Compositional complementarity and prebiotic ecology in the origin of life

Hypothesis: bacteria live on the edge of phase transitions with a cell cycle regulated by a water-clock

A fundamental problem in biology is how cells obtain the reproducible, coherent phenotypes needed for natural selection to act or, put differently, how cells manage to limit their exploration of the vastness of phenotype space. A subset of this problem is how they regulate their cell cycle. Bacteria, like eukaryotic cells, are highly structured and contain scores of hyperstructures or assemblies of molecules and macromolecules. The existence and functioning of certain of these hyperstructures depend on phase transitions. Here, I propose a conceptual framework to facilitate the development of water-clock hypotheses in which cells use water to generate phenotypes by living 'on the edge of phase transitions'. I give an example of such a hypothesis in the case of the bacterial cell cycle and show how it offers a relatively novel 'view from here' that brings together a range of different findings about hyperstructures, phase transitions and water and that can be integrated with other hypotheses about differentiation, metabolism and the origins of life.

Hunting the Cell Cycle Snark

In this very personal hunt for the meaning of the bacterial cell cycle, the snark, I briefly revisit and update some of the mechanisms we and many others have proposed to regulate the bacterial cell cycle. These mechanisms, which include the dynamics of calcium, membranes, hyperstructures, and networks, are based on physical and physico-chemical concepts such as ion condensation, phase transition, crowding, liquid crystal immiscibility, collective vibrational modes, reptation, and water availability. I draw on ideas from subjects such as the 'prebiotic ecology' and phenotypic diversity to help with the hunt. Given the fundamental nature of the snark, I would expect that its capture would make sense of other parts of biology. The route, therefore, followed by the hunt has involved trying to answer questions like "why do cells replicate their DNA?", "why is DNA replication semi-conservative?", "why is DNA a double helix?", "why do cells divide?", "is cell division a spandrel?", and "how are catabolism and anabolism balanced?". Here, I propose some relatively unexplored, experimental approaches to testing snark-related hypotheses and, finally, I propose some possibly original ideas about DNA packing, about phase separations, and about computing with populations of virtual bacteria.

Reactions Driven by Primitive Nonbiological Polyesters

All life on Earth is composed of cells, which are built from and run by biological reactions and structures. These reactions and structures are generally the result of action by cellular biomolecules, which are indispensable for the function and survival of all living organisms. Specifically, biological catalysis, namely by protein enzymes, but also by other biomolecules including nucleic acids, is an essential component of life. How the biomolecules themselves that perform biological catalysis came to exist in the first place is a major unanswered question that plagues researchers to this day, which is generally the focus of the origins of life (OoL) research field. Based on current knowledge, it is generally postulated that early Earth was full of a myriad of different chemicals, and that these chemicals reacted in specific ways that led to the emergence of biochemistry, cells, and later, life. In particular, a significant part of OoL research focuses on the synthesis, evolution, and function of biomolecules potentially present under early Earth conditions, as a way to understand their eventual transition into modern life. However, this narrative overlooks possibilities that other molecules contributed to the OoL, as while biomolecules that led to life were certainly present on early Earth, at the same time, other molecules that may not have strict, direct biological lineage were also widely and abundantly present. For example, hydroxy acids, although playing a role in metabolism or as parts of certain biological structures, are not generally considered to be as essential to modern biology as amino acids (a chemically similar monomer), and thus research in the OoL field tends to perhaps focus more on amino acids than hydroxy acids. However, their likely abundance on early Earth coupled with their ability to spontaneously condense into polymers (i.e., polyesters) make hydroxy acids, and their subsequent products, functions, and reactions, a reasonable target of investigation for prebiotic chemists. Whether "non-biological" hydroxy acids or polyesters can contribute to the emergence of life on early Earth is an inquiry that deserves attention within the OoL community, as this knowledge can also contribute to our understanding of the plausibility of extraterrestrial life that does not exactly use the biochemical set found in terrestrial organisms. While some demonstrations have been made with respect to compartment assembly, compartmentalization, and growth of primitive polyester-based systems, whether these "non-biological" polymers can contribute any catalytic function and/or drive primitive reactions is still an important step toward the development of early life. Here, we review research both from the OoL field as well as from industry and applied sciences regarding potential catalysis or reaction driven by "non-biological" polyesters in various forms: as linear polymers, as hyperbranched polyesters, and as membraneless microdroplets.

The ecology-evolution continuum and the origin of life

Prior research on evolutionary mechanisms during the origin of life has mainly assumed the existence of populations of discrete entities with information encoded in genetic polymers. Recent theoretical advances in autocatalytic chemical ecology establish a broader evolutionary framework that allows for adaptive complexification prior to the emergence of bounded individuals or genetic encoding. This framework establishes the formal equivalence of cells, ecosystems and certain localized chemical reaction systems as autocatalytic chemical ecosystems (ACEs): food-driven (open) systems that can grow due to the action of autocatalytic cycles (ACs). When ACEs are organized in meta-ecosystems, whether they be populations of cells or sets of chemically similar environmental patches, evolution, defined as change in AC frequency over time, can occur. In cases where ACs are enriched because they enhance ACE persistence or dispersal ability, evolution is adaptive and can build complexity. In particular, adaptive evolution can explain the emergence of self-bounded units (e.g. protocells) and genetic inheritance mechanisms. Recognizing the continuity between ecological and evolutionary change through the lens of autocatalytic chemical ecology suggests that the origin of life should be seen as a general and predictable outcome of driven chemical ecosystems rather than a phenomenon requiring specific, rare conditions.

Assessment of Stoichiometric Autocatalysis across Element Groups

Autocatalysis has been proposed to play critical roles during abiogenesis. These proposals are at odds with a limited number of known examples of abiotic (and, in particular, inorganic) autocatalytic systems that might reasonably function in a prebiotic environment. In this study, we broadly assess the occurrence of stoichiometries that can support autocatalytic chemical systems through comproportionation. If the product of a comproportionation reaction can be coupled with an auxiliary oxidation or reduction pathway that furnishes a reactant, then a Comproportionation-based Autocatalytic Cycle (CompAC) can exist. Using this strategy, we surveyed the literature published in the past two centuries for reactions that can be organized into CompACs that consume some chemical species as food to synthesize more autocatalysts. 226 CompACs and 44 Broad-sense CompACs were documented, and we found that each of the 18 groups, lanthanoid series, and actinoid series in the periodic table has at least two CompACs. Our findings demonstrate that stoichiometric relationships underpinning abiotic autocatalysis could broadly exist across a range of geochemical and cosmochemical conditions, some of which are substantially different from the modern Earth. Meanwhile, the observation of some autocatalytic systems requires effective spatial or temporal separation between the food chemicals while allowing comproportionation and auxiliary reactions to proceed, which may explain why naturally occurring autocatalytic systems are not frequently observed. The collated CompACs and the conditions in which they might plausibly support complex, "life-like" chemical dynamics can directly aid an expansive assessment of life's origins and provide a compendium of alternative hypotheses concerning false-positive biosignatures.

Environmental Stability and Its Importance for the Emergence of Darwinian Evolution

The emergence of Darwinian evolution represents a central point in the history of life as we know it. However, it is generally assumed that the environments in which life appeared were hydrothermal environments, with highly variable conditions in terms of pH, temperature or redox levels. Are evolutionary processes favored to appear in such settings, where the target of biological adaptation changes over time? How would the first evolving populations compete with non-evolving populations? Using a numerical model, we explore the effect of environmental variation on the outcome of the competition between evolving and non-evolving populations of protocells. Our study found that, while evolving protocells consistently outcompete non-evolving populations in stable environments, they are outcompeted in variable environments when environmental variations occur on a timescale similar to the average duration of a generation. This is due to the energetic burden represented by adaptation to the wrong environmental conditions. Since the timescale of temperature variation in natural hydrothermal settings overlaps with the average prokaryote generation time, the current work indicates that a solution must have been found by early life to overcome this threshold.

Open Questions about the Roles of DnaA, Related Proteins, and Hyperstructure Dynamics in the Cell Cycle

The DnaA protein has long been considered to play the key role in the initiation of chromosome replication in modern bacteria. Many questions about this role, however, remain unanswered. Here, we raise these questions within a framework based on the dynamics of hyperstructures, alias large assemblies of molecules and macromolecules that perform a function. In these dynamics, hyperstructures can (1) emit and receive signals or (2) fuse and separate from one another. We ask whether the DnaA-based initiation hyperstructure acts as a logic gate receiving information from the membrane, the chromosome, and metabolism to trigger replication; we try to phrase some of these questions in terms of DNA supercoiling, strand opening, glycolytic enzymes, SeqA, ribonucleotide reductase, the macromolecular synthesis operon, post-translational modifications, and metabolic pools. Finally, we ask whether, underpinning the regulation of the cell cycle, there is a physico-chemical clock inherited from the first protocells, and whether this clock emits a single signal that triggers both chromosome replication and cell division.

The origin of genetic and metabolic systems: Evolutionary structuralinsights

DNA is derived from reverse transcription and its origin is related to reverse transcriptase, DNA polymerase and integrase. The gene structure originated from the evolution of the first RNA polymerase. Thus, an explanation of the origin of the genetic system must also explain the evolution of these enzymes. This paper proposes a polymer structure model, termed the stable complex evolution model, which explains the evolution of enzymes and functional molecules. Enzymes evolved their functions by forming locally tightly packed complexes with specific substrates. A metabolic reaction can therefore be considered to be the result of adaptive evolution in this way when a certain essential molecule is lacking in a cell. The evolution of the primitive genetic and metabolic systems was thus coordinated and synchronized. According to the stable complex model, almost all functional molecules establish binding affinity and specific recognition through complementary interactions, and functional molecules therefore have the nature of being auto-reactive. This is thermodynamically favorable and leads to functional duplication and self-organization. Therefore, it can be speculated that biological systems have a certain tendency to maintain functional stability or are influenced by an inherent selective power. The evolution of dormant bacteria may support this hypothesis, and inherent selectivity can be unified with natural selection at the molecular level.

"Sea Water" Supplemented with Calcium Phosphate and Magnesium Sulfate in a Long-Term Miller-Type Experiment Yields Sugars, Nucleic Acids Bases, Nucleosides, Lipids, Amino Acids, and Oligopeptides

The standard approach to exploring prebiotic chemistry is to use a small number of highly purified reactants and to attempt to optimize the conditions required to produce a particular end product. However, purified reactants do not exist in nature. We have previously proposed that what drives prebiotic evolution are complex chemical ecologies. Therefore, we have begun to explore what happens if one substitutes "sea water", with its complex mix of minerals and salts, for distilled water in the classic Miller experiment. We have also adapted the apparatus to permit it to be regassed at regular intervals so as to maintain a relatively constant supply of methane, hydrogen, and ammonia. The "sea water" used in the experiments was created from Mediterranean Sea salt with the addition of calcium phosphate and magnesium sulfate. Tests included several types of mass spectrometry, an ATP-monitoring device capable of measuring femtomoles of ATP, and a high-sensitivity cAMP enzyme-linked immunoadsorption assay. As expected, amino acids appeared within a few days of the start of the experiment and accumulated thereafter. Sugars, including glucose and ribose, followed as did long-chain fatty acids (up to C20). At three-to-five weeks after starting the experiment, ATP was repeatedly detected. Thus, we have shown that it is possible to produce a "one-pot synthesis" of most of the key chemical prerequisites for living systems within weeks by mimicking more closely the complexity of real-world chemical ecologies.

Novel Apparatuses for Incorporating Natural Selection Processes into Origins-of-Life Experiments to Produce Adaptively Evolving Chemical Ecosystems

Origins-of-life chemical experiments usually aim to produce specific chemical end-products such as amino acids, nucleic acids or sugars. The resulting chemical systems do not evolve or adapt because they lack natural selection processes. We have modified Miller origins-of-life apparatuses to incorporate several natural, prebiotic physicochemical selection factors that can be tested individually or in tandem: freezing-thawing cycles; drying-wetting cycles; ultraviolet light-dark cycles; and catalytic surfaces such as clays or minerals. Each process is already known to drive important origins-of-life chemical reactions such as the production of peptides and synthesis of nucleic acid bases and each can also destroy various reactants and products, resulting selection within the chemical system. No previous apparatus has permitted all of these selection processes to work together. Continuous synthesis and selection of products can be carried out over many months because the apparatuses can be re-gassed. Thus, long-term chemical evolution of chemical ecosystems under various combinations of natural selection may be explored for the first time. We argue that it is time to begin experimenting with the long-term effects of such prebiotic natural selection processes because they may have aided biotic life to emerge by taming the combinatorial chemical explosion that results from unbounded chemical syntheses.

Protocells: Milestones and Recent Advances

The origin of life is still one of humankind's great mysteries. At the transition between nonliving and living matter, protocells, initially featureless aggregates of abiotic matter, gain the structure and functions necessary to fulfill the criteria of life. Research addressing protocells as a central element in this transition is diverse and increasingly interdisciplinary. The authors review current protocell concepts and research directions, address milestones, challenges and existing hypotheses in the context of conditions on the early Earth, and provide a concise overview of current protocell research methods.

Potassium at the Origins of Life: Did Biology Emerge from Biotite in Micaceous Clay?

Intracellular potassium concentrations, [K+], are high in all types of living cells, but the origins of this K+ are unknown. The simplest hypothesis is that life emerged in an environment that was high in K+. One such environment is the spaces between the sheets of the clay mineral mica. The best mica for life's origins is the black mica, biotite, because it has a high content of Mg++ and because it has iron in various oxidation states. Life also has many of the characteristics of the environment between mica sheets, giving further support for the possibility that mica was the substrate on and within which life emerged. Here, a scenario for life's origins is presented, in which the necessary processes and components for life arise in niches between mica sheets; vesicle membranes encapsulate these processes and components; the resulting vesicles fuse, forming protocells; and eventually, all of the necessary components and processes are encapsulated within individual cells, some of which survive to seed the early Earth with life. This paper presents three new foci for the hypothesis of life's origins between mica sheets: (1) that potassium is essential for life's origins on Earth; (2) that biotite mica has advantages over muscovite mica; and (3) that micaceous clay is a better environment than isolated mica for life's origins.

Co-Evolution of Opioid and Adrenergic Ligands and Receptors: Shared, Complementary Modules Explain Evolution of Functional Interactions and Suggest Novel Engineering Possibilities

Cross-talk between opioid and adrenergic receptors is well-characterized and involves second messenger systems, the formation of receptor heterodimers, and the presence of extracellular allosteric binding regions for the complementary ligand; however, the evolutionary origins of these interactions have not been investigated. We propose that opioid and adrenergic ligands and receptors co-evolved from a common set of modular precursors so that they share binding functions. We demonstrate the plausibility of this hypothesis through a review of experimental evidence for molecularly complementary modules and report unexpected homologies between the two receptor types. Briefly, opioids form homodimers also bind adrenergic compounds; opioids bind to conserved extracellular regions of adrenergic receptors while adrenergic compounds bind to conserved extracellular regions of opioid receptors; opioid-like modules appear in both sets of receptors within key ligand-binding regions. Transmembrane regions associated with homodimerization of each class of receptors are also highly conserved across receptor types and implicated in heterodimerization. This conservation of multiple functional modules suggests opioid–adrenergic ligand and receptor co-evolution and provides mechanisms for explaining the evolution of their crosstalk. These modules also suggest the structure of a primordial receptor, providing clues for engineering receptor functions.

Competitive Coherence Generates Qualia in Bacteria and Other Living Systems

The relevance of bacteria to subjective experiences or qualia is underappreciated. Here, I make four proposals. Firstly, living systems traverse sequences of active states that determine their behaviour; these states result from competitive coherence, which depends on connectivity-based competition between a Next process and a Now process, whereby elements in the active state at time n+1 are chosen between the elements in the active state at time n and those elements in the developing n+1 state. Secondly, bacteria should help us link the mental to the physical world given that bacteria were here first, are highly complex, influence animal behaviour and dominate the Earth. Thirdly, the operation of competitive coherence to generate active states in bacteria, brains and other living systems is inseparable from qualia. Fourthly, these qualia become particularly important to the generation of active states in the highest levels of living systems, namely, the ecosystem and planetary levels.

Origin of Life: The Point of No Return

Origin of life research is one of the greatest scientific frontiers of mankind. Many hypotheses have been proposed to explain how life began. Although different hypotheses emphasize different initial phenomena, all of them agree around one important concept: at some point, along with the chain of events toward life, Darwinian evolution emerged. There is no consensus, however, how this occurred. Frequently, the mechanism leading to Darwinian evolution is not addressed and it is assumed that this problem could be solved later, with experimental proof of the hypothesis. Here, the author first defines the minimum components required for Darwinian evolution and then from this standpoint, analyzes some of the hypotheses for the origin of life. Distinctive features of Darwinian evolution and life rooted in the interaction between information and its corresponding structure/function are then reviewed. Due to the obligatory dependency of the information and structure subject to Darwinian evolution, these components must be locked in their origin. One of the most distinctive characteristics of Darwinian evolution in comparison with all other processes is the establishment of a fundamentally new level of matter capable of evolving and adapting. Therefore, the initiation of Darwinian evolution is the "point of no return" after which life begins. In summary: a definition and a mechanism for Darwinian evolution are provided together with a critical analysis of some of the hypotheses for the origin of life.

Prebiotic oligomerization and self-assembly of structurally diverse xenobiological monomers

Prebiotic chemists often study how modern biopolymers, e.g., peptides and nucleic acids, could have originated in the primitive environment, though most contemporary biomonomers don't spontaneously oligomerize under mild conditions without activation or catalysis. However, life may not have originated using the same monomeric components that it does presently. There may be numerous non-biological (or "xenobiological") monomer types that were prebiotically abundant and capable of facile oligomerization and self-assembly. Many modern biopolymers degrade abiotically preferentially via processes which produce thermodynamically stable ring structures, e.g. diketopiperazines in the case of proteins and 2', 3'-cyclic nucleotide monophosphates in the case of RNA. This weakness is overcome in modern biological systems by kinetic control, but this need not have been the case for primitive systems. We explored here the oligomerization of a structurally diverse set of prebiotically plausible xenobiological monomers, which can hydrolytically interconvert between cyclic and acyclic forms, alone or in the presence of glycine under moderate temperature drying conditions. These monomers included various lactones, lactams and a thiolactone, which varied markedly in their stability, propensity to oligomerize and apparent modes of initiation, and the oligomeric products of some of these formed self-organized microscopic structures which may be relevant to protocell formation.

An ecological framework for the analysis of prebiotic chemical reaction networks

It is becoming widely accepted that very early in life's origin, even before the emergence of genetic encoding, reaction networks of diverse small chemicals might have manifested key properties of life, namely self-propagation and adaptive evolution. To explore this possibility, we formalize the dynamics of chemical reaction networks within the framework of chemical ecosystem ecology. To capture the idea that life-like chemical systems are maintained out of equilibrium by fluxes of energy-rich food chemicals, we model chemical ecosystems in well-mixed compartments that are subject to constant dilution by a solution with a fixed concentration of input chemicals. Modelling all chemical reactions as fully reversible, we show that seeding an autocatalytic cycle with tiny amounts of one or more of its member chemicals results in logistic growth of all member chemicals in the cycle. This finding justifies drawing an instructive analogy between an autocatalytic cycle and a biological species. We extend this finding to show that pairs of autocatalytic cycles can exhibit competitive, predator-prey, or mutualistic associations just like biological species. Furthermore, when there is stochasticity in the environment, particularly in the seeding of autocatalytic cycles, chemical ecosystems can show complex dynamics that can resemble evolution. The evolutionary character is especially clear when the network architecture results in ecological precedence, which makes a system's trajectory historically contingent on the order in which cycles are seeded. For all its simplicity, the framework developed here helps explain the onset of adaptive evolution in prebiotic chemical reaction networks, and can shed light on the origin of key biological attributes such as thermodynamic irreversibility and genetic encoding.

Chemical Ecosystem Selection on Mineral Surfaces Reveals Long-Term Dynamics Consistent with the Spontaneous Emergence of Mutual Catalysis

How did chemicals first become organized into systems capable of self-propagation and adaptive evolution? One possibility is that the first evolvers were chemical ecosystems localized on mineral surfaces and composed of sets of molecular species that could catalyze each other’s formation. We used a bottom-up experimental framework, chemical ecosystem selection (CES), to evaluate this perspective and search for surface-associated and mutually catalytic chemical systems based on the changes in chemistry that they are expected to induce. Here, we report the results of preliminary CES experiments conducted using a synthetic “prebiotic soup” and pyrite grains, which yielded dynamical patterns that are suggestive of the emergence of mutual catalysis. While more research is needed to better understand the specific patterns observed here and determine whether they are reflective of self-propagation, these results illustrate the potential power of CES to test competing hypotheses for the emergence of protobiological chemical systems.

Mutual Enhancement of Opioid and Adrenergic Receptors by Combinations of Opioids and Adrenergic Ligands Is Reflected in Molecular Complementarity of Ligands: Drug Development Possibilities

Crosstalk between opioid and adrenergic receptors is well characterized and due to interactions between second messenger systems, formation of receptor heterodimers, and extracellular allosteric binding regions. Both classes of receptors bind both sets of ligands. We propose here that receptor crosstalk may be mirrored in ligand complementarity. We demonstrate that opioids bind to adrenergic compounds with micromolar affinities. Additionally, adrenergic compounds bind with micromolar affinities to extracellular loops of opioid receptors while opioids bind to extracellular loops of adrenergic receptors. Thus, each compound type can bind to the complementary receptor, enhancing the activity of the other compound type through an allosteric mechanism. Screening for ligand complementarity may permit the identification of other mutually-enhancing sets of compounds as well as the design of novel combination drugs or tethered compounds with improved duration and specificity of action.

Emergence of a "Cyclosome" in a Primitive Network Capable of Building "Infinite" Proteins

We argue for the existence of an RNA sequence, called the AL (for ALpha) sequence, which may have played a role at the origin of life; this role entailed the AL sequence helping generate the first peptide assemblies via a primitive network. These peptide assemblies included "infinite" proteins. The AL sequence was constructed on an economy principle as the smallest RNA ring having one representative of each codon's synonymy class and capable of adopting a non-functional but nevertheless evolutionarily stable hairpin form that resisted denaturation due to environmental changes in pH, hydration, temperature, etc. Long subsequences from the AL ring resemble sequences from tRNAs and 5S rRNAs of numerous species like the proteobacterium, Rhodobacter sphaeroides. Pentameric subsequences from the AL are present more frequently than expected in current genomes, in particular, in genes encoding some of the proteins associated with ribosomes like tRNA synthetases. Such relics may help explain the existence of universal sequences like exon/intron frontier regions, Shine-Dalgarno sequence (present in bacterial and archaeal mRNAs), CRISPR and mitochondrial loop sequences.

Does the Semiconservative Nature of DNA Replication Facilitate Coherent Phenotypic Diversity?

It has been clear for over sixty years that the principal method whereby cells replicate and segregate their DNA is semiconservative. It is much less clear why it should be like this rather than, say, conservative. Recently, evidence has accumulated that supports the hypothesis that one of the functions of the cell cycle is to generate phenotypically different daughter cells, even in nondifferentiating bacteria such as Escherichia coli Evidence has also accumulated that the bacterial phenotype is determined by the functioning of extended assemblies of macromolecules termed hyperstructures. One class of these hyperstructures is attached dynamically to a DNA strand by the coupling of transcription and translation. Previously, we proposed in the strand segregation model that one set of hyperstructures accompanies one parental strand into one daughter cell while another set of hyperstructures accompanies the other parental strand into the other daughter cell. This epigenetic mechanism results in daughter cells having different phenotypes. Here, I propose that one of the reasons why semiconservative replication has been selected is because it allows the generation of a population containing cells with very different growth rates even in steady-state conditions.

Successive Paradigm Shifts in the Bacterial Cell Cycle and Related Subjects

A paradigm shift in one field can trigger paradigm shifts in other fields. This is illustrated by the paradigm shifts that have occurred in bacterial physiology following the discoveries that bacteria are not unstructured, that the bacterial cell cycle is not controlled by the dynamics of peptidoglycan, and that the growth rates of bacteria in the same steady-state population are not at all the same. These paradigm shifts are having an effect on longstanding hypotheses about the regulation of the bacterial cell cycle, which appear increasingly to be inadequate. I argue that, just as one earthquake can trigger others, an imminent paradigm shift in the regulation of the bacterial cell cycle will have repercussions or "paradigm quakes" on hypotheses about the origins of life and about the regulation of the eukaryotic cell cycle.

The Ribosome as a Missing Link in Prebiotic Evolution III: Over-Representation of tRNA- and rRNA-Like Sequences and Plieofunctionality of Ribosome-Related Molecules Argues for the Evolution of Primitive Genomes from Ribosomal RNA Modules

We propose that ribosomal RNA (rRNA) formed the basis of the first cellular genomes, and provide evidence from a review of relevant literature and proteonomic tests. We have proposed previously that the ribosome may represent the vestige of the first self-replicating entity in which rRNAs also functioned as genes that were transcribed into functional messenger RNAs (mRNAs) encoding ribosomal proteins. rRNAs also encoded polymerases to replicate itself and a full complement of the transfer RNAs (tRNAs) required to translate its genes. We explore here a further prediction of our “ribosome-first” theory: the ribosomal genome provided the basis for the first cellular genomes. Modern genomes should therefore contain an unexpectedly large percentage of tRNA- and rRNA-like modules derived from both sense and antisense reading frames, and these should encode non-ribosomal proteins, as well as ribosomal ones with key cell functions. Ribosomal proteins should also have been co-opted by cellular evolution to play extra-ribosomal functions. We review existing literature supporting these predictions. We provide additional, new data demonstrating that rRNA-like sequences occur at significantly higher frequencies than predicted on the basis of mRNA duplications or randomized RNA sequences. These data support our “ribosome-first” theory of cellular evolution.

An Insulin-Like Modular Basis for the Evolution of Glucose Transporters (GLUT) with Implications for Diabetes

Glucose transporters (GLUT) are twelve-transmembrane spanning proteins that contain two pores capable of transporting glucose and dehydroascorbate in and out of cells. The mechanism by which transport is effected is unknown. An evolutionarily-based hypothesis for the mechanism of glucose transport is presented here based on reports that insulin has multiple binding sites for glucose. It is proposed that insulin-like peptides were incorporated as modular elements into transmembrane proteins during evolution, resulting in glucose transporting capacity. Homology searching reveals that all GLUT contain multiple copies of insulin-like regions. These regions map onto a model of GLUT in positions that define the glucose transport cores. This observation provides a mechanism for glucose transport involving the diffusion of glucose from one insulin-like glucose-binding region to another. It also suggests a mechanism by which glucose disregulation may occur in both type 1 and type 2 diabetes: insulin rapidly self-glycates under hyperglycemic conditions. Insulin-like regions of GLUT may also self-glycate rapidly, thereby interfering with transport of glucose into cells and disabling GLUT sensing of blood glucose levels. All aspects of the hypothesis are experimentally testable.

Diversity and survival of artificial lifeforms under sedimentation and random motion

Cellular automata are often used to explore the numerous possible scenarios of what could have occurred at the origins of life and before, during the prebiotic ages, when very simple molecules started to assemble and organise into larger catalytic or informative structures, or to simulate ecosystems. Artificial self-maintained spatial structures emerge in cellular automata and are often used to represent molecules or living organisms. They converge generally towards homogeneous stationary soups of still-life creatures. It is hard for an observer to believe they are similar to living systems, in particular because nothing is moving anymore within such simulated environments after few computation steps, because they present isotropic spatial organisation, because the diversity of self-maintained morphologies is poor, and because when stationary states are reached the creatures are immortal. Natural living systems, on the contrary, are composed of a high diversity of creatures in interaction having limited lifetimes and generally present a certain anisotropy of their spatial organisation, in particular frontiers and interfaces. In the present work, we propose that the presence of directional weak fields such as gravity may counter-balance the excess of mixing and disorder caused by Brownian motion and favour the appearance of specific regions, i.e. different strata or environmental layers, in which physical-chemical conditions favour the emergence and the survival of self-maintained spatial structures including living systems. We test this hypothesis by way of numerical simulations of a very simplified ecosystem model. We use the well-known Game of Life to which we add rules simulating both sedimentation forces and thermal agitation. We show that this leads to more active (vitality and biodiversity) and robust (survival) dynamics. This effectively suggests that coupling such physical processes to reactive systems allows the separation of environments into different milieux and could constitute a simple mechanism to form ecosystem frontiers or elementary interfaces that would protect and favour the development of fragile auto-poietic systems.

Prebiotic Lipidic Amphiphiles and Condensing Agents on the Early Earth

It is still uncertain how the first minimal cellular systems evolved to the complexity required for life to begin, but it is obvious that the role of amphiphilic compounds in the origin of life is one of huge relevance. Over the last four decades a number of studies have demonstrated how amphiphilic molecules can be synthesized under plausibly prebiotic conditions. The majority of these experiments also gave evidence for the ability of so formed amphiphiles to assemble in closed membranes of vesicles that, in principle, could have compartmented first biological processes on early Earth, including the emergence of self-replicating systems. For a competitive selection of the best performing molecular replicators to become operative, some kind of bounded units capable of harboring them are indispensable. Without the competition between dynamic populations of different compartments, life itself could not be distinguished from an otherwise disparate array or network of molecular interactions. In this review, we describe experiments that demonstrate how different prebiotically-available building blocks can become precursors of phospholipids that form vesicles. We discuss the experimental conditions that resemble plausibly those of the early Earth (or elsewhere) and consider the analytical methods that were used to characterize synthetic products. Two brief sections focus on phosphorylating agents, catalysts and coupling agents with particular attention given to their geochemical context. In Section 5, we describe how condensing agents such as cyanamide and urea can promote the abiotic synthesis of phospholipids. We conclude the review by reflecting on future studies of phospholipid compartments, particularly, on evolvable chemical systems that include giant vesicles composed of different lipidic amphiphiles.

Primordial evolvability: Impasses and challenges

While it is generally agreed that some kind of replicating non-living compounds were the precursors of life, there is much debate over their possible chemical nature. Metabolism-first approaches propose that mutually catalytic sets of simple organic molecules could be capable of self-replication and rudimentary chemical evolution. In particular, the graded autocatalysis replication domain (GARD) model, depicting assemblies of amphiphilic molecules, has received considerable interest. The system propagates compositional information across generations and is suggested to be a target of natural selection. However, evolutionary simulations indicate that the system lacks selectability (i.e. selection has negligible effect on the equilibrium concentrations). We elaborate on the lessons learnt from the example of the GARD model and, more widely, on the issue of evolvability, and discuss the implications for similar metabolism-first scenarios. We found that simple incorporation-type chemistry based on non-covalent bonds, as assumed in GARD, is unlikely to result in alternative autocatalytic cycles when catalytic interactions are randomly distributed. An even more serious problem stems from the lognormal distribution of catalytic factors, causing inherent kinetic instability of such loops, due to the dominance of efficiently catalyzed components that fail to return catalytic aid. Accordingly, the dynamics of the GARD model is dominated by strongly catalytic, but not auto-catalytic, molecules. Without effective autocatalysis, stable hereditary propagation is not possible. Many repetitions and different scaling of the model come to no rescue. Despite all attempts to show the contrary, the GARD model is not evolvable, in contrast to reflexively autocatalytic networks, complemented by rare uncatalyzed reactions and compartmentation. The latter networks, resting on the creation and breakage of chemical bonds, can generate novel ('mutant') autocatalytic loops from a given set of environmentally available compounds. Real chemical reactions that make or break covalent bonds, rather than mere incorporation of components, are necessary for open-ended evolvability. The issue of whether or not several concrete chemical systems (rather than singular curiosities) could realize reflexively autocatalytic macromolecular networks will ultimately determine the relevance of metabolism-first approaches to the origin of life, as stepping stones towards true open-endedness that requires the combination of rich combinatorial chemistry controlled by information stored in template replicators.

Emergence of life: Physical chemistry changes the paradigm

Origin of life research has been slow to advance not only because of its complex evolutionary nature (Franklin Harold: In Search of Cell History, 2014) but also because of the lack of agreement on fundamental concepts, including the question of ‘what is life?’. To re-energize the research and define a new experimental paradigm, we advance four premises to better understand the physicochemical complexities of life’s emergence:

Chemical and Darwinian (biological) evolutions are distinct, but become continuous with the appearance of heredity.

Earth’s chemical evolution is driven by energies of cycling (diurnal) disequilibria and by energies of hydrothermal vents.

Earth’s overall chemical complexity must be high at the origin of life for a subset of (complex) chemicals to phase separate and evolve into living states.

Macromolecular crowding in aqueous electrolytes under confined conditions enables evolution of molecular recognition and cellular self-organization.

We discuss these premises in relation to current ‘constructive’ (non-evolutionary) paradigm of origins research – the process of complexification of chemical matter ‘from the simple to the complex’. This paradigm artificially avoids planetary chemical complexity and the natural tendency of molecular compositions toward maximum disorder embodied in the second law of thermodynamics. Our four premises suggest an empirical program of experiments involving complex chemical compositions under cycling gradients of temperature, water activity and electromagnetic radiation.

Why do bacteria divide?

The problem of not only how but also why cells divide can be tackled using recent ideas. One idea from the origins of life – Life as independent of its constituents – is that a living entity like a cell is a particular pattern of connectivity between its constituents. This means that if the growing cell were just to get bigger the average connectivity between its constituents per unit mass – its cellular connectivity – would decrease and the cell would lose its identity. The solution is division which restores connectivity. The corollary is that the cell senses decreasing cellular connectivity and uses this information to trigger division. A second idea from phenotypic diversity – Life on the Scales of Equilibria – is that a bacterium must find strategies that allow it to both survive and grow. This means that it has learnt to reconcile the opposing constraints that these strategies impose. The solution is that the cell cycle generates daughter cells with different phenotypes based on sufficiently complex equilibrium (E) and non-equilibrium (NE) cellular compounds and structures appropriate for survival and growth, respectively, alias ‘hyperstructures.’ The corollary is that the cell senses both the quantity of E material and the intensity of use of NE material and then uses this information to trigger the cell cycle. A third idea from artificial intelligence – Competitive Coherence – is that a cell selects the active subset of elements that actively determine its phenotype from a much larger set of available elements. This means that the selection of an active subset of a specific size and composition must be done so as to generate both a coherent cell state, in which the cell’s contents work together harmoniously, and a coherent sequence of cell states, each coherent with respect to itself and to an unpredictable environment. The solution is the use of a range of mechanisms ranging from hyperstructure dynamics to the cell cycle itself.

Quasispecies in population of compositional assemblies

BACKGROUND

The quasispecies model refers to information carriers that undergo self-replication with errors. A quasispecies is a steady-state population of biopolymer sequence variants generated by mutations from a master sequence. A quasispecies error threshold is a minimal replication accuracy below which the population structure breaks down. Theory and experimentation of this model often refer to biopolymers, e.g. RNA molecules or viral genomes, while its prebiotic context is often associated with an RNA world scenario. Here, we study the possibility that compositional entities which code for compositional information, intrinsically different from biopolymers coding for sequential information, could show quasispecies dynamics.

RESULTS

We employed a chemistry-based model, graded autocatalysis replication domain (GARD), which simulates the network dynamics within compositional molecular assemblies. In GARD, a compotype represents a population of similar assemblies that constitute a quasi-stationary state in compositional space. A compotype's center-of-mass is found to be analogous to a master sequence for a sequential quasispecies. Using single-cycle GARD dynamics, we measured the quasispecies transition matrix (Q) for the probabilities of transition from one center-of-mass Euclidean distance to another. Similarly, the quasispecies' growth rate vector (A) was obtained. This allowed computing a steady state distribution of distances to the center of mass, as derived from the quasispecies equation. In parallel, a steady state distribution was obtained via the GARD equation kinetics. Rewardingly, a significant correlation was observed between the distributions obtained by these two methods. This was only seen for distances to the compotype center-of-mass, and not to randomly selected compositions. A similar correspondence was found when comparing the quasispecies time dependent dynamics towards steady state. Further, changing the error rate by modifying basal assembly joining rate of GARD kinetics was found to display an error catastrophe, similar to the standard quasispecies model. Additional augmentation of compositional mutations leads to the complete disappearance of the master-like composition.

CONCLUSIONS

Our results show that compositional assemblies, as simulated by the GARD formalism, portray significant attributes of quasispecies dynamics. This expands the applicability of the quasispecies model beyond sequence-based entities, and potentially enhances validity of GARD as a model for prebiotic evolution.

Looked at life from both sides now

As the molecular top–down causality emerging through comparative genomics is combined with the bottom–up dynamic chemical networks of biochemistry, the molecular symbiotic relationships driving growth of the tree of life becomes strikingly apparent. These symbioses can be mutualistic or parasitic across many levels, but most foundational is the complex and intricate mutualism of nucleic acids and proteins known as the central dogma of biological information flow. This unification of digital and analog molecular information within a common chemical network enables processing of the vast amounts of information necessary for cellular life. Here we consider the molecular information pathways of these dynamic biopolymer networks from the perspective of their evolution and use that perspective to inform and constrain pathways for the construction of mutualistic polymers.

The ribosome as a missing link in the evolution of life

Many steps in the evolution of cellular life are still mysterious. We suggest that the ribosome may represent one important missing link between compositional (or metabolism-first), RNA-world (or genes-first) and cellular (last universal common ancestor) approaches to the evolution of cells. We present evidence that the entire set of transfer RNAs for all twenty amino acids are encoded in both the 16S and 23S rRNAs of Escherichia coli K12; that nucleotide sequences that could encode key fragments of ribosomal proteins, polymerases, ligases, synthetases, and phosphatases are to be found in each of the six possible reading frames of the 16S and 23S rRNAs; and that every sequence of bases in rRNA has information encoding more than one of these functions in addition to acting as a structural component of the ribosome. Ribosomal RNA, in short, is not just a structural scaffold for proteins, but the vestigial remnant of a primordial genome that may have encoded a self-organizing, self-replicating, auto-catalytic intermediary between macromolecules and cellular life.

Molecular complementarity between simple, universal molecules and ions limited phenotype space in the precursors of cells

Background

Fundamental problems faced by the protocells and their modern descendants include how to go from one phenotypic state to another; escape from a basin of attraction in the space of phenotypes; reconcile conflicting growth and survival strategies (and thereby live on ‘the scales of equilibria’); and create a coherent, reproducible phenotype from a multitude of constituents.

Presentation of the hypothesis

The solutions to these problems are likely to be found with the organic and inorganic molecules and inorganic ions that constituted protocells, which we term SUMIs for Simple Universal Molecules and Ions. These SUMIs probably included polyphosphate (PolyP) as a source of energy and of phosphate; poly-(R)-3-hydroxybutyrate (PHB) as a source of carbon and as a transporter in association with PolyP; polyamines as a source of nitrogen; lipids as precursors of membranes; as well as peptides, nucleic acids, and calcium. Here, we explore the hypothesis that the direct interactions between PHB, PolyP, polyamines and lipids – modulated by calcium – played a central role in solving the fundamental problems faced by early and modern cells.

Testing the hypothesis

We review evidence that SUMIs (1) were abundant and available to protocells; (2) are widespread in modern cells; (3) interact with one another and other cellular constituents to create structures with new functions surprisingly similar to those of proteins and RNA; (4) are essential to creating coherent phenotypes in modern bacteria. SUMIs are therefore natural candidates for reducing the immensity of phenotype space and making the transition from a “primordial soup” to living cells.

Implications of the hypothesis

We discuss the relevance of the SUMIs and their interactions to the ideas of molecular complementarity, composomes (molecular aggregates with hereditary properties based on molecular complementarity), and a prebiotic ecology of co-evolving populations of composomes. In particular, we propose that SUMIs might limit the initial phenotype space of composomes in a coherent way. As examples, we propose that acidocalcisomes arose from interactions and self-selection among SUMIs and that the phosphorylation of proteins in modern cells had its origin in the covalent modification of proteins by PHB.

Reviewers

This article was reviewed by Doron Lancet and Kepa Ruiz-Mirazo.

What properties of life are universal? Substance-free, scale-free life

One approach to answering the question of what properties of life are universal is to try to answer the question of what are the essential properties of biology's best understood model organism, Escherichia coli. One of these properties is competitive coherence whereby E. coli reconciles the generation of a coherent cell state with the generation of a coherent sequence of cell states. The second property is differentiation which occurs ineluctably when E. coli divides. The third property is dualism which is how E. coli navigates between the two main attractors of phenotypes - survival and growth - which are based on quasi-equilibrium and non-equilibrium structures, respectively. The fourth property is complementarity: the interactions between the molecules and macromolecules that constitute E. coli protect them from degradation and confer new properties. The fifth property is multi-scale existence: E. coli exists at levels extending from the bacterium to the global super-organism. The sixth property is maintenance of connectivity; growth alters connectivity and, in the case of E. coli, alters the phenotype. The seventh property is the combination of intensity sensing (the constituents can work no harder) and quantity sensing (too much unused material has been made); this combination is used by E. coli to drive its cell cycle and thereby generate an environmentally adapted population of cells. The eighth property is subjective experience which exists even at the level of a single E. coli but which only becomes important at higher levels of organisation. I propose that the search for life at other times and in other places be based on the above eight universal properties and be independent of both particular substances and spatio-temporal scales.

New approaches to the problem of generating coherent, reproducible phenotypes

Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. Both competitive coherence and life on the scales deal with the problem of reconciling conflicting constraints. Here, we bring together these concepts in the common framework of hyperstructures and make predictions that may be tested using a learning program, Coco, and secondary ion mass spectrometry.

Plasmids as scribbling pads for operon formation and propagation

Many bacterial genes are in operons and the process whereby operons are formed is therefore fundamental. To help elucidate this process, we propose in the Scribbling Pad hypothesis that bacteria have been constantly using plasmids for genetic experimentation and, in particular, for the construction of operons. This hypothesis simultaneously solves the problems of the creation of operons and the way operons are propagated. We cite results in the literature to support the hypothesis and make experimental predictions to test it.

Sensor potency of the moonlighting enzyme-decorated cytoskeleton: the cytoskeleton as a metabolic sensor

Background

There is extensive evidence for the interaction of metabolic enzymes with the eukaryotic cytoskeleton. The significance of these interactions is far from clear.

Presentation of the hypothesis

In the cytoskeletal integrative sensor hypothesis presented here, the cytoskeleton senses and integrates the general metabolic activity of the cell. This activity depends on the binding to the cytoskeleton of enzymes and, depending on the nature of the enzyme, this binding may occur if the enzyme is either active or inactive but not both. This enzyme-binding is further proposed to stabilize microtubules and microfilaments and to alter rates of GTP and ATP hydrolysis and their levels.

Testing the hypothesis

Evidence consistent with the cytoskeletal integrative sensor hypothesis is presented in the case of glycolysis. Several testable predictions are made. There should be a relationship between post-translational modifications of tubulin and of actin and their interaction with metabolic enzymes. Different conditions of cytoskeletal dynamics and enzyme-cytoskeleton binding should reveal significant differences in local and perhaps global levels and ratios of ATP and GTP. The different functions of moonlighting enzymes should depend on cytoskeletal binding.

Implications of the hypothesis

The physical and chemical effects arising from metabolic sensing by the cytoskeleton would have major consequences on cell shape, dynamics and cell cycle progression. The hypothesis provides a framework that helps the significance of the enzyme-decorated cytoskeleton be determined.

A modular hierarchy-based theory of the chemical origins of life based on molecular complementarity

Albert Szent-Gyorgyi once defined discovery as seeing what everyone else sees and thinking what no one else thinks. I often find that phenomena that are obvious to other people are not obvious to me. Molecular complementarity is one of these phenomena: while rare among any random set of compounds, it is ubiquitous in living systems. Because every molecule in a living system binds more or less specifically to several others, we now speak of "interactomes". What explains the ubiquity of molecular complementarity in living systems? What might such an explanation reveal about the chemical origins of life and the principles that have governed its evolution? Beyond this, what might complementarity tell us about the optimization of integrated systems in general? My research combines theoretical and experimental approaches to molecular complementarity relating to evolution from prebiotic chemical systems to superorganismal interactions. Experimentally, I have characterized complementarity involving specific binding between small molecules and explored how these small-molecule modules have been incorporated into macromolecular systems such as receptors and transporters. Several general principles have emerged from this research. Molecules that bind to each other almost always alter each other's physiological effects; and conversely, molecules that have antagonistic or synergistic physiological effects almost always bind to each other. This principle suggests a chemical link between biological structure and function. Secondly, modern biological systems contain an embedded molecular paleontology based on complementarity that can reveal their chemical origins. This molecular paleontology is often manifested through modules involving small, molecularly complementary subunits that are built into modern macromolecular structures such as receptors and transporters. A third principle is that complementary modules are conserved and repurposed at every stage of evolution. Molecular complementarity plays critical roles in the evolution of chemical systems and resolves a significant number of outstanding problems in the emergence of complex systems. All physical and mathematical models of organization within complex systems rely upon nonrandom linkage between components. Molecular complementarity provides a naturally occurring nonrandom linker. More importantly, the formation of hierarchically organized stable modules vastly improves the probability of achieving self-organization, and molecular complementarity provides a mechanism by which hierarchically organized stable modules can form. Finally, modularity based on molecular complementarity produces a means for storing and replicating information. Linear replicating molecules such as DNA or RNA are not required to transmit information from one generation of compounds to the next: compositional replication is as ubiquitous in living systems as genetic replication and is equally important to its functions. Chemical systems composed of complementary modules mediate this compositional replication and gave rise to linear replication schemes. In sum, I propose that molecular complementarity is ubiquitous in living systems because it provides the physicochemical basis for modular, hierarchical ordering and replication necessary for the evolution of the chemical systems upon which life is based. I conjecture that complementarity more generally is an essential agent that mediates evolution at every level of organization.

Chromosome Replication in Escherichia coli: Life on the Scales

At all levels of Life, systems evolve on the 'scales of equilibria'. At the level of bacteria, the individual cell must favor one of two opposing strategies and either take risks to grow or avoid risks to survive. It has been proposed in the Dualism hypothesis that the growth and survival strategies depend on non-equilibrium and equilibrium hyperstructures, respectively. It has been further proposed that the cell cycle itself is the way cells manage to balance the ratios of these types of hyperstructure so as to achieve the compromise solution of living on the two scales. Here, we attempt to re-interpret a major event, the initiation of chromosome replication in Escherichia coli, in the light of scales of equilibria. This entails thinking in terms of hyperstructures as responsible for intensity sensing and quantity sensing and how this sensing might help explain the role of the DnaA protein in initiation of replication. We outline experiments and an automaton approach to the cell cycle that should test and refine the scales concept.

Field-Control, Phase-Transitions, and Life's Emergence

Instances of critical-like characteristics in living systems at each organizational level (bio-molecules to ecosystems) as well as the spontaneous emergence of computation (Langton), do suggest the relevance of self-organized criticality (SOC). But extrapolating complex bio-systems to life's origins, brings up a paradox: how could simple organics - lacking the "soft-matter" response properties of today's complex bio-molecules - have dissipated energy from primordial reactions (eventually reducing CO(2)) in a controlled manner for their "ordering"? Nevertheless, a causal link of life's macroscopic irreversible dynamics to the microscopic reversible laws of statistical mechanics is indicated via the "functional-takeover" of a soft magnetic scaffold by organics (c.f. Cairns-Smith's "crystal-scaffold"). A field-controlled structure offers a mechanism for boot-strapping - bottom-up assembly with top-down control: its super-paramagnetic colloidal components obey reversible dynamics, but its dissipation of magnetic (H)-field energy for aggregation breaks time-reversal symmetry. The responsive adjustments of the controlled (host) mineral system to environmental changes would bring about mutual coupling between random organic sets supported by it; here the generation of long-range correlations within organic (guest) networks could include SOC-like mechanisms. And, such cooperative adjustments enable the selection of the functional configuration by altering the inorganic dipolar network's capacity to assist a spontaneous process. A non-equilibrium dynamics could now drive the kinetically oriented system (trimming the phase-space via sterically coupled organics) toward a series of phase-transitions with appropriate organic replacements "taking-over" its functions. Where available, experiments are cited in support of these speculations and for designing appropriate tests.

How did metabolism and genetic replication get married?

In addressing the question of the origins of the relationship between metabolism and genetic replication, we consider the implications of a prebiotic, fission-fusion, ecology of composomes. We emphasise the importance of structures and non-specific catalysis on interfaces created by structures. From the assumption that the bells of the metabolism-replication wedding still echo in modern cells, we argue that the functional assemblies of macromolecules that constitute hyperstructures in modern bacteria are the descendants of composomes and that interactions at the hyperstructure level control the cell cycle. A better understanding of the cell cycle should help understand the original metabolism-replication marriage. This understanding requires new concepts such as metabolic signalling, metabolic sensing and Dualism, which entails the cells in a population varying the ratios of equilibrium to non-equilibrium hyperstructures so as to maximise the chances of both survival and growth. A deeper understanding of the coupling between metabolism and replication may also require a new view of cell cycle functions in creating a coherent diversity of phenotypes and in narrowing the combinatorial catalytic space. To take these ideas into account, we propose the Accordion model in which a dynamic interface between lipid domains catalysed monomer to polymer reactions and became decorated with peptides and nucleotides that favoured their own catalysis. In this model, metabolism, replication, differentiation and division all began together at the interface between extended equilibrium structures within protocells or composomes.

Excess mutual catalysis is required for effective evolvability

It is widely accepted that autocatalysis constitutes a crucial facet of effective replication and evolution (e.g., in Eigen's hypercycle model). Other models for early evolution (e.g., by Dyson, Gánti, Varela, and Kauffman) invoke catalytic networks, where cross-catalysis is more apparent. A key question is how the balance between auto- (self-) and cross- (mutual) catalysis shapes the behavior of model evolving systems. This is investigated using the graded autocatalysis replication domain (GARD) model, previously shown to capture essential features of reproduction, mutation, and evolution in compositional molecular assemblies. We have performed numerical simulations of an ensemble of GARD networks, each with a different set of lognormally distributed catalytic values. We asked what is the influence of the catalytic content of such networks on beneficial evolution. Importantly, a clear trend was observed, wherein only networks with high mutual catalysis propensity (p(mc)) allowed for an augmented diversity of composomes, quasi-stationary compositions that exhibit high replication fidelity. We have reexamined a recent analysis that showed meager selection in a single GARD instance and for a few nonstationary target compositions. In contrast, when we focused here on compotypes (clusters of composomes) as targets for selection in populations of compositional assemblies, appreciable selection response was observed for a large portion of the networks simulated. Further, stronger selection response was seen for high p(mc) values. Our simulations thus demonstrate that GARD can help analyze important facets of evolving systems, and indicate that excess mutual catalysis over self-catalysis is likely to be important for the emergence of molecular systems capable of evolutionlike behavior.

Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life

This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

Evolution before genes

Background

Our current understanding of evolution is so tightly linked to template-dependent replication of DNA and RNA molecules that the old idea from Oparin of a self-reproducing 'garbage bag' ('coacervate') of chemicals that predated fully-fledged cell-like entities seems to be farfetched to most scientists today. However, this is exactly the kind of scheme we propose for how Darwinian evolution could have occurred prior to template replication.

Results

We cannot confirm previous claims that autocatalytic sets of organic polymer molecules could undergo evolution in any interesting sense by themselves. While we and others have previously imagined inhibition would result in selectability, we found that it produced multiple attractors in an autocatalytic set that cannot be selected for. Instead, we discovered that if general conditions are satisfied, the accumulation of adaptations in chemical reaction networks can occur. These conditions are the existence of rare reactions producing viable cores (analogous to a genotype), that sustains a molecular periphery (analogous to a phenotype).

Conclusions

We conclude that only when a chemical reaction network consists of many such viable cores, can it be evolvable. When many cores are enclosed in a compartment there is competition between cores within the same compartment, and when there are many compartments, there is between-compartment competition due to the phenotypic effects of cores and their periphery at the compartment level. Acquisition of cores by rare chemical events, and loss of cores at division, allows macromutation, limited heredity and selectability, thus explaining how a poor man's natural selection could have operated prior to genetic templates. This is the only demonstration to date of a mechanism by which pre-template accumulation of adaptation could occur.

Reviewers

This article was reviewed by William Martin and Eugene Koonin.

DNA movies and panspermia

There are several ways that our species might try to send a message to another species separated from us by space and/or time. Synthetic biology might be used to write an epitaph to our species, or simply “Kilroy was here”, in the genome of a bacterium via the patterns of either (1) the codons to exploit Life's non-equilibrium character or (2) the bases themselves to exploit Life's quasi-equilibrium character. We suggest here how DNA movies might be designed using such patterns. We also suggest that a search for mechanisms to create and preserve such patterns might lead to a better understanding of modern cells. Finally, we argue that the cutting-edge microbiology and synthetic biology needed for the Kilroy project would put origin-of-life studies in the vanguard of research.