Systems protobiology: origin of life in lipid catalytic networks

Turbulent coherent structures and early life below the Kolmogorov scale

Major evolutionary transitions, including the emergence of life, likely occurred in aqueous environments. While the role of water’s chemistry in early life is well studied, the effects of water’s ability to manipulate population structure are less clear. Population structure is known to be critical, as effective replicators must be insulated from parasites. Here, we propose that turbulent coherent structures, long-lasting flow patterns which trap particles, may serve many of the properties associated with compartments — collocalization, division, and merging — which are commonly thought to play a key role in the origins of life and other evolutionary transitions. We substantiate this idea by simulating multiple proposed metabolisms for early life in a simple model of a turbulent flow, and find that balancing the turnover times of biological particles and coherent structures can indeed enhance the likelihood of these metabolisms overcoming extinction either via parasitism or via a lack of metabolic support. Our results suggest that group selection models may be applicable with fewer physical and chemical constraints than previously thought, and apply much more widely in aqueous environments.

Models of the origin of life generally require a mechanism to structure emerging populations. Here, Krieger et al. develop spatial models showing that coherent structures arising in turbulent flows in aquatic environments could have provided compartments that facilitated the origin of life.

Footprints of a Singular 22-Nucleotide RNA Ring at the Origin of Life

(1) Background: Previous experimental observations and theoretical hypotheses have been providing insight into a hypothetical world where an RNA hairpin or ring may have debuted as the primary informational and functional molecule. We propose a model revisiting the architecture of RNA-peptide interactions at the origin of life through the evolutionary dynamics of RNA populations. (2) Methods: By performing a step-by-step computation of the smallest possible hairpin/ring RNA sequences compatible with building up a variety of peptides of the primitive network, we inferred the sequence of a singular docosameric RNA molecule, we call the ALPHA sequence. Then, we searched for any relics of the peptides made from ALPHA in sequences deposited in the different public databases. (3) Results: Sequence matching between ALPHA and sequences from organisms among the earliest forms of life on Earth were found at high statistical relevance. We hypothesize that the frequency of appearance of relics from ALPHA sequence in present genomes has a functional necessity. (4) Conclusions: Given the fitness of ALPHA as a supportive sequence of the framework of all existing theories, and the evolution of Archaea and giant viruses, it is anticipated that the unique properties of this singular archetypal ALPHA sequence should prove useful as a model matrix for future applications, ranging from synthetic biology to DNA computing.

Molecules to Microbes

How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.

Compositional heterogeneity confers selective advantage to model protocellular membranes during the origins of cellular life

Protocellular membranes are thought to be composed of mixtures of single chain amphiphiles, such as fatty acids and their derivatives, moieties that would have been part of the complex prebiotic chemical landscape. The composition and physico-chemical properties of these prebiological membranes would have been significantly affected and regulated by their environment. In this study, pertinent properties were systematically characterized, under early Earth conditions. Two different fatty acids were mixed with their respective alcohol and/or glycerol monoester derivatives to generate combinations of binary and tertiary membrane systems. Their properties were then evaluated as a function of multiple factors including their stability under varying pH, varying Mg²⁺ ion concentrations, dilution regimes, and their permeability to calcein. Our results demonstrate how environmental constraints would have acted as important prebiotic selection pressures to shape the evolution of prebiological membranes. The study also illustrates that compositionally diverse membrane systems are more stable and robust to multiple selection pressures, thereby making them more suitable for supporting protocellular life.

Origin of viruses: primordial replicators recruiting capsids from hosts

Viruses are ubiquitous parasites of cellular life and the most abundant biological entities on Earth. It is widely accepted that viruses are polyphyletic, but a consensus scenario for their ultimate origin is still lacking. Traditionally, three scenarios for the origin of viruses have been considered: descent from primordial, precellular genetic elements, reductive evolution from cellular ancestors and escape of genes from cellular hosts, achieving partial replicative autonomy and becoming parasitic genetic elements. These classical scenarios give different timelines for the origin(s) of viruses and do not explain the provenance of the two key functional modules that are responsible, respectively, for viral genome replication and virion morphogenesis. Here, we outline a 'chimeric' scenario under which different types of primordial, selfish replicons gave rise to viruses by recruiting host proteins for virion formation. We also propose that new groups of viruses have repeatedly emerged at all stages of the evolution of life, often through the displacement of ancestral structural and genome replication genes.

The generality of transient compartmentalization and its associated error thresholds

Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the presence of mutations and noise in replication, as both can be detrimental the survival of compartments. Our study comprises situations where compartments contain uncoupled autocatalytic reactions feeding on a common resource, and systems based on RNA molecules copied by replicases, following a recent experimental study. Using the theory of branching processes, we show analytically that two regimes are possible. In the diffusion-limited regime, replication is asynchronous which leads to a large variability in the composition of compartments. In contrast, in a replication-limited regime, the growth is synchronous and thus the compositional variability is low. Typically, simple autocatalysts are in the former regime, while polymeric replicators can access the latter. For deterministic growth dynamics, we introduce mutations that turn functional replicators into parasites. We derive the phase boundary separating coexistence or parasite dominance as a function of relative growth, inoculation size and mutation rate. We show that transient compartmentalization allows coexistence beyond the classical error threshold, above which the parasite dominates. Our findings invite to revisit major prebiotic transitions, notably the transitions towards cooperation, complex polymers and cell division.

Polyesters as a Model System for Building Primitive Biologies from Non-Biological Prebiotic Chemistry

A variety of organic chemicals were likely available on prebiotic Earth. These derived from diverse processes including atmospheric and geochemical synthesis and extraterrestrial input, and were delivered to environments including oceans, lakes, and subaerial hot springs. Prebiotic chemistry generates both molecules used by modern organisms, such as proteinaceous amino acids, as well as many molecule types not used in biochemistry. As prebiotic chemical diversity was likely high, and the core of biochemistry uses a rather small set of common building blocks, the majority of prebiotically available organic compounds may not have been those used in modern biochemistry. Chemical evolution was unlikely to have been able to discriminate which molecules would eventually be used in biology, and instead, interactions among compounds were governed simply by abundance and chemical reactivity. Previous work has shown that likely prebiotically available α-hydroxy acids can combinatorially polymerize into polyesters that self-assemble to create new phases which are able to compartmentalize other molecule types. The unexpectedly rich complexity of hydroxy acid chemistry and the likely enormous structural diversity of prebiotic organic chemistry suggests chemical evolution could have been heavily influenced by molecules not used in contemporary biochemistry, and that there is a considerable amount of prebiotic chemistry which remains unexplored.

Selection from a pool of self-assembling lipid replicators

Replication and compartmentalization are fundamental to living systems and may have played important roles in life’s origins. Selection in compartmentalized autocatalytic systems might provide a way for evolution to occur and for life to arise from non-living systems. Herein we report selection in a system of self-reproducing lipids where a predominant species can emerge from a pool of competitors. The lipid replicators are metastable and their out-of-equilibrium population can be sustained by feeding the system with starting materials. Phase separation is crucial for selective surfactant formation as well as autocatalytic kinetics; indeed, no selection is observed when all reacting species are dissolved in the same phase. Selectivity is attributed to a kinetically controlled process where the rate of monomer formation determines which replicator building blocks are the fittest. This work reveals how kinetics of a phase-separated autocatalytic reaction may be used to control the population of out-of-equilibrium replicators in time.

Selection in compartmentalized self-replicating systems might provide a way for life to arise from abiotic environments. Here, the authors explore selection in a system of transient autocatalytic lipids and find that autocatalytic kinetics and phase separation are the key selection factors.

Introduction to virus origins and their role in biological evolution

Viruses are diverse parasites of cells and extremely abundant. They might have arisen during an early phase of the evolution of life on Earth dominated by ribonucleic acid or RNA-like macromolecules, or when a cellular world was already well established. The theories of the origin of life on Earth shed light on the possible origin of primitive viruses or virus-like genetic elements in our biosphere. Some features of present-day viruses, notably error-prone replication, might be a consequence of the selective forces that mediated their ancestral origin. Two views on the role of viruses in our biosphere predominate; viruses considered as opportunistic, selfish elements, and viruses considered as active participants in the construction of the cellular world via the lateral transfer of genes. These two models have a bearing on viruses being considered predominantly as disease agents or predominantly as cooperators in the shaping of differentiated cellular organisms.

Membranes Composed of Lipopeptides and Liponucleobases Inspired Protolife Evolution

Amino acids and peptides have been demonstrated to form lipoamino acids and lipopeptides under presumed prebiotic conditions, and readily form liposomes. Of the common nucleobases, adenine forms a liponucleobase even below 100 °C. Adenine as well as other nucleobases can also be derivatized with ethylene carbonate (and likely other similar compounds) onto which fatty acids can be attached. The fatty acid tails along with appropriately functionalized nucleobases provide some solubility of liponucleobases in membranes. Such membranes would provide a structure in which three of biology's major components are closely associated and available for chemical interactions. Nucleobase-to-nucleobase interactions would ensure that the liponucleobases would have a uniquely different head-group relationship than other amphiphiles within a membrane, likely forming rafts due their π-π interactions and providing surface discontinuities that could serve as catalytic sites. The π-π bond distance in aromatic compounds is typically 0.34 nm, commensurate with that of the amine to carboxylate distance in alpha amino acids. This would have provided opportunity for hydrogen bonding between amino acids and the distal primary amines or tautomeric carbonyl/hydroxyl groups of two π-bonded nucleobases. Such bonding would weaken the covalent linkages within the amino acids, making them susceptible to forming peptide bonds with an adjacent amino acid, likely a lipoamino acid or lipopeptide. Were this second lipoamino acid bound to a third π-bonded nucleobase, it could result in orientation, destabilization and peptide formation. The stacked triplet of nucleobases might constitute the primordial codon triplet from which peptides were synthesized: primordial translation.

Membrane Lipid Composition and Amino Acid Excretion Patterns of Methanothermococcus okinawensis Grown in the Presence of Inhibitors Detected in the Enceladian Plume

Lipids and amino acids are regarded as important biomarkers for the search for extraterrestrial life in the Solar System. Such biomarkers may be used to trace methanogenic life on other planets or moons in the Solar System, such as Saturn's icy moon Enceladus. However, little is known about the environmental conditions shaping the synthesis of lipids and amino acids. Here, we present the lipid production and amino acid excretion patterns of the methanogenic archaeon Methanothermococcus okinawensis after exposing it to different multivariate concentrations of the inhibitors ammonium, formaldehyde, and methanol present in the Enceladian plume. M. okinawensis shows different patterns of lipid and amino acids excretion, depending on the amount of these inhibitors in the growth medium. While methanol did not show a significant impact on growth, lipid or amino acid production rates, ammonium and formaldehyde strongly affected these parameters. These findings are important for understanding the eco-physiology of methanogens on Earth and have implications for the use of biomarkers as possible signs of extraterrestrial life for future space missions in the Solar System.

The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold.

Probing complexity: thermodynamics and computational mechanics approaches to origins studies

This paper proposes new avenues for origins research that apply modern concepts from stochastic thermodynamics, information thermodynamics and complexity science. Most approaches to the emergence of life prioritize certain compounds, reaction pathways, environments or phenomena. What they all have in common is the objective of reaching a state that is recognizably alive, usually positing the need for an evolutionary process. As with life itself, this correlates with a growth in the complexity of the system over time. Complexity often takes the form of an intuition or a proxy for a phenomenon that defies complete understanding. However, recent progress in several theoretical fields allows the rigorous computation of complexity. We thus propose that measurement and control of the complexity and information content of origins-relevant systems can provide novel insights that are absent in other approaches. Since we have no guarantee that the earliest forms of life (or alien life) used the same materials and processes as extant life, an appeal to complexity and information processing provides a more objective and agnostic approach to the search for life's beginnings. This paper gives an accessible overview of the three relevant branches of modern thermodynamics. These frameworks are not commonly applied in origins studies, but are ideally suited to the analysis of such non-equilibrium systems. We present proposals for the application of these concepts in both theoretical and experimental origins settings.

Survival of Self-Replicating Molecules under Transient Compartmentalization with Natural Selection

The problem of the emergence and survival of self-replicating molecules in origin-of-life scenarios is plagued by the error catastrophe, which is usually escaped by considering effects of compartmentalization, as in the stochastic corrector model. By addressing the problem in a simple system composed of a self-replicating molecule (a replicase) and a parasite molecule that needs the replicase for copying itself, we show that transient (rather than permanent) compartmentalization is sufficient to the task. We also exhibit a regime in which the concentrations of the two kinds of molecules undergo sustained oscillations. Our model should be relevant not only for origin-of-life scenarios but also for describing directed evolution experiments, which increasingly rely on transient compartmentalization with pooling and natural selection.

Enceladus: First Observed Primordial Soup Could Arbitrate Origin-of-Life Debate

A recent breakthrough publication has reported complex organic molecules in the plumes emanating from the subglacial water ocean of Saturn's moon Enceladus (Postberg et al., 2018, Nature 558:564-568). Based on detailed chemical scrutiny, the authors invoke primordial or endogenously synthesized carbon-rich monomers (<200 u) and polymers (up to 8000 u). This appears to represent the first reported extraterrestrial organics-rich water body, a conceivable milieu for early steps in life's origin ("prebiotic soup"). One may ask which origin-of-life scenario appears more consistent with the reported molecular configurations on Enceladus. The observed monomeric organics are carbon-rich unsaturated molecules, vastly different from present-day metabolites, amino acids, and nucleotide bases, but quite chemically akin to simple lipids. The organic polymers are proposed to resemble terrestrial insoluble kerogens and humic substances, as well as refractory organic macromolecules found in carbonaceous chondritic meteorites. The authors posit that such polymers, upon long-term hydrous interactions, might break down to micelle-forming amphiphiles. In support of this, published detailed analyses of the Murchison chondrite are dominated by an immense diversity of likely amphiphilic monomers. Our specific quantitative model for compositionally reproducing lipid micelles is amphiphile-based and benefits from a pronounced organic diversity. It thus contrasts with other origin models, which require the presence of very specific building blocks and are expected to be hindered by excess of irrelevant compounds. Thus, the Enceladus finds support the possibility of a pre-RNA Lipid World scenario for life's origin.

Twenty Years of "Lipid World": A Fertile Partnership with David Deamer

"The Lipid World" was published in 2001, stemming from a highly effective collaboration with David Deamer during a sabbatical year 20 years ago at the Weizmann Institute of Science in Israel. The present review paper highlights the benefits of this scientific interaction and assesses the impact of the lipid world paper on the present understanding of the possible roles of amphiphiles and their assemblies in the origin of life. The lipid world is defined as a putative stage in the progression towards life's origin, during which diverse amphiphiles or other spontaneously aggregating small molecules could have concurrently played multiple key roles, including compartment formation, the appearance of mutually catalytic networks, molecular information processing, and the rise of collective self-reproduction and compositional inheritance. This review brings back into a broader perspective some key points originally made in the lipid world paper, stressing the distinction between the widely accepted role of lipids in forming compartments and their expanded capacities as delineated above. In the light of recent advancements, we discussed the topical relevance of the lipid worldview as an alternative to broadly accepted scenarios, and the need for further experimental and computer-based validation of the feasibility and implications of the individual attributes of this point of view. Finally, we point to possible avenues for exploring transition paths from small molecule-based noncovalent structures to more complex biopolymer-containing proto-cellular systems.

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.

Possible Roles of Amphiphilic Molecules in the Origin of Biological Homochirality

A review. The question of homochirality is an intriguing problem in the field of chemistry, and is deeply related to the origin of life. Though amphiphiles and their supramolecular assembly have attracted less attention compared to biomacromolecules such as RNA and proteins, the lipid world hypothesis sheds new light on the origin of life. This review describes how amphiphilic molecules are possibly involved in the scenario of homochirality. Some prebiotic conditions relevant to amphiphilic molecules will also be described. It could be said that the chiral properties of amphiphilic molecules have various interesting features such as compositional information, spontaneous formation, the ability to exchange components, fission and fusion, adsorption, and permeation. This review aims to clarify the roles of amphiphiles regarding homochirality, and to determine what kinds of physical properties of amphiphilic molecules could have played a role in the scenario of homochirality.

Molecules to Microbes

How did life begin on Earth? And is there life elsewhere in the Cosmos? Challenging questions, indeed. The series of conferences established by NoR CEL in 2013, addresses these very same questions. The basis for this paper is the summary report of oral presentations that were delivered by NoR CEL’s network members during the 2018 Athens conference and, as such, disseminates the latest research which they have put forward. More in depth material can be found by consulting the contributors referenced papers. Overall, the outcome of this conspectus on the conference demonstrates a case for the existence of “probable chemistry” during the prebiotic epoch.

Membraneless polyester microdroplets as primordial compartments at the origins of life

Compartmentalization was likely essential for primitive chemical systems during the emergence of life, both for preventing leakage of important components, i.e., genetic materials, and for enhancing chemical reactions. Although life as we know it uses lipid bilayer-based compartments, the diversity of prebiotic chemistry may have enabled primitive living systems to start from other types of boundary systems. Here, we demonstrate membraneless compartmentalization based on prebiotically available organic compounds, α-hydroxy acids (αHAs), which are generally coproduced along with α-amino acids in prebiotic settings. Facile polymerization of αHAs provides a model pathway for the assembly of combinatorially diverse primitive compartments on early Earth. We characterized membraneless microdroplets generated from homo- and heteropolyesters synthesized from drying solutions of αHAs endowed with various side chains. These compartments can preferentially and differentially segregate and compartmentalize fluorescent dyes and fluorescently tagged RNA, providing readily available compartments that could have facilitated chemical evolution by protecting, exchanging, and encapsulating primitive components. Protein function within and RNA function in the presence of certain droplets is also preserved, suggesting the potential relevance of such droplets to various origins of life models. As a lipid amphiphile can also assemble around certain droplets, this further shows the droplets' potential compatibility with and scaffolding ability for nascent biomolecular systems that could have coexisted in complex chemical systems. These model compartments could have been more accessible in a "messy" prebiotic environment, enabling the localization of a variety of protometabolic and replication processes that could be subjected to further chemical evolution before the advent of the Last Universal Common Ancestor.

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.

In search of a primitive signaling code

Cells must have preceded by simpler chemical systems (protocells) that had the capacity of a spontaneous self-assembly process and the ability to confine chemical reaction networks together with a form of information. The presence of lipid molecules in the early Earth conditions is sufficient to ensure the occurrence of spontaneous self-assembly processes, not defined by genetic information, but related to their chemical amphiphilic nature. Ribozymes are plausible molecules for early life, being the first small polynucleotides made up of random oligomers or formed by non-enzymatic template copying. Compartmentalization represents a strategy for the evolution of ribozymes; the attachment of ribozymes to surfaces, such as formed by lipid micellar aggregates may be particular relevant if the surface itself catalyzes RNA polymerization.It is conceivable that the transition from pre-biotic molecular aggregates to cellular life required the coevolution of the RNA world, capable of synthesizing specific, instead of statistical proteins, and of the Lipid world, with a transition from micellar aggregates to semipermeable vesicles. Small molecules available in the prebiotic inventory might promote RNA stability and the evolution of hydrophobic micellar aggregates into membrane-delimited vesicles. The transition from ribozymes catalyzing the assembly of statistical polypeptides to the synthesis of proteins, required the appearance of the genetic code; the transition from hydrophobic platforms favoring the stability of ribozymes and of nascent polypeptides to the selective transport of reagents through a membrane, required the appearance of the signal transduction code.A further integration between the RNA and Lipid worlds can be advanced, taking into account the emerging roles of phospholipid aggregates not only in ensuring stability to ribozymes by compartmentalization, but also in a crucial step of evolution through natural selection mechanisms, based on signal transduction pathways that convert environmental changes into biochemical responses that could vary according to the context. Here I present evidences on the presence of traces of the evolution of a signal transduction system in extant cells, which utilize a phosphoinositide signaling system located both at nucleoplasmic level as well as at the plasma membrane, based on the very same molecules but responding to different rules. The model herewith proposed is based on the following assumptions on the biomolecules of extant organisms: i) amphiphils can be converted into structured aggregates by hydrophobic forces thus giving rise to functional platforms for the interaction of other biomolecules and to their compartmentalization; ii) fundamental biochemical pathways, including protein synthesis, can be sustained by natural ribozymes of ancient origin; iii) ribozymes and nucleotide-derived coenzymes could have existed long before protein enzymes emerged; iv) signaling molecules, both derived from phospholipids and from RNAs could have guided the evolution of complex metabolic processes before the emergence of proteins.

Investigating Prebiotic Protocells for A Comprehensive Understanding of the Origins of Life: A Prebiotic Systems Chemistry Perspective

Protocells are supramolecular systems commonly used for numerous applications, such as the formation of self-evolvable systems, in systems chemistry and synthetic biology. Certain types of protocells imitate plausible prebiotic compartments, such as giant vesicles, that are formed with the hydration of thin films of amphiphiles. These constructs can be studied to address the emergence of life from a non-living chemical network. They are useful tools since they offer the possibility to understand the mechanisms underlying any living cellular system: Its formation, its metabolism, its replication and its evolution. Protocells allow the investigation of the synergies occurring in a web of chemical compounds. This cooperation can explain the transition between chemical (inanimate) and biological systems (living) due to the discoveries of emerging properties. The aim of this review is to provide an overview of relevant concept in prebiotic protocell research.

Towards a General Definition of Life

A new definition of life is proposed and discussed in the present article. It is formulated by modifying and extending NASA's working definition of life, which postulates that life is a "self-sustaining chemical system capable of Darwinian evolution". The new definition includes a thermodynamical aspect of life as a far from equilibrium system and considers the flow of information from the environment to the living system. In our derivation of the definition of life we have assumed the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems that only subsequently acquired the capacity of genetic heredity. The new proposed definition of life is independent of the mode of evolution, regardless of whether Lamarckian or Darwinian evolution operated at the origins of life and throughout evolutionary history. The new definition of life presented herein is formulated in a minimal manner and it is general enough that it does not distinguish between individual (metabolic) network and the collective (ecological) one. The newly proposed definition of life may be of interest for astrobiology, research into the origins of life or for efforts to produce synthetic or artificial life, and it furthermore may also have implications in the cognitive and computer sciences.

Protobiotic Systems Chemistry Analyzed by Molecular Dynamics

Systems chemistry has been a key component of origin of life research, invoking models of life's inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular dynamics has provided an experimental tool to study complex biological phenomena such as protein folding, ligand-receptor interactions, and micellar formation, growth, and fission. The detailed molecular definition of GARD and its inter-molecular catalytic interactions make it highly compatible with molecular dynamics analyses. We present a roadmap for simulating GARD's kinetic and thermodynamic behavior using various molecular dynamics methodologies. We review different approaches for testing the validity of the GARD model by following micellar accretion and fission events and examining compositional changes over time. Near-future computational advances could provide empirical delineation for further system complexification, from simple compositional non-covalent assemblies towards more life-like protocellular entities with covalent chemistry that underlies metabolism and genetic encoding.

Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions

The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible pathway for life emergence, and is by no means be a demonstration of how life really emerged. The best we can hope for is to indicate plausible chemical–physical conditions and mechanisms that might lead to self-organizing and autopoietic systems. Here we present a stochastic simulation, based on chemical reactions already observed in prebiotic environments, that might help in the design of new experiments. We will show how the definition of simple rules for the synthesis of random peptides may lead to the appearance of networks of autocatalytic cycles and the emergence of memory.