The ambivalent role of water at the origins of life

The tri-flow adaptiveness of codes in major evolutionary transitions

Life codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to enduring flow architecture everywhere, in both engineered and natural flow systems. Beginning approximately 4 billion years ago, the most basic level for transmitting genetic material to offspring was initiated by protocell division. Evidence from ribosomes suggests that protocells transmitted comma-free or circular codes, preceding the evolution of standard genetic code. This rudimentary information flow within protocells is likely to have first emerged within the geo-energetic and geospatial constraints of hydrothermal vents. A broad-gauged hypothesis is that major evolutionary transitions overcame such constraints with tri-flow adaptations. The interconnected triple flows incorporated energy-converting, spatiotemporal, and code-based informational dynamics. Such tri-flow adaptations stacked sequence splicing code on top of protein-DNA recognition code in eukaryotes, prefiguring the transition to sexual reproduction. Sex overcame the spatiotemporal-energetic constraints of binary fission with further code stacking. Examples are tubulin code and transcription initiation code in vertebrates. In a later evolutionary transition, language reduced metabolic-spatiotemporal constraints on inheritance by stacking phonetic, phonological, and orthographic codes. In organisms that reproduce sexually, each major evolutionary transition is shown to be a tri-flow adaptation that adds new levels of code-based informational exchange. Evolving biological complexity is also shown to increase the nongenetic transmissibility of code.

Materials Genes of CO2 Hydrogenation on Supported Cobalt Catalysts: An Artificial Intelligence Approach Integrating Theoretical and Experimental Data

Designing materials for catalysis is challenging because the performance is governed by an intricate interplay of various multiscale phenomena, such as the chemical reactions on surfaces and the materials' restructuring during the catalytic process. In the case of supported catalysts, the role of the support material can be also crucial. Here, we address this intricacy challenge by a symbolic-regression artificial intelligence (AI) approach. We identify the key physicochemical parameters correlated with the measured performance, out of many offered candidate parameters characterizing the materials, reaction environment, and possibly relevant underlying phenomena. Importantly, these parameters are obtained by both experiments and ab initio simulations. The identified key parameters might be called "materials genes", in analogy to genes in biology: they correlate with the property or function of interest, but the explicit physical relationship is not (necessarily) known. To demonstrate the approach, we investigate the CO2 hydrogenation catalyzed by cobalt nanoparticles supported on silica. Crucially, the silica support is modified with the additive metals magnesium, calcium, titanium, aluminum, or zirconium, which results in six materials with significantly different performances. These systems mimic hydrothermal vents, which might have produced the first organic molecules on Earth. The key parameters correlated with the CH3OH selectivity reflect the reducibility of cobalt species, the adsorption strength of reaction intermediates, and the chemical nature of the additive metal. By using an AI model trained on basic elemental properties of the additive metals (e.g., ionization potential) as physicochemical parameters, new additives are suggested. The predicted CH3OH selectivity of cobalt catalysts supported on silica modified with vanadium and zinc is confirmed by new experiments.

Enzymic recognition of amino acids drove the evolution of primordial genetic codes

How genetic information gained its exquisite control over chemical processes needed to build living cells remains an enigma. Today, the aminoacyl-tRNA synthetases (AARS) execute the genetic codes in all living systems. But how did the AARS that emerged over three billion years ago as low-specificity, protozymic forms then spawn the full range of highly-specific enzymes that distinguish between 22 diverse amino acids? A phylogenetic reconstruction of extant AARS genes, enhanced by analysing modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades, resulting in a total of 36 families of AARS catalytic domains. Small structural modules that differentiate one AARS family from another played pivotal roles in discriminating between amino acid side chains, thereby expanding the genetic code and refining its precision. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that were not synthesised until later in the evolution of the code. The most probable evolutionary route for an emergent amino acid type to establish a place in the code was by recruiting older, less specific AARS, rather than adapting contemporary lineages. This process, retrofunctionalisation, differs from previously described mechanisms through which amino acids would enter the code.

The Moon-Forming Impact and the Autotrophic Origin of Life

The Moon-forming impact vaporized part of Earth's mantle, and turned the rest into a magma ocean, from which carbon dioxide degassed into the atmosphere, where it stayed until water rained out to form the oceans. The rain dissolved CO2 and made it available to react with transition metal catalysts in the Earth's crust so as to ultimately generate the organic compounds that form the backbone of microbial metabolism. The Moon-forming impact was key in building a planet with the capacity to generate life in that it converted carbon on Earth into a homogeneous and accessible substrate for organic synthesis. Today all ecosystems, without exception, depend upon primary producers, organisms that fix CO2 . According to theories of autotrophic origin, it has always been that way, because autotrophic theories posit that the first forms of life generated all the molecules needed to build a cell from CO2 , forging a direct line of continuity between Earth's initial CO2 -rich atmosphere and the first microorganisms. By modern accounts these were chemolithoautotrophic archaea and bacteria that initially colonized the crust and still inhabit that environment today.

The Role of the CuCl Active Complex in the Stereoselectivity of the Salt-Induced Peptide Formation Reaction: Insights from Density Functional Theory Calculations

The salt-induced peptide formation (SIPF) reaction is a prebiotically plausible mechanism for the spontaneous polymerization of amino acids into peptides on early Earth. Experimental investigations of the SIPF reaction have found that in certain conditions, the l enantiomer is more reactive than the d enantiomer, indicating its potential role in the rise of biohomochirality. Previous work hypothesized that the distortion of the CuCl active complex toward a tetrahedral-like structure increases the central chirality on the Cu ion, which amplifies the inherent parity-violating energy differences between l- and d-amino acid enantiomers, leading to stereoselectivity. Computational evaluations of this theory have been limited to the protonated-neutral l + l forms of the CuCl active complex. Here, density functional theory methods were used to compare the energies and geometries of the homochiral (l + l and d + d) and heterochiral (l + d) CuCl-amino acid complexes for both the positive-neutral and neutral-neutral forms for alanine, valine, and proline. Significant energy differences were not observed between different chiral active complexes (i.e., d + d, l + l vs. l + d), and the distortions of active complexes between stereoselective systems and non-selective systems were not consistent, indicating that the geometry of the active complex is not the primary driver of the observed stereoselectivity of the SIPF reaction.

On the potential roles of phosphorus in the early evolution of energy metabolism

Energy metabolism in extant life is centered around phosphate and the energy-dense phosphoanhydride bonds of adenosine triphosphate (ATP), a deeply conserved and ancient bioenergetic system. Yet, ATP synthesis relies on numerous complex enzymes and has an autocatalytic requirement for ATP itself. This implies the existence of evolutionarily simpler bioenergetic pathways and potentially primordial alternatives to ATP. The centrality of phosphate in modern bioenergetics, coupled with the energetic properties of phosphorylated compounds, may suggest that primordial precursors to ATP also utilized phosphate in compounds such as pyrophosphate, acetyl phosphate and polyphosphate. However, bioavailable phosphate may have been notably scarce on the early Earth, raising doubts about the roles that phosphorylated molecules might have played in the early evolution of life. A largely overlooked phosphorus redox cycle on the ancient Earth might have provided phosphorus and energy, with reduced phosphorus compounds potentially playing a key role in the early evolution of energy metabolism. Here, we speculate on the biological phosphorus compounds that may have acted as primordial energy currencies, sources of environmental energy, or sources of phosphorus for the synthesis of phosphorylated energy currencies. This review encompasses discussions on the evolutionary history of modern bioenergetics, and specifically those pathways with primordial relevance, and the geochemistry of bioavailable phosphorus on the ancient Earth. We highlight the importance of phosphorus, not only in the form of phosphate, to early biology and suggest future directions of study that may improve our understanding of the early evolution of bioenergetics.

Gravity's effect on biology

Gravity is a fundamental interaction that permeates throughout our Universe. On Earth, gravity gives weight to physical objects, and has been a constant presence throughout terrestrial biological evolution. Thus, gravity has shaped all biological functions, some examples include the growth of plants (e.g., gravitropism), the structure and morphology of biological parts in multicellular organisms, to its effects on our physiological function when humans travel into space. Moreover, from an evolutionary perspective, gravity has been a constant force on biology, and life, to our understanding, should have no reason to not experience the effects of gravity. Interestingly, there appear to be specific biological mechanisms that activate in the absence of gravity, with the space environment the only location to study the effects of a lack of gravity on biological systems. Thus, in this perspective piece, biological adaptations from the cellular to the whole organism levels to the presence and absence of gravity will be organized and described, as well as outlining future areas of research for gravitational biological investigations to address. Up to now, we have observed and shown how gravity effects biology at different levels, with a few examples including genetic (e.g., cell cycle, metabolism, signal transduction associated pathways, etc.), biochemically (e.g., cytoskeleton, NADPH oxidase, Yes-associated protein, etc.), and functionally (e.g., astronauts experiencing musculoskeletal and cardiovascular deconditioning, immune dysfunction, etc., when traveling into space). Based from these observations, there appear to be gravity-sensitive and specific pathways across biological organisms, though knowledge gaps of the effects of gravity on biology remain, such as similarities and differences across species, reproduction, development, and evolutionary adaptations, sex-differences, etc. Thus, here an overview of the literature is provided for context of gravitational biology research to-date and consideration for future studies, as we prepare for long-term occupation of low-Earth Orbit and cis-Lunar space, and missions to the Moon and Mars, experiencing the effects of Lunar and Martian gravity on biology, respectively, through our Artemis program.

The Nature of the Low-Temperature Crossover of Water in Hard Confinement

The dynamics of water confined in mesoporous MIP (2-3 nm pores in size) with silica gel (secondary silica; further, the abbreviation SG will be used) and MAP (10-35 nm pores in size) without SG borosilicate glasses have been studied by broadband dielectric spectroscopy (BDS), nuclear magnetic resonance (NMR), and differential scanning calorimetry (DSC). MIP samples contain secondary silica inside the pores and provide a confinement size of about 2-3 nm, whereas MAP samples are free of secondary silica and provide a confinement size of about 10-35 nm. It is shown by BDS and NMR techniques that water exhibits a dynamic crossover of around 180 K when it is confined in MIP samples. By contrast, water confined in larger pores (MAP) does not exhibit any changes in its relaxation behavior. It is also shown that the crossover temperature depends on the hydration level (the higher the hydration level, the lower the crossover temperature). Below the crossover temperature, we find that water reorientation is isotropic (NMR) and that the temperature-dependent dielectric relaxation strength (BDS) follows the tendency expected for a solid-like material. In contrast, water reorientation is related to long-range diffusion above the crossover temperature, and the dielectric relaxation strength follows the tendency expected for a liquid-like material. Furthermore, the calorimetric results are compatible with crossing a glass transition near 180 K. Finally, the results are discussed within the Gibbs-Thomson model. In this framework, the crossover could be related to ice crystals melting.

Temporal nanofluid environments induce prebiotic condensation in water

Water is a problem in understanding chemical evolution towards life's origins on Earth. Although all known life is being based on water key prebiotic reactions are inhibited by it. The prebiotic plausibility of current strategies to circumvent this paradox is questionable regarding the principle that evolution builds on existing pathways. Here, we report a straightforward way to overcome the water paradox in line with evolutionary conservatism. By utilising a molecular deposition method as a physicochemical probe, we uncovered a synergy between biomolecule assembly and temporal nanofluid conditions that emerge within transient nanoconfinements of water between suspended particles. Results from fluorometry, quantitative PCR, melting curve analysis, gel electrophoresis and computational modelling reveal that such conditions induce nonenzymatic polymerisation of nucleotides and promote basic cooperation between nucleotides and amino acids for RNA formation. Aqueous particle suspensions are a geochemical ubiquitous and thus prebiotic highly plausible setting. Harnessing nanofluid conditions in this setting for prebiotic syntheses is consistent with evolutionary conservatism, as living cells also work with temporal nanoconfined water for biosynthesis. Our findings add key insights required to understand the transition from geochemistry to biochemistry and open up systematic pathways to water-based green chemistry approaches in materials science and nanotechnology.

Confinement effect on hydrolysis in small lipid vesicles

In living organisms most chemical reactions take place within the confines of lipid-membrane bound compartments, while confinement within the bounds of a lipid membrane is thought to be a key step in abiogenesis. In previous work we demonstrated that confinement in the aqueous cavity of a lipid vesicle affords protection against hydrolysis, a phenomenon that we term here confinement effect (C _e) and that we attributed to the interaction with the lipid membrane. Here, we show that both the size and the shape of the cavity of the vesicle modulate the C _e. We link this observation to the packing of the lipid following changes in membrane curvature, and formulate a mathematical model that relates the C _e to the radius of a spherical vesicle and the packing parameter of the lipids. These results suggest that the shape of the compartment where a molecule is located plays a major role in controlling the chemical reactivity of non-enzymatic reactions. Moreover, the mathematical treatment we propose offers a useful tool for the design of vesicles with predictable reaction rates of the confined molecules, e.g., drug delivery vesicles with confined prodrugs. The results also show that a crude form of signal transduction, devoid of complex biological machinery, can be achieved by any external stimuli that drastically changes the structure of the membrane, like the osmotic shocks used in the present work.

Modern biophysical view of electromagnetic processes of the phenomenon of life of living biological systems as a promising basis for the development of complex medicine: the role of water

The results of a theoretical study of the role of water in electromagnetic generation and in the process of realizing the phenomenon of life are presented in the article. This article is a continuation of the theoretical study of the team of authors, which was published in the Journal of Complexity in Health Sciences, Vol. 5, Issue 1, 2022, p. 22-34. The aim of the theoretical study was to generalize the available scientific physical and biological knowledge of modern science about the role of water in the electromagnetic processes of the phenomenon of life at the cellular level in order to deepen the fundamental knowledge of Complex Medicine. This study is a fragment of research work on “Development of algorithms and technologies for implementing a Healthy Lifestyle in patients with Noncommunicable Diseases based on the study of functional status” (state registration number 0121U108237: UDC 613 616-056-06: 616.1/9-03). General scientific methods and theoretical methods were used in this theoretical study. The main conclusions of the theoretical study were made as follows: 1) Тhe “30/11 helix” is the main most typical fragmentary element of water self-organization into fractal structures and it forms energy-intensive fractal crystalline filamentous water structures in living biological systems, supported by energy constantly coming from biopolymers, and forming large constantly growing hierarchical structures that unite all the water of a living organism in a dynamic balance of opposite processes of destruction and growth of its energy-intensive crystalline structures; 2) Water has a key role in the process of transmission and perception of the coherent energy of a soliton through self-organizing fractal energy-intensive paramagnetic crystalline structures in living biological systems; 3) The phenomenon of biological life at the micro level is characterized by the presence of a state of water binding/organization into energy-intensive crystalline structures due to the constant supply of coherent energy from biopolymers and stops when this energy flow disappears, which corresponds to the onset of the phenomenon of biological death and is manifested by the degradation of energy-intensive fractal crystalline self-organization of water to an unbound water state. solution devoid of so-called biological anomalies.

A prebiotic basis for ATP as the universal energy currency

ATP is universally conserved as the principal energy currency in cells, driving metabolism through phosphorylation and condensation reactions. Such deep conservation suggests that ATP arose at an early stage of biochemical evolution. Yet purine synthesis requires 6 phosphorylation steps linked to ATP hydrolysis. This autocatalytic requirement for ATP to synthesize ATP implies the need for an earlier prebiotic ATP equivalent, which could drive protometabolism before purine synthesis. Why this early phosphorylating agent was replaced, and specifically with ATP rather than other nucleoside triphosphates, remains a mystery. Here, we show that the deep conservation of ATP might reflect its prebiotic chemistry in relation to another universally conserved intermediate, acetyl phosphate (AcP), which bridges between thioester and phosphate metabolism by linking acetyl CoA to the substrate-level phosphorylation of ADP. We confirm earlier results showing that AcP can phosphorylate ADP to ATP at nearly 20% yield in water in the presence of Fe3+ ions. We then show that Fe3+ and AcP are surprisingly favoured. A wide range of prebiotically relevant ions and minerals failed to catalyse ADP phosphorylation. From a panel of prebiotic phosphorylating agents, only AcP, and to a lesser extent carbamoyl phosphate, showed any significant phosphorylating potential. Critically, AcP did not phosphorylate any other nucleoside diphosphate. We use these data, reaction kinetics, and molecular dynamic simulations to infer a possible mechanism. Our findings might suggest that the reason ATP is universally conserved across life is that its formation is chemically favoured in aqueous solution under mild prebiotic conditions.

Frontiers in Prebiotic Chemistry and Early Earth Environments

The Prebiotic Chemistry and Early Earth Environments (PCE₃) Consortium is a community of researchers seeking to understand the origins of life on Earth and in the universe. PCE₃ is one of five Research Coordination Networks (RCNs) within NASA’s Astrobiology Program. Here we report on the inaugural PCE₃ workshop, intended to cross-pollinate, transfer information, promote cooperation, break down disciplinary barriers, identify new directions, and foster collaborations. This workshop, entitled, “Building a New Foundation”, was designed to propagate current knowledge, identify possibilities for multidisciplinary collaboration, and ultimately define paths for future collaborations. Presentations addressed the likely conditions on early Earth in ways that could be incorporated into prebiotic chemistry experiments and conceptual models to improve their plausibility and accuracy. Additionally, the discussions that followed among workshop participants helped to identify within each subdiscipline particularly impactful new research directions. At its core, the foundational knowledge base presented in this workshop should underpin future workshops and enable collaborations that bridge the many disciplines that are part of PCE₃.

On the prebiotic selection of nucleotide anomers: A computational study

Present-day known predominance of the β- over the α-anomers in nucleosides and nucleotides emerges from a thermodynamic analysis of their assembly from their components, i.e. bases, sugars, and a phosphate group. Furthermore, the incorporation of uracil into RNA and thymine into DNA rather than the other way around is also predicted from the calculations. An interplay of kinetics and thermodynamics must have driven evolutionary selection of life's building blocks. In this work, based on quantum chemical calculations, we focus on the latter control as a tool for “natural selection”.

Role of geochemical protoenzymes (geozymes) in primordial metabolism: specific abiotic hydride transfer by metals to the biological redox cofactor NAD. FEBS J 2021;289:3148-3162. [PMID: 34923745 PMCID: PMC9306933 DOI: 10.1111/febs.16329]

Hydrogen gas, H₂, is generated in serpentinizing hydrothermal systems, where it has supplied electrons and energy for microbial communities since there was liquid water on Earth. In modern metabolism, H₂ is converted by hydrogenases into organically bound hydrides (H^–), for example, the cofactor NADH. It transfers hydrides among molecules, serving as an activated and biologically harnessed form of H₂. In serpentinizing systems, minerals can also bind hydrides and could, in principle, have acted as inorganic hydride donors—possibly as a geochemical protoenzyme, a ‘geozyme’— at the origin of metabolism. To test this idea, we investigated the ability of H₂ to reduce NAD⁺ in the presence of iron (Fe), cobalt (Co) and nickel (Ni), metals that occur in serpentinizing systems. In the presence of H₂, all three metals specifically reduce NAD⁺ to the biologically relevant form, 1,4‐NADH, with up to 100% conversion rates within a few hours under alkaline aqueous conditions at 40 °C. Using Henry's law, the partial pressure of H₂ in our reactions corresponds to 3.6 mm, a concentration observed in many modern serpentinizing systems. While the reduction of NAD⁺ by Ni is strictly H₂‐dependent, experiments in heavy water (²H₂O) indicate that native Fe can reduce NAD⁺ both with and without H₂. The results establish a mechanistic connection between abiotic and biotic hydride donors, indicating that geochemically catalysed, H₂‐dependent NAD⁺ reduction could have preceded the hydrogenase‐dependent reaction in evolution.

Photoswitchable single-stranded DNA-peptide coacervate formation as a dynamic system for reaction control

In cells, segregation allows for diverse biochemical reactions to take place simultaneously. Such intricate regulation of cellular processes is achieved through the dynamic formation and disassembly of membraneless organelles via liquid-liquid phase separation (LLPS). Herein, we demonstrate the light-controlled formation and disassembly of liquid droplets formed from a complex of polylysine (pLys) and arylazopyrazole (AAP)-conjugated single-stranded DNA. Photoswitchablility of droplet formation was also shown to be applicable to the control of chemical reactions; imine formation and a DNAzyme-catalyzed oxidation reaction were accelerated in the presence of droplets. These outcomes were reversed upon droplet disassembly. Our results demonstrate that the photoswitchable droplet formation system is a versatile model for the regulation of reactions through dynamic LLPS.

•

Incorporating AAP enabled light-controlled droplet formation with ssDNA and pLys

•

Droplets were reversibly formed or disassembled without altering sample composition

•

Photoswitchability depended on sequence and ionic interactions but not flexibility

•

Photoswitchable droplet formation accelerated uncatalyzed and catalyzed reactions

Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA)

Though all theories for the origin of life require a source of energy to promote primordial chemical reactions, the nature of energy that drove the emergence of metabolism at origins is still debated. We reasoned that evidence for the nature of energy at origins should be preserved in the biochemical reactions of life itself, whereby changes in free energy, ΔG, which determine whether a reaction can go forward or not, should help specify the source. By calculating values of ΔG across the conserved and universal core of 402 individual reactions that synthesize amino acids, nucleotides and cofactors from H2, CO2, NH3, H2S and phosphate in modern cells, we find that 95-97% of these reactions are exergonic (ΔG ≤ 0 kJ⋅mol-1) at pH 7-10 and 80-100°C under nonequilibrium conditions with H2 replacing biochemical reductants. While 23% of the core's reactions involve ATP hydrolysis, 77% are ATP-independent, thermodynamically driven by ΔG of reactions involving carbon bonds. We identified 174 reactions that are exergonic by -20 to -300 kJ⋅mol-1 at pH 9 and 80°C and that fall into ten reaction types: six pterin dependent alkyl or acyl transfers, ten S-adenosylmethionine dependent alkyl transfers, four acyl phosphate hydrolyses, 14 thioester hydrolyses, 30 decarboxylations, 35 ring closure reactions, 31 aromatic ring formations, and 44 carbon reductions by reduced nicotinamide, flavins, ferredoxin, or formate. The 402 reactions of the biosynthetic core trace to the last universal common ancestor (LUCA), and reveal that synthesis of LUCA's chemical constituents required no external energy inputs such as electric discharge, UV-light or phosphide minerals. The biosynthetic reactions of LUCA uncover a natural thermodynamic tendency of metabolism to unfold from energy released by reactions of H2, CO2, NH3, H2S, and phosphate.

Computational Study of the Stability of Natural Amino Acid isomers

The secular debate on the origin of life on our planet represents one of the open challenges for the scientific community. In this endeavour, chemistry has a pivotal role in disclosing novel scenarios that allow us to understand how the formation of simple organic molecules would be possible in the early primitive geological ages of Earth. Amino acids play a crucial role in biological processes. They are known to be formed in experiments simulating primitive conditions and were found in meteoric samples retrieved throughout the years. Understanding their formation is a key step for prebiotic chemistry. Following this reasoning, we performed a computational investigation over 100'000 structural isomers of natural amino acids. The results we have found suggest that natural amino acids are among the most thermodynamically stable structures and, therefore, one of the most probable ones to be synthesised among their possible isomers.

'Whole Organism', Systems Biology, and Top-Down Criteria for Evaluating Scenarios for the Origin of Life

While most advances in the study of the origin of life on Earth (OoLoE) are piecemeal, tested against the laws of chemistry and physics, ultimately the goal is to develop an overall scenario for life's origin(s). However, the dimensionality of non-equilibrium chemical systems, from the range of possible boundary conditions and chemical interactions, renders the application of chemical and physical laws difficult. Here we outline a set of simple criteria for evaluating OoLoE scenarios. These include the need for containment, steady energy and material flows, and structured spatial heterogeneity from the outset. The Principle of Continuity, the fact that all life today was derived from first life, suggests favoring scenarios with fewer non-analog (not seen in life today) to analog (seen in life today) transitions in the inferred first biochemical pathways. Top-down data also indicate that a complex metabolism predated ribozymes and enzymes, and that full cellular autonomy and motility occurred post-LUCA. Using these criteria, we find the alkaline hydrothermal vent microchamber complex scenario with a late evolving exploitation of the natural occurring pH (or Na⁺ gradient) by ATP synthase the most compelling. However, there are as yet so many unknowns, we also advocate for the continued development of as many plausible scenarios as possible.

To What Inanimate Matter Are We Most Closely Related and Does the Origin of Life Harbor Meaning?

The question concerning the meaning of life is important, but it immediately confronts the present authors with insurmountable obstacles from a philosophical standpoint, as it would require us to define not only what we hold to be life, but what we hold to be meaning in addition, requiring us to do both in a properly researched context. We unconditionally surrender to that challenge. Instead, we offer a vernacular, armchair approach to life’s origin and meaning, with some layman’s thoughts on the meaning of origins as viewed from the biologist’s standpoint. One can observe that biologists generally approach the concept of biological meaning in the context of evolution. This is the basis for the broad resonance behind Dobzhansky’s appraisal that “Nothing in biology makes sense except in the light of evolution”. Biologists try to understand living things in the historical context of how they arose, without giving much thought to the definition of what life or living things are, which for a biologist is usually not an interesting question in the practical context of daily dealings with organisms. Do humans generally understand life’s meaning in the context of history? If we consider the problem of life’s origin, the question of what constitutes a living thing becomes somewhat more acute for the biologist, though not more answerable, because it is inescapable that there was a time when there were no organisms on Earth, followed by a time when there were, the latter time having persisted in continuity to the present. This raises the question of where, in that transition, chemicals on Earth became alive, requiring, in turn, a set of premises for how life arose in order to conceptualize the problem in relation to organisms we know today, including ourselves, which brings us to the point of this paper: In the same way that cultural narratives for origins always start with a setting, scientific narratives for origins also always start with a setting, a place on Earth or elsewhere where we can imagine what happened for the sake of structuring both the problem and the narrative for its solution. This raises the question of whether scientific origins settings convey meaning to humans in that they suggest to us from what kind of place and what kinds of chemicals we are descended, that is, to which inanimate things we are most closely related.

The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors

The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H₂, CO₂, and ammonia (NH₃) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO₂ is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO₂, and the circumstance that the core’s main products are far more reduced than CO₂ indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H₂, inorganic carbon, and NH₃ in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Such conditions are very similar to those found in serpentinizing hydrothermal systems.

Chemical Garden Membranes in Temperature-Controlled Microfluidic Devices

Thin-walled tubes that classically form when metal salts react with sodium silicate solution are known as chemical gardens. They share similarities with the porous, catalytic materials in hydrothermal vent chimneys, and both structures are exposed to steep pH gradients that, combined with thermal factors, might have provided the free energy for prebiotic chemistry on early Earth. We report temperature effects on the shape, composition, and opacity of chemical gardens. Tubes grown at high temperature are more opaque, indicating changes to the membrane structure or thickness. To study this dependence, we developed a temperature-controlled microfluidic device, which allows the formation of analogous membranes at the interface of two coflowing reactant solutions. For the case of Ni(OH)₂, membranes thicken according to a diffusion-controlled mechanism. In the studied range of 10-40 °C, the effective diffusion coefficient is independent of temperature. This suggests that counteracting processes are at play (including an increased solubility) and that the opacity of chemical garden tubes arises from changes in internal morphology. The latter could be linked to experimentally observed dendritic structures within the membranes.

Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

Speciation, an evolutionary process by which new species form, is ultimately responsible for the incredible biodiversity that we observe on Earth every day. Such biodiversity is one of the critical features which contributes to the survivability of biospheres and modern life. While speciation and biodiversity have been amply studied in organismic evolution and modern life, it has not yet been applied to a great extent to understanding the evolutionary dynamics of primitive life. In particular, one unanswered question is at what point in the history of life did speciation as a phenomenon emerge in the first place. Here, we discuss the mechanisms by which speciation could have occurred before the origins of life in the context of chemical evolution. Specifically, we discuss that primitive compartments formed before the emergence of the last universal common ancestor (LUCA) could have provided a mechanism by which primitive chemical systems underwent speciation. In particular, we introduce a variety of primitive compartment structures, and associated functions, that may have plausibly been present on early Earth, followed by examples of both discriminate and indiscriminate speciation affected by primitive modes of compartmentalization. Finally, we discuss modern technologies, in particular, droplet microfluidics, that can be applied to studying speciation phenomena in the laboratory over short timescales. We hope that this discussion highlights the current areas of need in further studies on primitive speciation phenomena while simultaneously proposing directions as important areas of study to the origins of life.

A Few Experimental Suggestions Using Minerals to Obtain Peptides with a High Concentration of L-Amino Acids and Protein Amino Acids

The peptides/proteins of all living beings on our planet are mostly made up of 19 L-amino acids and glycine, an achiral amino acid. Arising from endogenous and exogenous sources, the seas of the prebiotic Earth could have contained a huge diversity of biomolecules (including amino acids), and precursors of biomolecules. Thus, how were these amino acids selected from the huge number of available amino acids and other molecules? What were the peptides of prebiotic Earth made up of? How were these peptides synthesized? Minerals have been considered for this task, since they can preconcentrate amino acids from dilute solutions, catalyze their polymerization, and even make the chiral selection of them. However, until now, this problem has only been studied in compartmentalized experiments. There are separate experiments showing that minerals preconcentrate amino acids by adsorption or catalyze their polymerization, or separate L-amino acids from D-amino acids. Based on the [GADV]-protein world hypothesis, as well as the relative abundance of amino acids on prebiotic Earth obtained by Zaia, several experiments are suggested. The main goal of these experiments is to show that using minerals it is possible, at least, to obtain peptides whose composition includes a high quantity of L-amino acids and protein amino acids (PAAs). These experiments should be performed using hydrothermal environments and wet/dry cycles. In addition, for hydrothermal environment experiments, it is very important to use one of the suggested artificial seawaters, and for wet/dry environments, it is important to perform the experiments in distilled water and diluted salt solutions. Finally, from these experiments, we suggest that, without an RNA world or even a pre genetic world, a small peptide set could emerge that better resembles modern proteins.