RNA Oligomerization in Laboratory Analogues of Alkaline Hydrothermal Vent Systems

Abiotic formation of hexoses and disaccharides in aqueous microdroplets

Understanding the chemical reactions that led to the origin of life is a fundamental challenge of chemistry. The formose reaction, an abiotic pathway to monosaccharides, provides a mechanism of sugar formation from simple aldehydes and ketones. However, the reaction requires the addition of base, metal catalysts, and is prone to side reactions, leaving questions about how such processes could have occurred on a primitive Earth. The abiotic formation of more complex sugars, such as disaccharides also require catalysts, and remains underexplored compared to other classes of biomolecules. This study investigates the role of microdroplets in the formation of hexoses and their subsequent condensation reactions to produce disaccharides, without the need for catalysts. The microdroplet-mediated synthesis of fructose and sorbose from glyceraldehyde or dihydroxyacetone, as well as that of disaccharides from various pentoses or hexoses, was monitored via mass spectrometery. Products were confirmed by high resolution mass spectrometry and tandem mass spectrometry. The product distribution of glucose disaccharides was determined by matching the relative intensities of product ions to a mixture of six disaccharide and showed a maximum yield of 9.4% or 1.7 µg min-1 emitter. This study demonstrates the abiotic formation of monosaccharides and disaccharides, such as xylobiose and maltose, providing a possible link between prebiotic sugar synthesis and extant carbohydrate biochemistry. Hexose formation and disaccharide synthesis are driven by the unique air water interface of microdroplets, where partial solvation, pH extremes, and fast mass transfer kinetics enable abiotic transformations.

Prebiotic Nucleoside Phosphorylation in a Simulated Deep-Sea Supercritical Carbon Dioxide-Water Two-Phase Environment

Prebiotic synthesis of complex organic molecules in water-rich environments has been a long-standing challenge. In the modern deep sea, emission of liquid CO2 has been observed in multiple locations, which indicates the existence of benthic CO2 pools. Recently, a liquid/supercritical CO2 (ScCO2) hypothesis has been proposed that a two-phase ScCO2-water environment could lead to efficient dehydration and condensation of organics. To confirm this hypothesis, we conducted a nucleoside phosphorylation reaction in a hydrothermal reactor creating ScCO2-water two-phase environment. After 120 h of uridine, cytosine, guanosine, and adenosine phosphorylation at 68.9°C, various nucleoside monophosphates (NMPs), nucleotide diphosphates, and carbamoyl nucleosides were produced. The addition of urea enhanced the overall production of phosphorylated species with 5'-NMPs, the major products that reached over 10% yield. As predicted, phosphorylation did not proceed in the fully aqueous environment without ScCO2. Further, a glass window reactor was introduced for direct observation of the two-phase environment, where the escape of water into the ScCO2 phase was observed. These results are similar to those of a wet-dry cycle experiment simulating the terrestrial hot spring environment, indicating that the presence of ScCO2 can create a comparatively dry condition in the deep sea. In addition, the high acidity present in the aqueous phase further supports nucleotide synthesis by enabling the release of orthophosphate from the hydroxyapatite mineral solving the phosphate problem. Thus, the present study highlights the potential of the unique ScCO2-water two-phase environment to drive prebiotic nucleotide synthesis and likely induce condensation reactions of various organic and inorganic compounds in the deep-sea CO2 pool on Earth and potentially other ocean worlds.

Qualitative Monitoring of Proto-Peptide Condensation by Differential FTIR Spectroscopy

Condensation processes such as wet-dry cycling are thought to have played significant roles in the emergence of proto-peptides. Here, we describe a simple and low-cost method, differential Fourier transform infrared (FTIR) spectroscopy, for qualitative analysis of peptide condensation products in model primordial reactions. We optimize differential FTIR for depsipeptides and apply this method to investigate their polymerization in the presence of extraterrestrial dust simulants.

White and green rust chimneys accumulate RNA in a ferruginous chemical garden

Mechanisms of nucleic acid accumulation were likely critical to life's emergence in the ferruginous oceans of the early Earth. How exactly prebiotic geological settings accumulated nucleic acids from dilute aqueous solutions, is poorly understood. As a possible solution to this concentration problem, we simulated the conditions of prebiotic low-temperature alkaline hydrothermal vents in co-precipitation experiments to investigate the potential of ferruginous chemical gardens to accumulate nucleic acids via sorption. The injection of an alkaline solution into an artificial ferruginous solution under anoxic conditions (O2  < 0.01% of present atmospheric levels) and at ambient temperatures, caused the precipitation of amakinite ("white rust"), which quickly converted to chloride-containing fougerite ("green rust"). RNA was only extractable from the ferruginous solution in the presence of a phosphate buffer, suggesting RNA in solution was bound to Fe2+ ions. During chimney formation, this iron-bound RNA rapidly accumulated in the white and green rust chimney structure from the surrounding ferruginous solution at the fastest rates in the initial white rust phase and correspondingly slower rates in the following green rust phase. This represents a new mechanism for nucleic acid accumulation in the ferruginous oceans of the early Earth, in addition to wet-dry cycles and may have helped to concentrate RNA in a dilute prebiotic ocean.

Alkaline vents recreated in two dimensions to study pH gradients, precipitation morphology, and molecule accumulation

Alkaline vents (AVs) are hypothesized to have been a setting for the emergence of life, by creating strong gradients across inorganic membranes within chimney structures. In the past, three-dimensional chimney structures were formed under laboratory conditions; however, no in situ visualization or testing of the gradients was possible. We develop a quasi-two-dimensional microfluidic model of AVs that allows spatiotemporal visualization of mineral precipitation in low-volume experiments. Upon injection of an alkaline fluid into an acidic, iron-rich solution, we observe a diverse set of precipitation morphologies, mainly controlled by flow rate and ion concentration. Using microscope imaging and pH-dependent dyes, we show that finger-like precipitates can facilitate formation and maintenance of microscale pH gradients and accumulation of dispersed particles in confined geometries. Our findings establish a model to investigate the potential of gradients across a semipermeable boundary for early compartmentalization, accumulation, and chemical reactions at the origins of life.

Mineral-Mediated Oligoribonucleotide Condensation: Broadening the Scope of Prebiotic Possibilities on the Early Earth

The origin of life on earth requires the synthesis of protobiopolymers in realistic geologic environments along strictly abiotic pathways that rely on inorganic phases (such as minerals) instead of cellular machinery to promote condensation. One such class of polymer central to biochemistry is the polynucleotides, and oligomerization of activated ribonucleotides has been widely studied. Nonetheless, the range of laboratory conditions tested to date is limited and the impact of realistic early Earth conditions on condensation reactions remains unexplored. Here, we investigate the potential for a variety of minerals to enhance oligomerization using ribonucleotide monomers as one example to model condensation under plausible planetary conditions. The results show that several minerals differing in both structure and composition enhance oligomerization. Sulfide minerals yielded oligomers of comparable lengths to those formed in the presence of clays, with galena being the most effective, yielding oligonucleotides up to six bases long. Montmorillonite continues to excel beyond other clays. Chemical pretreatment of the clay was not required, though maximum oligomer lengths decreased from ~11 to 6 bases. These results demonstrate the diversity of mineral phases that can impact condensation reactions and highlight the need for greater consideration of environmental context when assessing prebiotic synthesis and the origin of life.

A heated rock crack captures and polymerizes primordial DNA and RNA

Life is based on informational polymers such as DNA or RNA. For their polymerization, high concentrations of complex monomer building blocks are required. Therefore, the dilution by diffusion poses a major problem before early life could establish a non-equilibrium of compartmentalization. Here, we explored a natural non-equilibrium habitat to polymerize RNA and DNA. A heat flux across thin rock cracks is shown to accumulate and maintain nucleotides. This boosts the polymerization to RNA and DNA inside the crack. Moreover, the polymers remain localized, aiding both the creation of longer polymers and fostering downstream evolutionary steps. In a closed system, we found single nucleotides concentrate 10⁴-fold at the bottom of the crack compared to the top after 24 hours. We detected enhanced polymerization for 2 different activation chemistries: aminoimidazole-activated DNA nucleotides and 2',3'-cyclic RNA nucleotides. The copolymerization of 2',3'-cGMP and 2',3'-cCMP in the thermal pore showed an increased heterogeneity in sequence composition compared to isothermal drying. Finite element models unravelled the combined polymerization and accumulation kinetics and indicated that the escape of the nucleotides from such a crack is negligible over a time span of years. The thermal non-equilibrium habitat establishes a cell-like compartment that actively accumulates nucleotides for polymerization and traps the resulting oligomers. We argue that the setting creates a pre-cellular non-equilibrium steady state for the first steps of molecular evolution.

Multivariate Analysis Applied to Microwave-Driven Cyanide Polymerization: A Statistical View of a Complex System

For the first time, chemometrics was applied to the recently reported microwave-driven cyanide polymerization. Fast, easy, robust, low-cost, and green-solvent processes are characteristic of these types of reactions. These economic and environmental benefits, originally inspired by the constraints imposed by plausible prebiotic synthetic conditions, have taken advantage of the development of a new generation of HCN-derived multifunctional materials. HCN-derived polymers present tunable properties by temperature and reaction time. However, the apparently random behavior observed in the evolution of cyanide polymerizations, assisted by microwave radiation over time at different temperatures, leads us to study this highly complex system using multivariate analytical tools to have a proper view of the system. Two components are sufficient to explain between 84 and 98% of the total variance in the data in all principal component analyses. In addition, two components explain more than 91% of the total variance in the data in the case of principal component analysis for categorical data. These consistent statistical results indicate that microwave-driven polymerization is a more robust process than conventional thermal syntheses but also that plausible prebiotic chemistry in alkaline subaerial environments could be more complex than in the aerial part of these systems, presenting a clear example of the "messy chemistry" approach of interest in the research about the origins of life. In addition, the methodology discussed herein could be useful for the data analysis of extraterrestrial samples and for the design of soft materials, in a feedback view between prebiotic chemistry and materials science.

Prebiotic Chemistry Experiments Using Microfluidic Devices

Microfluidic devices are small tools mostly consisting of one or more channels, with dimensions between one and hundreds of microns, where small volumes of fluids are manipulated. They have extensive use in the biomedical and chemical fields; however, in prebiotic chemistry, they only have been employed recently. In prebiotic chemistry, just three types of microfluidic devices have been used: the first ones are Y-form devices with laminar co-flow, used to study the precipitation of minerals in hydrothermal vents systems; the second ones are microdroplet devices that can form small droplets capable of mimic cellular compartmentalization; and the last ones are devices with microchambers that recreate the microenvironment inside rock pores under hydrothermal conditions. In this review, we summarized the experiments in the field of prebiotic chemistry that employed microfluidic devices. The main idea is to incentivize their use and discuss their potential to perform novel experiments that could contribute to unraveling some prebiotic chemistry questions.

Controlled self-assembly of chemical gardens enables fabrication of heterogeneous chemobrionic materials

Chemical gardens are an example of a chemobrionic system that typically result in abiotic macro-, micro- and nano- material architectures, with formation driven by complex out-of-equilibrium reaction mechanisms. From a technological perspective, controlling chemobrionic processes may hold great promise for the creation of novel, compositionally diverse and ultimately, useful materials and devices. In this work, we engineer an innovative custom-built liquid exchange unit that enables us to control the formation of tubular chemical garden structures grown from the interface between calcium loaded hydrogel and phosphate solution. We show that systematic displacement of phosphate solution with water (H₂O) can halt self-assembly, precisely control tube height and purify structures in situ. Furthermore, we demonstrate the fabrication of a heterogeneous chemobrionic composite material composed of aligned, high-aspect ratio calcium phosphate channels running through an otherwise dense matrix of poly(2-hydroxyethyl methacrylate) (pHEMA). Given that the principles we derive can be broadly applied to potentially control various chemobrionic systems, this work paves the way for fabricating multifunctional materials that may hold great potential in a variety of application areas, such as regenerative medicine, catalysis and microfluidics.

Plausible Emergence and Self Assembly of a Primitive Phospholipid from Reduced Phosphorus on the Primordial Earth

How life arose on the primitive Earth is one of the biggest questions in science. Biomolecular emergence scenarios have proliferated in the literature but accounting for the ubiquity of oxidized (+ 5) phosphate (PO43-) in extant biochemistries has been challenging due to the dearth of phosphate and molecular oxygen on the primordial Earth. A compelling body of work suggests that exogenous schreibersite ((Fe,Ni)3P) was delivered to Earth via meteorite impacts during the Heavy Bombardment (ca. 4.1-3.8 Gya) and there converted to reduced P oxyanions (e.g., phosphite (HPO32-) and hypophosphite (H2PO2-)) and phosphonates. Inspired by this idea, we review the relevant literature to deduce a plausible reduced phospholipid analog of modern phosphatidylcholines that could have emerged in a primordial hydrothermal setting. A shallow alkaline lacustrine basin underlain by active hydrothermal fissures and meteoritic schreibersite-, clay-, and metal-enriched sediments is envisioned. The water column is laden with known and putative primordial hydrothermal reagents. Small system dimensions and thermal- and UV-driven evaporation further concentrate chemical precursors. We hypothesize that a reduced phospholipid arises from Fischer-Tropsch-type (FTT) production of a C8 alkanoic acid, which condenses with an organophosphinate (derived from schreibersite corrosion to hypophosphite with subsequent methylation/oxidation), to yield a reduced protophospholipid. This then condenses with an α-amino nitrile (derived from Strecker-type reactions) to form the polar head. Preliminary modeling results indicate that reduced phospholipids do not aggregate rapidly; however, single layer micelles are stable up to aggregates with approximately 100 molecules.

Experimental Approaches for Testing the Hypothesis of the Emergence of Life at Submarine Alkaline Vents

Since the pioneering experimental work performed by Urey and Miller around 70 years ago, several experimental works have been developed for approaching the question of the origin of life based on very few well-constructed hypotheses. In recent years, attention has been drawn to the so-called alkaline hydrothermal vents model (AHV model) for the emergence of life. Since the first works, perspectives from complexity sciences, bioenergetics and thermodynamics have been incorporated into the model. Consequently, a high number of experimental works from the model using several tools have been developed. In this review, we present the key concepts that provide a background for the AHV model and then analyze the experimental approaches that were motivated by it. Experimental tools based on hydrothermal reactors, microfluidics and chemical gardens were used for simulating the environments of early AHVs on the Hadean Earth (~4.0 Ga). In addition, it is noteworthy that several works used techniques from electrochemistry to investigate phenomena in the vent-ocean interface for early AHVs. Their results provided important parameters and details that are used for the evaluation of the plausibility of the AHV model, and for the enhancement of it.

A Lizardite-HCN Interaction Leading the Increasing of Molecular Complexity in an Alkaline Hydrothermal Scenario: Implications for Origin of Life Studies

Hydrogen cyanide, HCN, is considered a fundamental molecule in chemical evolution. The named HCN polymers have been suggested as precursors of important bioorganics. Some novel researches have focused on the role of mineral surfaces in the hydrolysis and/or polymerization of cyanide species, but until now, their role has been unclear. Understanding the role of minerals in chemical evolution processes is crucial because minerals undoubtedly interacted with the organic molecules formed on the early Earth by different process. Therefore, we simulated the probable interactions between HCN and a serpentinite-hosted alkaline hydrothermal system. We studied the effect of serpentinite during the thermolysis of HCN at basic conditions (i.e., HCN 0.15 M, 50 h, 100 °C, pH > 10). The HCN-derived thermal polymer and supernatant formed after treatment were analyzed by several complementary analytical techniques. The results obtained suggest that: (I) the mineral surfaces can act as mediators in the mechanisms of organic molecule production such as the polymerization of HCN; (II) the thermal and physicochemical properties of the HCN polymer produced are affected by the presence of the mineral surface; and (III) serpentinite seems to inhibit the formation of bioorganic molecules compared with the control (without mineral).

Theoretical Constraints Imposed by Gradient Detection and Dispersal on Microbial Size in Astrobiological Environments

The capacity to sense gradients efficiently and acquire information about the ambient environment confers many advantages such as facilitating movement toward nutrient sources or away from toxic chemicals. The amplified dispersal evinced by organisms endowed with motility is possibly beneficial in related contexts. Hence, the connections between information acquisition, motility, and microbial size are explored from an explicitly astrobiological standpoint. By using prior theoretical models, the constraints on organism size imposed by gradient detection and motility are elucidated in the form of simple heuristic scaling relations. It is argued that environments such as alkaline hydrothermal vents, which are distinguished by the presence of steep gradients, might be conducive to the existence of "small" microbes (with radii of ≳0.1 μm) in principle, when only the above two factors are considered; other biological functions (e.g., metabolism and genetic exchange) could, however, regulate the lower bound on microbial size and elevate it. The derived expressions are potentially applicable to a diverse array of settings, including those entailing solvents other than water; for example, the lakes and seas of Titan. The article concludes with a brief exposition of how this formalism may be of practical and theoretical value to astrobiology.

Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules

Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing to their replication. A possible mechanism to repress parasite amplification is compartmentalization that segregates parasitic molecules and limits their access to functional genetic molecules. Although extent cells encapsulate genomes within lipid-based membranes, more primitive materials or simple geological processes could have provided compartmentalization on early Earth. In this review, we summarize the current understanding of the types and roles of primitive compartmentalization regarding sustainable replication of genetic molecules, especially from the perspective of the prevention of parasite replication. In addition, we also describe the ability of several environments to selectively accumulate longer genetic molecules, which could also have helped select functional genetic molecules rather than fast-replicating short parasitic molecules.

Elements for the Origin of Life on Land: A Deep-Time Perspective from the Pilbara Craton of Western Australia

For decades, deep sea hydrothermal vents have been a preferred setting for the Origin of Life, but "The Water Problem" as relates to polymerization of organic molecules, together with a propensity to dilute critical prebiotic elements as well as a number of other crucial factors, suggests that a terrestrial hot spring field with the capacity for wet-dry cycling and element concentration may represent a more likely candidate. Here, we investigate a 3.5 billion-year-old, anoxic hot spring setting from the Pilbara Craton (Australia) and show that its hydrothermal veins and compositionally varied pools and springs concentrated all of the essential elements required for prebiotic chemistry (including B, Zn, Mn, and K, in addition to C, H, N, O, P, and S). Temporal variability (seasonal to decadal), together with the known propensity of hot springs for wet-dry cycling and information exchange, would lead to innovation pools with peaks of fitness for developing molecules. An inference from the chemical complexity of the Pilbara analogue is that life could perhaps get started quickly on planets with volcanoes, silicate rocks, an exposed land surface, and water, ingredients that should form the backbone in the search for life in the Universe.

Characterization of HCN-Derived Thermal Polymer: Implications for Chemical Evolution

Hydrogen cyanide (HCN)-derived polymers have been recognized as sources of relevant organic molecules in prebiotic chemistry and material sciences. However, there are considerable gaps in the knowledge regarding the polymeric nature, the physicochemical properties, and the chemical pathways along polymer synthesis. HCN might have played an important role in prebiotic hydrothermal environments; however, only few experiments use cyanide species considering hydrothermal conditions. In this work, we synthesized an HCN-derived thermal polymer simulating an alkaline hydrothermal environment (i.e., HCN (l) 0.15 M, 50 h, 100 °C, pH approximately 10) and characterized its chemical structure, thermal behavior, and the hydrolysis effect. Elemental analysis and infrared spectroscopy suggest an important oxidation degree. The thermal behavior indicates that the polymer is more stable compared to other HCN-derived polymers. The mass spectrometric thermal analysis showed the gradual release of several volatile compounds along different thermal steps. The results suggest a complicate macrostructure formed by amide and hydroxyl groups, which are joined to the main reticular chain with conjugated bonds (C=O, N=O, –O–C=N). The hydrolysis treatment showed the pH conditions for the releasing of organics. The study of the synthesis of HCN-derived thermal polymers under feasible primitive hydrothermal conditions is relevant for considering hydrothermal vents as niches of chemical evolution on early Earth.

Exo-Ocean Exploration with Deep-Sea Sensor and Platform Technologies

One of Saturn's largest moons, Enceladus, possesses a vast extraterrestrial ocean (i.e., exo-ocean) that is increasingly becoming the hotspot of future research initiatives dedicated to the exploration of putative life. Here, a new bio-exploration concept design for Enceladus' exo-ocean is proposed, focusing on the potential presence of organisms across a wide range of sizes (i.e., from uni- to multicellular and animal-like), according to state-of-the-art sensor and robotic platform technologies used in terrestrial deep-sea research. In particular, we focus on combined direct and indirect life-detection capabilities, based on optoacoustic imaging and passive acoustics, as well as molecular approaches. Such biologically oriented sampling can be accompanied by concomitant geochemical and oceanographic measurements to provide data relevant to exo-ocean exploration and understanding. Finally, we describe how this multidisciplinary monitoring approach is currently enabled in terrestrial oceans through cabled (fixed) observatories and their related mobile multiparametric platforms (i.e., Autonomous Underwater and Remotely Operated Vehicles, as well as crawlers, rovers, and biomimetic robots) and how their modified design can be used for exo-ocean exploration.

Factoring Origin of Life Hypotheses into the Search for Life in the Solar System and Beyond

Two widely-cited alternative hypotheses propose geological localities and biochemical mechanisms for life's origins. The first states that chemical energy available in submarine hydrothermal vents supported the formation of organic compounds and initiated primitive metabolic pathways which became incorporated in the earliest cells; the second proposes that protocells self-assembled from exogenous and geothermally-delivered monomers in freshwater hot springs. These alternative hypotheses are relevant to the fossil record of early life on Earth, and can be factored into the search for life elsewhere in the Solar System. This review summarizes the evidence supporting and challenging these hypotheses, and considers their implications for the search for life on various habitable worlds. It will discuss the relative probability that life could have emerged in environments on early Mars, on the icy moons of Jupiter and Saturn, and also the degree to which prebiotic chemistry could have advanced on Titan. These environments will be compared to ancient and modern terrestrial analogs to assess their habitability and biopreservation potential. Origins of life approaches can guide the biosignature detection strategies of the next generation of planetary science missions, which could in turn advance one or both of the leading alternative abiogenesis hypotheses.

Chemistry of Abiotic Nucleotide Synthesis

The chemistry of abiotic nucleotide synthesis of RNA and DNA in the context of their prebiotic origins on early earth is a continuing challenge. How did (or how can) the nucleotides form and assemble from the small molecule inventories and under conditions that prevailed on early earth 3.5-4 billion years ago? This review provides a background and up-to-date progress that will allow the reader to judge where the field stands currently and what remains to be achieved. We start with a brief primer on the biological synthesis of nucleotides, followed by an extensive focus on the prebiotic formation of the components of nucleotides-either via the synthesis of ribose and the canonical nucleobases and then joining them together or by building both the conjoined sugar and nucleobase, part-by-part-toward the ultimate goal of forming RNA and DNA by polymerization. The review will emphasize that there are-and will continue to be-many more questions than answers from the synthetic, mechanistic, and analytical perspectives. We wrap up the review with a cautionary note in this context about coming to conclusions as to whether the problem of chemistry of prebiotic nucleotide synthesis has been solved.

Chemobrionics: From Self-Assembled Material Architectures to the Origin of Life

Self-organizing precipitation processes, such as chemical gardens forming biomimetic micro- and nanotubular forms, have the potential to show us new fundamental science to explore, quantify, and understand nonequilibrium physicochemical systems, and shed light on the conditions for life's emergence. The physics and chemistry of these phenomena, due to the assembly of material architectures under a flux of ions, and their exploitation in applications, have recently been termed chemobrionics. Advances in understanding in this area require a combination of expertise in physics, chemistry, mathematical modeling, biology, and nanoengineering, as well as in complex systems and nonlinear and materials sciences, giving rise to this new synergistic discipline of chemobrionics.

Chemobrionic structures in tissue engineering: self-assembling calcium phosphate tubes as cellular scaffolds

A diverse range of complex patterns and mineralised hierarchical microstructures can be derived from chemobrionic systems. In this work, we explore chemobrionic calcium phosphate tubes as cellular scaffolds.

Survival of RNA Replicators is much Easier in Protocells than in Surface-Based, Spatial Systems

In RNA-World scenarios for the origin of life, replication is catalyzed by polymerase ribozymes. Replicating RNA systems are subject to invasion by non-functional parasitic strands. It is well-known that there are two ways to avoid the destruction of the system by parasites: spatial clustering in models with limited diffusion, or group selection in protocells. Here, we compare computational models of replication in spatial models and protocells as closely as possible in order to determine the relative importance of these mechanisms in the RNA World. For the survival of the polymerases, the replication rate must be greater than a minimum threshold value, k_min, and the mutation rate in replication must be less than a maximum value, M_max, which is known as the error threshold. For the protocell models, we find that k_min is substantially lower and M_max is substantially higher than for the equivalent spatial models; thus, the survival of polymerases is much easier in protocells than on surfaces. The results depend on the maximum number of strands permitted in one protocell or one lattice site in the spatial model, and on whether replication is limited by the supply of monomers or the population size of protocells. The substantial advantages that are seen in the protocell models relative to the spatial models are robust to changing these details. Thus, cooperative polymerases with limited accuracy would have found it much easier to operate inside lipid compartments, and this suggests that protocells may have been a very early step in the development of life. We consider cases where parasites have an equal replication rate to polymerases, and cases where parasites multiply twice as fast as polymerases. The advantage of protocell models over spatial models is increased when the parasites multiply faster.

Redox and pH gradients drive amino acid synthesis in iron oxyhydroxide mineral systems

Iron oxyhydroxide minerals, known to be chemically reactive and significant for elemental cycling, are thought to have been abundant in early-Earth seawater, sediments, and hydrothermal systems. In the anoxic Fe²⁺-rich early oceans, these minerals would have been only partially oxidized and thus redox-active, perhaps able to promote prebiotic chemical reactions. We show that pyruvate, a simple organic molecule that can form in hydrothermal systems, can undergo reductive amination in the presence of mixed-valence iron oxyhydroxides to form the amino acid alanine, as well as the reduced product lactate. Furthermore, geochemical gradients of pH, redox, and temperature in iron oxyhydroxide systems affect product selectivity. The maximum yield of alanine was observed when the iron oxyhydroxide mineral contained 1:1 Fe(II):Fe(III), under alkaline conditions, and at moderately warm temperatures. These represent conditions that may be found, for example, in iron-containing sediments near an alkaline hydrothermal vent system. The partially oxidized state of the precipitate was significant in promoting amino acid formation: Purely ferrous hydroxides did not drive reductive amination but instead promoted pyruvate reduction to lactate, and ferric hydroxides did not result in any reaction. Prebiotic chemistry driven by redox-active iron hydroxide minerals on the early Earth would therefore be strongly affected by geochemical gradients of E_h, pH, and temperature, and liquid-phase products would be able to diffuse to other conditions within the sediment column to participate in further reactions.

Binding of Nucleic Acid Components to the Serpentinite-Hosted Hydrothermal Mineral Brucite

The adsorption of nucleic acid components onto the serpentinite-hosted hydrothermal mineral brucite has been investigated experimentally by determining the equilibrium adsorption isotherms in aqueous solution. Thermodynamic characterization of the adsorption data has been performed using the extended triple-layer model (ETLM) to establish a model for the stoichiometry and equilibrium constants of surface complexes. Infrared characterization of the molecule-mineral complexes has helped gain insight into the molecular functional groups directly interacting with the mineral surface. Quantum mechanical calculations have been carried out to identify the possible complexes formed on surfaces by nucleic acid components and their binding configurations on mineral surfaces, both in the presence of water molecules and in water-free conditions. The results indicate that brucite favors adsorption of nucleotides with respect to nucleosides and nucleobases from dilute aqueous environments. The surface of this mineral is able to induce well-defined orientations of the molecules through specific molecule-mineral interactions. This result suggests plausible roles of the mineral brucite in assisting prebiotic molecular self-organization. Furthermore, the detection of the infrared spectroscopic features of such building blocks of life adsorbed on brucite at very low degrees of coverage provides important support to life detection investigations.

The origin of heredity in protocells

Here we develop a computational model that examines one of the first major biological innovations-the origin of heredity in simple protocells. The model assumes that the earliest protocells were autotrophic, producing organic matter from CO₂ and H₂ Carbon fixation was facilitated by geologically sustained proton gradients across fatty acid membranes, via iron-sulfur nanocrystals lodged within the membranes. Thermodynamic models suggest that organics formed this way should include amino acids and fatty acids. We assume that fatty acids partition to the membrane. Some hydrophobic amino acids chelate FeS nanocrystals, producing three positive feedbacks: (i) an increase in catalytic surface area; (ii) partitioning of FeS nanocrystals to the membrane; and (iii) a proton-motive active site for carbon fixing that mimics the enzyme Ech. These positive feedbacks enable the fastest-growing protocells to dominate the early ecosystem through a simple form of heredity. We propose that as new organics are produced inside the protocells, the localized high-energy environment is more likely to form ribonucleotides, linking RNA replication to its ability to drive protocell growth from the beginning. Our novel conceptualization sets out conditions under which protocell heredity and competition could arise, and points to where crucial experimental work is required.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.

Acetyl Phosphate as a Primordial Energy Currency at the Origin of Life

Metabolism is primed through the formation of thioesters via acetyl CoA and the phosphorylation of substrates by ATP. Prebiotic equivalents such as methyl thioacetate and acetyl phosphate have been proposed to catalyse analogous reactions at the origin of life, but their propensity to hydrolyse challenges this view. Here we show that acetyl phosphate (AcP) can be synthesised in water within minutes from thioacetate (but not methyl thioacetate) under ambient conditions. AcP is stable over hours, depending on temperature, pH and cation content, giving it an ideal poise between stability and reactivity. We show that AcP can phosphorylate nucleotide precursors such as ribose to ribose-5-phosphate and adenosine to adenosine monophosphate, at modest (~2%) yield in water, and at a range of pH. AcP can also phosphorylate ADP to ATP in water over several hours at 50 °C. But AcP did not promote polymerization of either glycine or AMP. The amino group of glycine was preferentially acetylated by AcP, especially at alkaline pH, hindering the formation of polypeptides. AMP formed small stacks of up to 7 monomers, but these did not polymerise in the presence of AcP in aqueous solution. We conclude that AcP can phosphorylate biologically meaningful substrates in a manner analogous to ATP, promoting the origins of metabolism, but is unlikely to have driven polymerization of macromolecules such as polypeptides or RNA in free solution. This is consistent with the idea that a period of monomer (cofactor) catalysis preceded the emergence of polymeric enzymes or ribozymes at the origin of life.

Effects of salinity on the adsorption of nucleotides onto phyllosilicates

In the context of the origin of life, phyllosilicate surfaces might favor the adsorption, concentration and reactivity of otherwise diluted prebiotic molecules. The primitive oceanic seafloor was certainly rich in Fe-Mg-rich phyllosilicates. The salinity of the primitive seawater remains largely unknown. Values ranging from 1 to 15 times modern salinity have been proposed and the salt composition of the primitive ocean also remains elusive although it may have played a role in the interactions between nucleotides and mineral surfaces. Therefore we studied the adsorption of 5'-monophosphate deoxyguanosine (dGMP) as a model nucleotide onto a Fe-rich swelling clay, i.e. nontronite, and an Al-rich phyllosilicate, i.e. pyrophyllite, for comparison. Experiments were carried out at atmospheric pressure, 25 °C and natural pH, with a series of salts NaCl, MgCl₂, CaCl₂, MgSO₄, NaH₂PO₄ and LaCl₃ in order to evaluate the effect of cations and anions on dGMP adsorption. The present study shows that nucleotides are adsorbed on both phyllosilicates via a ligand exchange mechanism. The phosphate group of the nucleotide is adsorbed on the lateral metal hydroxyls of the broken edges of phyllosilicates. The presence of divalent cations or molecular anions, such as phosphate or sulfate, tends to inhibit this interaction on mineral surfaces. However, in the presence of divalent cations, cationic bridging on the basal surfaces of the swelling clay also occurs and could induce a higher retention capacity of the swelling clays compared to non-swelling phyllosilicates in primitive and modern natural environments.

Probing of molecular replication and accumulation in shallow heat gradients through numerical simulations

How can living matter arise from dead matter? All known living systems are built around information stored in RNA and DNA. To protect this information against molecular degradation and diffusion, the second law of thermodynamics imposes the need for a non-equilibrium driving force. Following a series of successful experiments using thermal gradients, we have shown that heat gradients across sub-millimetre pores can drive accumulation, replication, and selection of ever longer molecules, implementing all the necessary parts for Darwinian evolution. For these lab experiments to proceed with ample speed, however, the temperature gradients have to be quite steep, reaching up to 30 K per 100 μm. Here we use computer simulations based on experimental data to show that 2000-fold shallower temperature gradients - down to 100 K over one metre - can still drive the accumulation of protobiomolecules. This finding opens the door for various environments to potentially host the origins of life: volcanic, water-vapour, or hydrothermal settings. Following the trajectories of single molecules in simulation, we also find that they are subjected to frequent temperature oscillations inside these pores, facilitating e.g. template-directed replication mechanisms. The tilting of the pore configuration is the central strategy to achieve replication in a shallow temperature gradient. Our results suggest that shallow thermal gradients across porous rocks could have facilitated the formation of evolutionary machines, significantly increasing the number of potential sites for the origin of life on young rocky planets.

Toy trains, loaded dice and the origin of life: dimerization on mineral surfaces under periodic drive with Gaussian inputs

In a major extension of previous work, we model the putative hydrothermal rock pore setting for the origin of life on Earth as a series of coupled continuous flow units (the toy train). Perfusing through this train are reactants that set up thermochemical and pH oscillations, and an activated nucleotide that produces monomer and dimer monophosphates. The dynamical equations that model this system are thermally self-consistent. In an innovative step that breaks some new ground, we build stochasticity of the inputs into the model. The computational results infer various constraints and conditions on, and insights into, chemical evolution and the origin of life and its physical setting: long, interconnected porous structures with longitudinal non-uniformity would have been favourable, and the ubiquitous pH dependences of biology may have been established in the prebiotic era. We demonstrate the important role of Gaussian fluctuations of the inputs in driving polymerization, evolution and diversification. In particular, we find that the probability distribution of the resulting output fluctuations is left-skewed and right-weighted (the loaded dice), which could favour chemical evolution towards a living RNA world. We tentatively name this distribution 'Goldilocks'. These results also vindicate the general approach of constructing and running a simple model to learn important new information about a complex system.

Origin of the RNA world: The fate of nucleobases in warm little ponds

Before the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favorable environments on early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet-dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA. We couple Earth's early evolution with complex prebiotic chemistry in these environments. We find that RNA polymers must have emerged very quickly after the deposition of meteorites (less than a few years). Their constituent nucleobases were primarily meteoritic in origin and not from interplanetary dust particles. Ponds appeared as continents rose out of the early global ocean, but this increasing availability of "targets" for meteorites was offset by declining meteorite bombardment rates. Moreover, the rapid losses of nucleobases to pond seepage during wet periods, and to UV photodissociation during dry periods, mean that the synthesis of nucleotides and their polymerization into RNA occurred in just one to a few wet-dry cycles. Under these conditions, RNA polymers likely appeared before 4.17 billion years ago.

Can Life Begin on Enceladus? A Perspective from Hydrothermal Chemistry

Enceladus is a target of future missions designed to search for existing life or its precursors. Recent flybys of Enceladus by the Cassini probe have confirmed the existence of a long-lived global ocean laced with organic compounds and biologically available nitrogen. This immediately suggests the possibility that life could have begun and may still exist on Enceladus. Here we will compare the properties of two proposed sites for the origin of life on Earth-hydrothermal vents on the ocean floor and hydrothermal volcanic fields at the surface-and ask whether similar conditions could have fostered the origin of life on Enceladus. The answer depends on which of the two sites would be more conducive for the chemical evolution leading to life's origin. A hydrothermal vent origin would allow life to begin in the Enceladus ocean, but if the origin of life requires freshwater hydrothermal pools undergoing wet-dry cycles, the Enceladus ocean could be habitable but lifeless. These arguments also apply directly to Europa and indirectly to early Mars. Key Words: Enceladus-Hydrothermal vents-Hydrothermal fields-Origin of life. Astrobiology 17, 834-839.

Experimentally Testing Hydrothermal Vent Origin of Life on Enceladus and Other Icy/Ocean Worlds

We review various laboratory strategies and methods that can be utilized to simulate prebiotic processes and origin of life in hydrothermal vent systems on icy/ocean worlds. Crucial steps that could be simulated in the laboratory include simulations of water-rock chemistry (e.g., serpentinization) to produce hydrothermal fluids, the types of mineral catalysts and energy gradients produced in vent interfaces where hydrothermal fluids interface with the surrounding seawater, and simulations of biologically relevant chemistry in flow-through gradient systems (i.e., far-from-equilibrium experiments). We describe some examples of experimental designs in detail, which are adaptable and could be used to test particular hypotheses about ocean world energetics or mineral/organic chemistry. Enceladus among the ocean worlds provides an ideal test case, since the pressure at the ocean floor is more easily simulated in the lab. Results for Enceladus could be extrapolated with further experiments and modeling to understand other ocean worlds. Key Words: Enceladus-Ocean worlds-Icy worlds-Hydrothermal vent-Iron sulfide-Gradient. Astrobiology 17, 820-833.

Conjecture and hypothesis: The importance of reality checks

In origins of life research, it is important to understand the difference between conjecture and hypothesis. This commentary explores the difference and recommends alternative hypotheses as a way to advance our understanding of how life can begin on the Earth and other habitable planets. As an example of how this approach can be used, two conditions have been proposed for sites conducive to the origin of life: hydrothermal vents in salty seawater, and fresh water hydrothermal fields associated with volcanic landmasses. These are considered as alternative hypotheses and the accumulating weight of evidence for each site is described and analyzed.

The Role of Lipid Membranes in Life's Origin

At some point in early evolution, life became cellular. Assuming that this step was required for the origin of life, there would necessarily be a pre-existing source of amphihilic compounds capable of assembling into membranous compartments. It is possible to make informed guesses about the properties of such compounds and the conditions most conducive to their self-assembly into boundary structures. The membranes were likely to incorporate mixtures of hydrocarbon derivatives between 10 and 20 carbons in length with carboxylate or hydroxyl head groups. Such compounds can be synthesized by chemical reactions and small amounts were almost certainly present in the prebiotic environment. Membrane assembly occurs most readily in low ionic strength solutions with minimal content of salt and divalent cations, which suggests that cellular life began in fresh water pools associated with volcanic islands rather than submarine hydrothermal vents.