RNA and may have played a pivotal role in early metabolism. Based on current theories of prebiotic evolution, which attempt to explain the emergence of privileged organic building blocks, this Review discusses plausible hypotheses on the prebiotic formation of key elements within selected extant coenzymes. In combination with prebiotic RNA, coenzymes may have dramatically broadened early protometabolic networks and the catalytic scope of RNA during the evolution of life.

The coenzyme/protein pair and the molecular evolution of life

Covering: up to 2020What was first? Coenzymes or proteins? These questions are archetypal examples of causal circularity in living systems. Classically, this "chicken-and-egg" problem was discussed for the macromolecules RNA, DNA and proteins. This report focuses on coenzymes and cofactors and discusses the coenzyme/protein pair as another example of causal circularity in life. Reflections on the origin of life and hypotheses on possible prebiotic worlds led to the current notion that RNA was the first macromolecule, long before functional proteins and hence DNA. So these causal circularities of living systems were solved by a time travel into the past. To tackle the "chicken-and-egg" problem of the protein-coenzyme pair, this report addresses this problem by looking for clues (a) in the first hypothetical biotic life forms such as protoviroids and the last unified common ancestor (LUCA) and (b) in considerations and evidence of the possible prebiotic production of amino acids and coenzymes before life arose. According to these considerations, coenzymes and cofactors can be regarded as very old molecular players in the origin and evolution of life, and at least some of them developed independently of α-amino acids, which here are evolutionarily synonymous with proteins. Discussions on "chicken-and-egg" problems open further doors to the understanding of evolution.

Ribose Selected as Precursor to Life

The chemical or prebiotic evolution referred also to as pre-Darwinian evolution describes chemical reactions up to the origin of a self-replicating system that was capable of Darwinian evolution. These chemical processes took place on Earth between about 3.7 and 4.5 billion years ago when cellular life came into being. The pre-Darwinian chemical evolution usually assumes hereditary elements, but does not regard them as self-organizing processes. Physical and chemical self-organization led to uninterrupted pre-Darwinian and Darwinian evolution. Thus, it is not justified to distinguish between different types of evolution. From the many possible solutions, evolution selected among those reactions that generated catalytic networks incorporating chemical sequence information and under gradually changing circumstances produced a reproducible and stable living system that adapted to these conditions. Major issues in this review involve prebiotic reactions leading to genetic evolution involving (1) abiotic sources of components of ribonucleotides and xenobiotic nucleotides, (2) formation of prebiotic RNA, (3) development of genetic RNA from random-sequence noncoding RNA, (4) transition from RNA World to DNA Empire, (5) the role of oxygenic photosynthesis in genetic transitions, and (6) hierarchical arrangement of processes involved in the optimized genetic system.

Hidden Concepts in the History and Philosophy of Origins-of-Life Studies: a Workshop Report

In this review, we describe some of the central philosophical issues facing origins-of-life research and provide a targeted history of the developments that have led to the multidisciplinary field of origins-of-life studies. We outline these issues and developments to guide researchers and students from all fields. With respect to philosophy, we provide brief summaries of debates with respect to (1) definitions (or theories) of life, what life is and how research should be conducted in the absence of an accepted theory of life, (2) the distinctions between synthetic, historical, and universal projects in origins-of-life studies, issues with strategies for inferring the origins of life, such as (3) the nature of the first living entities (the "bottom up" approach) and (4) how to infer the nature of the last universal common ancestor (the "top down" approach), and (5) the status of origins of life as a science. Each of these debates influences the others. Although there are clusters of researchers that agree on some answers to these issues, each of these debates is still open. With respect to history, we outline several independent paths that have led to some of the approaches now prevalent in origins-of-life studies. These include one path from early views of life through the scientific revolutions brought about by Linnaeus (von Linn.), Wöhler, Miller, and others. In this approach, new theories, tools, and evidence guide new thoughts about the nature of life and its origin. We also describe another family of paths motivated by a" circularity" approach to life, which is guided by such thinkers as Maturana & Varela, Gánti, Rosen, and others. These views echo ideas developed by Kant and Aristotle, though they do so using modern science in ways that produce exciting avenues of investigation. By exploring the history of these ideas, we can see how many of the issues that currently interest us have been guided by the contexts in which the ideas were developed. The disciplinary backgrounds of each of these scholars has influenced the questions they sought to answer, the experiments they envisioned, and the kinds of data they collected. We conclude by encouraging scientists and scholars in the humanities and social sciences to explore ways in which they can interact to provide a deeper understanding of the conceptual assumptions, structure, and history of origins-of-life research. This may be useful to help frame future research agendas and bring awareness to the multifaceted issues facing this challenging scientific question.

A Proposal of the Ur-proteome

Herein we outline a plausible proteome, encoded by assuming a primeval RNY genetic code. We unveil the primeval phenotype by using only the RNA genotype; it means that we recovered the most ancestral proteome, mostly made of the 8 amino acids encoded by RNY triplets. By looking at those fragments, it is noticeable that they are positioned, not at catalytic sites, but in the cofactor binding sites. It implies that the stabilization of a molecule appeared long before its catalytic activity, and therefore the Ur-proteome comprised a set of proteins modules that corresponded to Cofactor Stabilizing Binding Sites (CSBSs), which we call the primitive bindome. With our method, we reconstructed the structures of the "first protein modules" that Sobolevsky and Trifonov (2006) found by using only RMSD. We also examine the probable cofactors that bound to them. We discuss the notion of CSBSs as the first proteins modules in progenotes in the context of several proposals about the primitive forms of life.

Remnants of an Ancient Metabolism without Phosphate

Phosphate is essential for all living systems, serving as a building block of genetic and metabolic machinery. However, it is unclear how phosphate could have assumed these central roles on primordial Earth, given its poor geochemical accessibility. We used systems biology approaches to explore the alternative hypothesis that a protometabolism could have emerged prior to the incorporation of phosphate. Surprisingly, we identified a cryptic phosphate-independent core metabolism producible from simple prebiotic compounds. This network is predicted to support the biosynthesis of a broad category of key biomolecules. Its enrichment for enzymes utilizing iron-sulfur clusters, and the fact that thermodynamic bottlenecks are more readily overcome by thioester rather than phosphate couplings, suggest that this network may constitute a "metabolic fossil" of an early phosphate-free nonenzymatic biochemistry. Our results corroborate and expand previous proposals that a putative thioester-based metabolism could have predated the incorporation of phosphate and an RNA-based genetic system. PAPERCLIP.

Life's utilization of B vitamins on early Earth

Coenzymes are essential across all domains of life. B vitamins (B₁ -thiamin, B₂ -riboflavin, B₃ -niacin, B₅ -pantothenate, B₆ -pyridoxine, B₇ -biotin, and B₁₂ -cobalamin) represent the largest class of coenzymes, which participate in a diverse set of reactions including C₁ -rearrangements, DNA repair, electron transfer, and fatty acid synthesis. B vitamin structures range from simple to complex heterocycles, yet, despite this complexity, multiple lines of evidence exist for their ancient origins including abiotic synthesis under putative early Earth conditions and/or meteorite transport. Thus, some of these critical coenzymes likely preceded life on Earth. Some modern organisms can synthesize their own B vitamins de novo while others must either scavenge them from the environment or establish a symbiotic relationship with a B vitamin producer. B vitamin requirements are widespread in some of the most ancient metabolisms including all six carbon fixation pathways, sulfate reduction, sulfur disproportionation, methanogenesis, acetogenesis, and photosynthesis. Understanding modern metabolic B vitamin requirements is critical for understanding the evolutionary conditions of ancient metabolisms as well as the biogeochemical cycling of critical elements such as S, C, and O.

A Prebiotic Synthesis of Pterins

The genesis of life on Earth is a hypothesis of evolutionary science that can be, at least partially, tested experimentally. The prebiotic synthesis of cofactors or coenzymes is a poorly explored issue, likely because their formation under plausible prebiotic conditions is not clear. In this sense, it has been proposed that the cofactors are "molecular fossils" of an early phase of life. In contrast, Eschenmoser and Loewenthal suggested a prebiotic hydrocyanic origin of cofactor building blocks. In the present paper, the formation of a set of pterins from cyanide polymerizations is demonstrated, showing that the main structure of some cofactors can be prebiotically formed. Indeed, it was observed that aqueous aerosols additionally increase the relative composition for pterins in the insoluble NH4CN polymers synthesized. The novel identification of pterins in NH4CN polymers, together with the previous detection of other important biomonomers, indicates that cyanide polymerizations were essential in the early state of prebiotic chemistry.

227 Views of RNA: Is RNA Unique in Its Chemical Isomer Space?

Ribonucleic acid (RNA) is one of the two nucleic acids used by extant biochemistry and plays a central role as the intermediary carrier of genetic information in transcription and translation. If RNA was involved in the origin of life, it should have a facile prebiotic synthesis. A wide variety of such syntheses have been explored. However, to date no one-pot reaction has been shown capable of yielding RNA monomers from likely prebiotically abundant starting materials, though this does not rule out the possibility that simpler, more easily prebiotically accessible nucleic acids may have preceded RNA. Given structural constraints, such as the ability to form complementary base pairs and a linear covalent polymer, a variety of structural isomers of RNA could potentially function as genetic platforms. By using structure-generation software, all the potential structural isomers of the ribosides (BC5H9O4, where B is nucleobase), as well as a set of simpler minimal analogues derived from them, that can potentially serve as monomeric building blocks of nucleic acid-like molecules are enumerated. Molecules are selected based on their likely stability under biochemically relevant conditions (e.g., moderate pH and temperature) and the presence of at least two functional groups allowing the monomers to be incorporated into linear polymers. The resulting structures are then evaluated by using molecular descriptors typically applied in quantitative structure-property relationship (QSPR) studies and predicted physicochemical properties. Several databases have been queried to determine whether any of the computed isomers had been synthesized previously. Very few of the molecules that emerge from this structure set have been previously described. We conclude that ribonucleosides may have competed with a multitude of alternative structures whose potential proto-biochemical roles and abiotic syntheses remain to be explored.

Autocatalytic sets in E. coli metabolism

Background

A central unsolved problem in early evolution concerns self-organization towards higher complexity in chemical reaction networks. In theory, autocatalytic sets have useful properties to help model such transitions. Autocatalytic sets are chemical reaction systems in which molecules belonging to the set catalyze the synthesis of other members of the set. Given an external supply of starting molecules – the food set – and the conditions that (i) all reactions are catalyzed by at least one molecule, and (ii) each molecule can be constructed from the food set by a sequence of reactions, the system becomes a reflexively autocatalytic food-generated network (RAF set). Autocatalytic networks and RAFs have been studied extensively as mathematical models for understanding the properties and parameters that influence self-organizational tendencies. However, despite their appeal, the relevance of RAFs for real biochemical networks that exist in nature has, so far, remained virtually unexplored.

Results

Here we investigate the best-studied metabolic network, that of Escherichia coli, for the existence of RAFs. We find that the largest RAF encompasses almost the entire E. coli cytosolic reaction network. We systematically study its structure by considering the impact of removing catalysts or reactions. We show that, without biological knowledge, finding the minimum food set that maintains a given RAF is NP-complete. We apply a randomized algorithm to find (approximately) smallest subsets of the food set that suffice to sustain the original RAF.

Conclusions

The existence of RAF sets within a microbial metabolic network indicates that RAFs capture properties germane to biological organization at the level of single cells. Moreover, the interdependency between the different metabolic modules, especially concerning cofactor biosynthesis, points to the important role of spontaneous (non-enzymatic) reactions in the context of early evolution.

Graphical Abstract

The evolution of information storage and heredity

Many important transitions in evolution are associated with novel ways of storing and transmitting information. The storage of information in DNA sequence, and its transmission through DNA replication, is a fundamental hereditary system in all extant organisms, but it is not the only way of storing and transmitting information, and has itself replaced, and evolved from, other systems. A system that transmits information can have limited heredity or indefinite heredity. With limited heredity, the number of different possible types is commensurate with, or below, that of the individuals. With indefinite heredity, the number of possible types greatly exceeds the number of individuals in any realistic system. Recent findings suggest that the emergence and subsequent evolution of very different hereditary systems, from autocatalytic chemical cycles to natural language, accompanied the major evolutionary transitions in the history of life.

Multiple B-vitamin depletion in large areas of the coastal ocean

B vitamins are some of the most commonly required biochemical cofactors in living systems. Therefore, cellular metabolism of marine vitamin-requiring (auxotrophic) phytoplankton and bacteria would likely be significantly compromised if B vitamins (thiamin B(1), riboflavin B(2), pyridoxine B(6), biotin B(7), and cobalamin B(12)) were unavailable. However, the factors controlling the synthesis, ambient concentrations, and uptake of these key organic compounds in the marine environment are still not well understood. Here, we report vertical distributions of five B vitamins (and the amino acid methionine) measured simultaneously along a latitudinal gradient through the contrasting oceanographic regimes of the southern California-Baja California coast in the Northeast Pacific margin. Although vitamin concentrations ranged from below the detection limits of our technique to 30 pM for B(2) and B(12) and to ∼500 pM for B(1), B(6), and B(7), each vitamin showed a different geographical and depth distribution. Vitamin concentrations were independent of each other and of inorganic nutrient levels, enriched primarily in the upper mesopelagic zone (depth of 100-300 m), and associated with water mass origin. Moreover, vitamin levels were below our detection limits (ranging from ≤0.18 pM for B(12) to ≤0.81 pM for B(1)) in extensive areas (100s of kilometers) of the coastal ocean, and thus may exert important constraints on the taxonomic composition of phytoplankton communities, and potentially also on rates of primary production and carbon sequestration.

Out of fuzzy chemistry: from prebiotic chemistry to metabolic networks

The origin of life on Earth was a chemical affair. So how did primitive biochemical systems originate from geochemical and cosmochemical processes on the young planet? Contemporary research into the origins of life subscribes to the Darwinian principle of material causes operating in an evolutionary context, as advocated by A. I. Oparin and J. B. S. Haldane in the 1920s. In its simplest form (e.g., a bacterial cell) extant biological complexity relies on the functional integration of metabolic networks and replicative genomes inside a lipid boundary. Different research programmes have explored the prebiotic plausibility of each of these autocatalytic subsystems and combinations thereof: self-maintained networks of small molecules, template chemistry, and self-reproductive vesicles. This tutorial review focuses on the debates surrounding the origin of metabolism and offers a brief overview of current studies on the evolution of metabolic networks. I suggest that a leitmotif in the origin and evolution of metabolism is the role played by catalysers' substrate ambiguity and multifunctionality.

Computational identification of obligatorily autocatalytic replicators embedded in metabolic networks

Small-molecular metabolic autocatalytic regulators, which are crucial to metabolic pathways, are identified in a novel systems-wide study in different organisms, revealing that in the enzymatic reactions of conserved autocatalytic cycles, the autocatalytic behavior of replicators varies.

Background

If chemical A is necessary for the synthesis of more chemical A, then A has the power of replication (such systems are known as autocatalytic systems). We provide the first systems-level analysis searching for small-molecular autocatalytic components in the metabolisms of diverse organisms, including an inferred minimal metabolism.

Results

We find that intermediary metabolism is invariably autocatalytic for ATP. Furthermore, we provide evidence for the existence of additional, organism-specific autocatalytic metabolites in the forms of coenzymes (NAD⁺, coenzyme A, tetrahydrofolate, quinones) and sugars. Although the enzymatic reactions of a number of autocatalytic cycles are present in most of the studied organisms, they display obligatorily autocatalytic behavior in a few networks only, hence demonstrating the need for a systems-level approach to identify metabolic replicators embedded in large networks.

Conclusion

Metabolic replicators are apparently common and potentially both universal and ancestral: without their presence, kick-starting metabolic networks is impossible, even if all enzymes and genes are present in the same cell. Identification of metabolic replicators is also important for attempts to create synthetic cells, as some of these autocatalytic molecules will presumably be needed to be added to the system as, by definition, the system cannot synthesize them without their initial presence.

On the chemistry and evolution of the pioneer organism

The theory of a chemo-autotrophic origin of life in a volcanic Iron-Sulfur World postulates the emergence of a pioneer organism within a flow of volcanic exhalations. The pioneer organism is characterized by a composite structure with an inorganic substructure and an organic superstructure. Within the surfaces of the inorganic substructure, iron, cobalt, nickel, and other transition-metal centers with sulfido, carbonyl, cyano, and other ligands are catalytically active, and promote the growth of the organic superstructure through carbon fixation, driven by the reducing potential of the volcanic exhalations. This pioneer organism is reproductive by an autocatalytic feedback effect, whereby some organic products serve as ligands for activating the catalytic metal centres whence they arise. This unitary structure-function relationship of the pioneer organism constitutes the 'Anlage' for two major strands of evolution: enzymatization and cellularization, whereby the upward evolution of life by increase of molecular complexity is grounded ultimately in the transition metal-catalyzed, synthetic redox chemistry of the pioneer organism.

Evolution of the genetic code

Comparative path lengths in amino acid biosynthesis and other molecular indicators of the timing of codon assignment were examined to reconstruct the main stages of code evolution. The codon tree obtained was rooted in the 4 N-fixing amino acids (Asp, Glu, Asn, Gln) and 16 triplets of the NAN set. This small, locally phased (commaless) code evidently arose from ambiguous translation on a poly(A) collector strand, in a surface reaction network. Copolymerisation of these amino acids yields polyanionic peptide chains, which could anchor uncharged amide residues to a positively charged mineral surface. From RNA virus structure and replication in vitro, the first genes seemed to be RNA segments spliced into tRNA. Expansion of the code reduced the risk of mutation to an unreadable codon. This step was conditional on initiation at the 5'-codon of a translated sequence. Incorporation of increasingly hydrophobic amino acids accompanied expansion. As codons of the NUN set were assigned most slowly, they received the most nonpolar amino acids. The origin of ferredoxin and Gln synthetase was traced to mid-expansion phase. Surface metabolism ceased by the end of code expansion, as cells bounded by a proteo-phospholipid membrane, with a protoATPase, had emerged. Incorporation of positively charged and aromatic amino acids followed. They entered the post-expansion code by codon capture. Synthesis of efficient enzymes with acid-base catalysis was then possible. Both types of aminoacyl-tRNA synthetases were attributed to this stage. tRNA sequence diversity and error rates in RNA replication indicate the code evolved within 20 million yr in the preIsuan era. These findings on the genetic code provide empirical evidence, from a contemporaneous source, that a surface reaction network, centred on C-fixing autocatalytic cycles, rapidly led to cellular life on Earth.

A classification of replicators and lambda-calculus models of biological organization

W. Fontana & L.W. Buss (Proc. Natn. Acad. Sci. U.S.A. 91, 757 (1994) and Bull. math. Biol. 56, 1 (1994) have put forward a scheme for a theory of biological organization based on the lambda-calculus. Their key innovation was to represent, with the aid of this calculus, a certain minimal chemistry. Although this idea is very promising, their concrete formulation could be improved if suggestions for the following items were incorporated: (i) a better coding of chemical reactions; (ii) a reinterpretation of the evolutionary behaviour of autocatalytic chemical networks; (iii) a better appreciation of morphological and genetic factors; (iv) a more complete embedding of the theory into the background of relevant earlier contributions. Confusion can be stopped by the application of a proper classification of replicators (important categories being: processive and modular, limited and unlimited hereditary replicators). Suggestions to facilitate improvement are made explicit in this paper. The most challenging task would be to model the transition from processive, limited hereditary replicators to modular replicators with limited and unlimited heredity.

The major evolutionary transitions

There is no theoretical reason to expect evolutionary lineages to increase in complexity with time, and no empirical evidence that they do so. Nevertheless, eukaryotic cells are more complex than prokaryotic ones, animals and plants are more complex than protists, and so on. This increase in complexity may have been achieved as a result of a series of major evolutionary transitions. These involved changes in the way information is stored and transmitted.

Did reflexive catalysts drive chemical evolution?

High-energy starting materials and energy sources on the primitive earth would have generated abundant and varied organic molecules of small or medium size. It is questionable, however, whether ordinary chemical evolution could have produced information-carrying polymers. The end point might have been a fixed steady state if some form of autocatalysis had not intervened. Autocatalytic synthesis is possible for small molecules as illustrated by the formose reaction, in which glycolaldehyde condenses with formaldehyde to form sugars, and resulting tetroses may cleave into two molecules of glycolaldehyde. This and other 'reflexive catalysts', some functioning in molecular aggregates, may have energized chemical evolution and carried it to a level at which RNA or an RNA analog could replicate itself.

Genetic information could be integrated extrinsically for simplest life forms

Polynucleotides and proteins coupled in mutual synthesis are widely believed to have been needed for the origin of life, but this theory encounters grave problems. Simple catalysts reproducing by positive feedback, sometimes advocated as an alternative, lack a built-in mechanism for generating and accumulating genetic information. Modern organisms, however, integrate genetic information by extrinsic in addition to intrinsic mechanisms, and extrinsic mechanisms were available even at the beginning of chemical evolution for any self-reproducing entities that might have appeared. Novel molecules were generated by reactions among prevailing molecules, and a catalyst multiplying by positive feedback would have transmitted structural information not only to progeny molecules of its kind, but to derivatives and by-products. New molecules derived immediately or remotely from successfully reproducing catalysts would be favored to have catalytic properties. New catalysts with effective positive feedback would increase autocatalytically and be integrated with others into a metabolizing system by natural selection.

The relationship between the biosynthetic paths to the amino acids and their coding. I: The aliphatic amino acids and proline

The genetic code could not have been fixed until the means for biosynthesis of the amino acids was at hand. The biosynthetic enzymes could not be optimized until the genetic code ceased to be rearranged. Therefore the development of the code and the development of the biosynthesis of the amino acids occurred concurrently. The present day biosynthetic pathways of amino acids, examined from this point of view, help to explain the present set of coded amino acids, in particular the absence of norvaline, norleucine, homoserine, ornithine, and alpha-aminobutyric acid. An order of development of biosyntheses is also proposed. Lysine was first, followed by valine and isoleucine. The more common primordial amino acids did not need biosyntheses so early. The central pathways of metabolism probably developed in response to a need for amino acid biosynthesis.

Evolution of structure in RNA

Evidence is presented that structures formed by RNA and by RNA in association with protein have evolved from simpler structures by successive unions among them. The progressively more complex molecular structures have conferred selective advantage in evolution by progressively enhancing the specificities of the biochemical reactions. Before each union, the RNAs which joined at the time of union belonged to separate reproducing species. The record of unions in RNA therefore reflects unions among species in the biosphere, tracing the evolution of life from quite simple reproducing molecules up to well developed organisms.

A neutral theory of biogenesis

The selective Darwinian theory of chemical evolution is critically reviewed and the tentative conclusion is reached that neither the theoretical analyses nor the experiments with phages can really prove it. An alternative proposal is put forth which considers the possibility that the biogenetic process has been driven by stochastic forces, e.g. it took place in the absence of Darwinian selection which, in turn, started only when the first protocells came into existence. The dynamics of the early self-organization of living structures should be understood in terms of self-assembly. The complexification of living matter is thus not represented as a gradual phenomenon but as a series of abrupt and relatively fast transitions consisting in the aggregation of pre-systems which had evolved by their own. The shift towards new and variegated states proposed by the bifurcation theory are not considered particularly relevant for reasons reported in the test, nor is it believed that dissipation can entirely account for the order observed in living cells.

The evolution of metabolic cycles

The function of the citric acid cycle is to convert efficiently the energy released during the combustion of acetate into the energy stored in the pyrophosphate bonds of ATP. The cycle is almost twice as efficient as feasible alternatives of acetate combustion, such as a direct pathway via glycollate, glyoxylate, formaldehyde and formate. The reason is that the first stage of acetate degradation cannot be a dehydrogenation; it must be an oxygenation by molecular oxygen. Thus the cycle must have evolved because in a competitive environment the chances of survival are greatest if resources are optimal. Analogous considerations apply to the evolution of other metabolic cycles.