Biochemical evolution III: polymerization on organophilic silica-rich surfaces, crystal-chemical modeling, formation of first cells, and geological clues

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.

Inorganic-organic coprecipitation: spontaneous formation of enclosed and porous silica compartments with enriched biopolymers

We show that it is possible to spontaneously form all-enclosed compartments with microporous shells and enriched biopolymers via simple coprecipitation of silica and biopolymers. The reaction involves mild conditions and tolerates the random mixing of multiple reagents. Such a synthetic advance points to a new direction for resolving the chicken-egg dilemma of how the early life forms were hosted: without a physical barrier it would be difficult to maintain organized reactions, but without organized reactions, it would be difficult to create a cell membrane. In our synthesis, the divalent cation Ca²⁺ plays a critical role in the co-precipitation and in creating hollow compartments after simple dilution with water. The precursor of silica, poly(silicic acid), is a negatively charged, cross-linked polymer. It could be co-precipitated with negatively charged biopolymers such as DNA and proteins, whereas the remaining silica precursor forms a conformal and microporous shell on the surface of the initial precipitate. After etching, the biopolymers are retained inside the hollow compartments. The fact that multiple favorable conditions are easily brought together in enclosed compartments opens new possibilities in theorizing the host of early life forms.

The Formation of RNA Pre-Polymers in the Presence of Different Prebiotic Mineral Surfaces Studied by Molecular Dynamics Simulations

We used all-atom Molecular Dynamics (MD) computer simulations to study the formation of pre-polymers between the four nucleotides in RNA (AMP, UMP, CMP, GMP) in the presence of different substrates that could have been present in a prebiotic environment. Pre-polymers are C3'-C5' hydrogen-bonded nucleotides that have been suggested to be the precursors of phosphodiester-bonded RNA polymers. We simulated wet-dry cycles by successively removing water molecules from the simulations, from ~60 to 3 water molecules per nucleotide. The nine substrates in this study include three clay minerals, one mica, one phosphate mineral, one silica, and two metal oxides. The substrates differ in their surface charge and ability to form hydrogen bonds with the nucleotides. From the MD simulations, we quantify the interactions between different nucleotides, and between nucleotides and substrates. For comparison, we included graphite as an inert substrate, which is not charged and cannot form hydrogen bonds. We also simulated the dehydration of a nucleotide-only system, which mimics the drying of small droplets. The number of hydrogen bonds between nucleotides and nucleotides and substrates was found to increase significantly when water molecules were removed from the systems. The largest number of C3'-C5' hydrogen bonds between nucleotides occurred in the graphite and nucleotide-only systems. While the surface of the substrates led to an organization and periodic arrangement of the nucleotides, none of the substrates was found to be a catalyst for pre-polymer formation, neither at full hydration, nor when dehydrated. While confinement and dehydration seem to be the main drivers for hydrogen bond formation, substrate interactions reduced the interactions between nucleotides in all cases. Our findings suggest that small supersaturated water droplets that could have been produced by geysers or springs on the primitive Earth may play an important role in non-enzymatic RNA polymerization.

Clays and the Origin of Life: The Experiments

There are three groups of scientists dominating the search for the origin of life: the organic chemists (the Soup), the molecular biologists (RNA world), and the inorganic chemists (metabolism and transient-state metal ions), all of which have experimental adjuncts. It is time for Clays and the Origin of Life to have its experimental adjunct. The clay data coming from Mars and carbonaceous chondrites have necessitated a review of the role that clays played in the origin of life on Earth. The data from Mars have suggested that Fe-clays such as nontronite, ferrous saponites, and several other clays were formed on early Mars when it had sufficient water. This raised the question of the possible role that these clays may have played in the origin of life on Mars. This has put clays front and center in the studies on the origin of life not only on Mars but also here on Earth. One of the major questions is: What was the catalytic role of Fe-clays in the origin and development of metabolism here on Earth? First, there is the recent finding of a chiral amino acid (isovaline) that formed on the surface of a clay mineral on several carbonaceous chondrites. This points to the formation of amino acids on the surface of clay minerals on carbonaceous chondrites from simpler molecules, e.g., CO₂, NH₃, and HCN. Additionally, there is the catalytic role of small organic molecules, such as dicarboxylic acids and amino acids found on carbonaceous chondrites, in the formation of Fe-clays themselves. Amino acids and nucleotides adsorb on clay surfaces on Earth and subsequently polymerize. All of these observations and more must be subjected to strict experimental analysis. This review provides an overview of what has happened and is now happening in the experimental clay world related to the origin of life. The emphasis is on smectite-group clay minerals, such as montmorillonite and nontronite.

Amino acid encapsulation in zeolite MOR: Effect of spatial confinement

In this study the absorption of glycine, α-alanine and β-alanine amino acids into the pores of the synthetic zeolite Na-mordenite was investigated with the aim of: (i) evaluating the effectiveness of the MOR framework type in amino acid adsorption (via vapor and aqueous loading); (ii) understanding the host-guest and guest-guest interactions to possibly design a tailor made material and a loading procedure able to maximize the amino acid adsorption; (iii) studying the effect of pressure on the adsorbed amino acids such as, for instance, possible amino acid condensation. The structural characterization, carried out with the combination of diffractometric and infrared spectroscopy analyses, shows that MOR can adsorb amino acids, which are found both in protonated/deprotonated (possibly also generating zwitterions) form. Vapor loading is ineffective for α-alanine, while it is effective in β-alanine and glycine adsorption, even if using different loading degrees. The shape and size of MOR channels make this zeolite suitable to accommodate a peptide. In a glycine loaded sample some molecules condensate to form cyclic dimers, while linear oligomers are detected only in a β-alanine MOR hybrid. The sample loaded with α-L-alanine from aqueous solution does not show the presence of amide bond signals, indicating that the molecules are mostly hosted in zwitterionic form in Na-MOR channels. The application of external baric stimuli does not induce substantial modifications in the structure of the glycine loaded zeolite; this result may be explained by the low number of molecules hosted in the channels. The amino acid amount within the zeolite pores is the most important reactivity parameter and an increased loading could induce chemical modifications.

Non-associative phase separation in an evaporating droplet as a model for prebiotic compartmentalization

The synthetic pathways of life’s building blocks are envisaged to be through a series of complex prebiotic reactions and processes. However, the strategy to compartmentalize and concentrate biopolymers under prebiotic conditions remains elusive. Liquid-liquid phase separation is a mechanism by which membraneless organelles form inside cells, and has been hypothesized as a potential mechanism for prebiotic compartmentalization. Associative phase separation of oppositely charged species has been shown to partition RNA, but the strongly negative charge exhibited by RNA suggests that RNA-polycation interactions could inhibit RNA folding and its functioning inside the coacervates. Here, we present a prebiotically plausible pathway for non-associative phase separation within an evaporating all-aqueous sessile droplet. We quantitatively investigate the kinetic pathway of phase separation triggered by the non-uniform evaporation rate, together with the Marangoni flow-driven hydrodynamics inside the sessile droplet. With the ability to undergo liquid-liquid phase separation, the drying droplets provide a robust mechanism for formation of prebiotic membraneless compartments, as demonstrated by localization and storage of nucleic acids, in vitro transcription, as well as a three-fold enhancement of ribozyme activity. The compartmentalization mechanism illustrated in this model system is feasible on wet organophilic silica-rich surfaces during early molecular evolution.

Prebiotic compartmentalization could prove essential for the evolution of life. Guo et al. show that liquid-liquid separation in an aqueous two-phase system driven by evaporation may already suffice to facilitate chemical processes required for the RNA world hypothesis.

A Hydrothermal-Sedimentary Context for the Origin of Life

Critical to the origin of life are the ingredients of life, of course, but also the physical and chemical conditions in which prebiotic chemical reactions can take place. These factors place constraints on the types of Hadean environment in which life could have emerged. Many locations, ranging from hydrothermal vents and pumice rafts, through volcanic-hosted splash pools to continental springs and rivers, have been proposed for the emergence of life on Earth, each with respective advantages and certain disadvantages. However, there is another, hitherto unrecognized environment that, on the Hadean Earth (4.5-4.0 Ga), would have been more important than any other in terms of spatial and temporal scale: the sedimentary layer between oceanic crust and seawater. Using as an example sediments from the 3.5-3.33 Ga Barberton Greenstone Belt, South Africa, analogous at least on a local scale to those of the Hadean eon, we document constant permeation of the porous, carbonaceous, and reactive sedimentary layer by hydrothermal fluids emanating from the crust. This partially UV-protected, subaqueous sedimentary environment, characterized by physical and chemical gradients, represented a widespread system of miniature chemical reactors in which the production and complexification of prebiotic molecules could have led to the origin of life. Key Words: Origin of life-Hadean environment-Mineral surface reactions-Hydrothermal fluids-Archean volcanic sediments. Astrobiology 18, 259-293.

Chance, necessity and the origins of life: a physical sciences perspective

Earth's 4.5-billion-year history has witnessed a complex sequence of high-probability chemical and physical processes, as well as 'frozen accidents'. Most models of life's origins similarly invoke a sequence of chemical reactions and molecular self-assemblies in which both necessity and chance play important roles. Recent research adds two important insights into this discussion. First, in the context of chemical reactions, chance versus necessity is an inherently false dichotomy-a range of probabilities exists for many natural events. Second, given the combinatorial richness of early Earth's chemical and physical environments, events in molecular evolution that are unlikely at limited laboratory scales of space and time may, nevertheless, be inevitable on an Earth-like planet at time scales of a billion years.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Hypothesis of Lithocoding: Origin of the Genetic Code as a "Double Jigsaw Puzzle" of Nucleobase-Containing Molecules and Amino Acids Assembled by Sequential Filling of Apatite Mineral Cellules

The hypothesis of direct coding, assuming the direct contact of pairs of coding molecules with amino acid side chains in hollow unit cells (cellules) of a regular crystal-structure mineral is proposed. The coding nucleobase-containing molecules in each cellule (named "lithocodon") partially shield each other; the remaining free space determines the stereochemical character of the filling side chain. Apatite-group minerals are considered as the most preferable for this type of coding (named "lithocoding"). A scheme of the cellule with certain stereometric parameters, providing for the isomeric selection of contacting molecules is proposed. We modelled the filling of cellules with molecules involved in direct coding, with the possibility of coding by their single combination for a group of stereochemically similar amino acids. The regular ordered arrangement of cellules enables the polymerization of amino acids and nucleobase-containing molecules in the same direction (named "lithotranslation") preventing the shift of coding. A table of the presumed "LithoCode" (possible and optimal lithocodon assignments for abiogenically synthesized α-amino acids involved in lithocoding and lithotranslation) is proposed. The magmatic nature of the mineral, abiogenic synthesis of organic molecules and polymerization events are considered within the framework of the proposed "volcanic scenario".

ESR study of interfacial hydration layers of polypeptides in water-filled nanochannels and in vitrified bulk solvents

There is considerable evidence for the essential role of surface water in protein function and structure. However, it is unclear to what extent the hydration water and protein are coupled and interact with each other. Here, we show by ESR experiments (cw, DEER, ESEEM, and ESE techniques) with spin-labeling and nanoconfinement techniques that the vitrified hydration layers can be evidently recognized in the ESR spectra, providing nanoscale understanding for the biological interfacial water. Two peptides of different secondary structures and lengths are studied in vitrified bulk solvents and in water-filled nanochannels of different pore diameter (6.1∼7.6 nm). The existence of surface hydration and bulk shells are demonstrated. Water in the immediate vicinity of the nitroxide label (within the van der Waals contacts, ∼0.35 nm) at the water-peptide interface is verified to be non-crystalline at 50 K, and the water accessibility changes little with the nanochannel dimension. Nevertheless, this water accessibility for the nanochannel cases is only half the value for the bulk solvent, even though the peptide structures remain largely the same as those immersed in the bulk solvents. On the other hand, the hydration density in the range of ∼2 nm from the nitroxide spin increases substantially with decreasing pore size, as the density for the largest pore size (7.6 nm) is comparable to that for the bulk solvent. The results demonstrate that while the peptides are confined but structurally unaltered in the nanochannels, their surrounding water exhibits density heterogeneity along the peptide surface normal. The causes and implications, especially those involving the interactions between the first hydration water and peptides, of these observations are discussed. Spin-label ESR techniques are proven useful for studying the structure and influences of interfacial hydration.

Mineral-organic interfacial processes: potential roles in the origins of life

Life is believed to have originated on Earth ∼4.4-3.5 Ga ago, via processes in which organic compounds supplied by the environment self-organized, in some geochemical environmental niches, into systems capable of replication with hereditary mutation. This process is generally supposed to have occurred in an aqueous environment and, likely, in the presence of minerals. Mineral surfaces present rich opportunities for heterogeneous catalysis and concentration which may have significantly altered and directed the process of prebiotic organic complexification leading to life. We review here general concepts in prebiotic mineral-organic interfacial processes, as well as recent advances in the study of mineral surface-organic interactions of potential relevance to understanding the origin of life.

Impact of mineral micropores on transport and fate of organic contaminants: a review

Nanometer-scale pores are abundant in porous geological media (soils, sediments, and aquifer materials), and may account for over >90% of total mineral surface areas. Sorption of organic contaminants in mineral micropores (<2 nm) plays a key role in controlling their fate and transport when the porous geological media have very low organic carbon contents (<0.1%). Significant adsorption of hydrophobic organic contaminants could only occur in the hydrophobic micropore spaces because of the strong competition from water. The rate of desorption from micropores is very slow due to hindered diffusion, resulting in distinct two-stage desorption behavior for microporous solids. Size exclusion effect prevents micropore-sorbed contaminants from being accessed by microorganisms and their extracellular enzymes, thus reducing their bioavailability and biodegradation rates. Results from recent studies indicate that sorption in micropores can also inhibit abiotic degradation of reactive contaminants by protecting them in confined spaces with little reactive water, slowing down hydrolysis and other water-mediated transformations. As a result of the inhibitory effect on abiotic and biotic transformations, and the slow desorption due to hindered diffusion, sorption in hydrophobic micropores of porous geological media can cause preservation of anthropogenic organic contaminants in the subsurface and may increase their persistence to the time scale of geological ages under appropriate conditions. From a practical perspective, understanding the role of mineral micropores is important in assessing the long-term ecotoxicological risk of organic contaminants in the subsurface and designing remediation strategies.

Pumice as a remarkable substrate for the origin of life

The context for the emergence of life on Earth sometime prior to 3.5 billion years ago is almost as big a puzzle as the definition of life itself. Hitherto, the problem has largely been addressed in terms of theoretical and experimental chemistry plus evidence from extremophile habitats like modern hydrothermal vents and meteorite impact structures. Here, we argue that extensive rafts of glassy, porous, and gas-rich pumice could have had a significant role in the origin of life and provided an important habitat for the earliest communities of microorganisms. This is because pumice has four remarkable properties. First, during eruption it develops the highest surface-area-to-volume ratio known for any rock type. Second, it is the only known rock type that floats as rafts at the air-water interface and then becomes beached in the tidal zone for long periods of time. Third, it is exposed to an unusually wide variety of conditions, including dehydration. Finally, from rafting to burial, it has a remarkable ability to adsorb metals, organics, and phosphates as well as to host organic catalysts such as zeolites and titanium oxides. These remarkable properties now deserve to be rigorously explored in the laboratory and the early rock record.

Adsorption of thymine and uracil on 1:1 clay mineral surfaces: comprehensive ab initio study on influence of sodium cation and water

This computational study performed using the density functional theory shows that hydrated and non-hydrated tetrahedral and octahedral kaolinite mineral surfaces in the presence of a cation adsorb the nucleic acid bases thymine and uracil well. Differences in the structure and chemistry of specific clay mineral surfaces led to a variety of DNA bases adsorption mechanisms. The energetically most predisposed positions for an adsorbate molecule on the mineral surface were revealed. The target molecule binding with the surface can be characterized as physisorption, which occurs mainly due to a cation-molecular oxygen interaction, with hydrogen bonds providing an additional stabilization. The adsorption strength is proportional to the number of intermolecular interactions formed between the target molecule and the surface. From the Atoms in Molecules analysis and comparison of binding energy values of studied systems it is concluded that the sorption activity of kaolinite minerals for thymine and uracil depends on various factors, among which are the structure and accessibility of the organic compounds. The adsorption is governed mostly by the surface type, its properties and presence of cation, which cause a selective binding of the nucleobase. Adsorbate stabilization on the mineral surface increases only slightly with explicit addition of water. Comparison of activity of different studied kaolinite mineral models reveals the following order for stabilization: octahedral-Na-water > octahedral-Na > tetrahedral-Na > tetrahedral-Na-water. Further investigation of the electrostatic potentials helps understanding of the adsorption process and confirmation of the active sites on the kaolinite mineral surfaces. Based on the conclusions that clay mineral affinity for DNA and RNA bases can vary due to different structural and chemical properties of the surface, a hypothesis on possible role of clays in the origin of life was made.

A demonstration of an affinity between pyrite and organic matter in a hydrothermal setting

One of the key-principles of the iron-sulphur world theory is to bring organic molecules close enough to interact with each other, using the surface of pyrite as a substrate in a hydrothermal setting. The present paper explores the relationship of pyrite and organic matter in a hydrothermal setting from the geological record; in hydrothermal calcite veins from Carboniferous limestones in central Ireland. Here, the organic matter is accumulated as coatings around, and through, pyrite grains. Most of the pyrite grains are euhedral-subhedral crystals, ranging in size from ca 0.1-0.5 mm in diameter, and they are scattered throughout the matrix of the vein calcite. The organic matter was deposited from a hydrothermal fluid at a temperature of at least 200°C, and gives a Raman signature of disordered carbon. This study points to an example from a hydrothermal setting in the geological record, demonstrating that pyrite can have a high potential for the concentration and accumulation of organic materials.

Mineral surfaces, geochemical complexities, and the origins of life

Crystalline surfaces of common rock-forming minerals are likely to have played several important roles in life's geochemical origins. Transition metal sulfides and oxides promote a variety of organic reactions, including nitrogen reduction, hydroformylation, amination, and Fischer-Tropsch-type synthesis. Fine-grained clay minerals and hydroxides facilitate lipid self-organization and condensation polymerization reactions, notably of RNA monomers. Surfaces of common rock-forming oxides, silicates, and carbonates select and concentrate specific amino acids, sugars, and other molecular species, while potentially enhancing their thermal stabilities. Chiral surfaces of these minerals also have been shown to separate left- and right-handed molecules. Thus, mineral surfaces may have contributed centrally to the linked prebiotic problems of containment and organization by promoting the transition from a dilute prebiotic "soup" to highly ordered local domains of key biomolecules.

On the beneficial role of silicon to organisms: a case study on the importance of silicon chemistry to metal accumulation in yeast

Silicon is involved in numerous important structural and functional roles in a wide range of organisms, including diatoms, plants, and humans, but clear mechanisms have been discovered only in diatoms and sponges. Silicate availability influences metal concentrations within various cell- and tissue-types, but a mechanism has not been discovered so far. In an earlier study on Baker's yeast Saccharomyces cerevisiae it was proposed that a chemical mechanism, rather than a biological one, is important. In the present study, the interaction of silicon with Baker's yeast is further investigated by studying the influence of zinc and magnesium on Si accumulation both at a low and a high silicate concentration in the medium. Si accumulation fitted well with Freundlich adsorption and Si release followed depolymerization kinetics, indicating that silicate adsorbs to the surface of the cell rather than being transported over the cell membrane. Subsequently, adsorbed silicate interacts with metal ions and, therefore, alters the cell's affinity for these ions. Since several metals are nutritional, these Si interactions can significantly change the growth and viability of organisms. In conclusion, the results show that chemistry is important in Si and metal accumulation in Baker's yeast, and suggest that similar mechanisms should be studied in detail in other organisms to unravel essential roles of Si.

Mineral interface in extreme habitats: a niche for primitive molecular evolution for the appearance of different forms of life on earth

Innumerable primitive membrane and protocell models in latter stages of chemical evolution are based on the properties of minerals' interfaces with primitive seawater. The ordering mechanism induced by mineral interfaces has been the basis of several prebiotic models of molecular complexification and compartmentalization towards the appearance and evolution of different forms of life. Since mineral-aqueous media interfaces have been considered as initial stages of prebiotic models dealing with the formation of energy-transducing systems, the interface formed by pyrite in the presence of artificial primitive seawater was chosen to show the functional richness of this special niche. Interfaces--especially sulphide interfaces--were proposed as suitable niches for a two-carbon extant metabolism, synthesis and polymerization of nucleotides--to form ancient RNA strands--and assembly of amino acids synthesized in its vicinity. Accumulation of precursors at sulphide interfaces could have avoided their dilution into the Hadean seas and provided a suitable geochemical environment for a variety of molecular interactions. In this essay, we present a short review of the proposed roles of mineral interfaces in chemical evolution towards the appearance of primitive membranes, which might have been relevant for the advent of cellular life before its divergent evolution and differentiation. This survey covers several previous studies on the early cycles of energy conservation and of the formation of molecules carrying genetic information.

Surfactant assemblies and their various possible roles for the origin(s) of life

A large number of surfactants (surface active molecules) are chemically simple compounds that can be obtained by simple chemical reactions, in some cases even under presumably prebiotic conditions. Surfactant assemblies are self-organized polymolecular aggregates of surfactants, in the simplest case micelles, vesicles, hexagonal and cubic phases. It may be that these different types of surfactant assemblies have played various, so-far underestimated important roles in the processes that led to the formation of the first living systems. Although nucleic acids are key players in the formation of cells as we know them today (RNA world hypothesis), it is still unclear how RNA could have been formed under prebiotic conditions. Surfactants with their self-organizing properties may have assisted, controlled and compartimentalized some of the chemical reactions that eventually led to the formation of molecules like RNA. Therefore, surfactants were possibly very important in prebiotic times in the sense that they may have been involved in different physical and chemical processes that finally led to a transformation of non-living matter to the first cellular form(s) of life. This hypothesis is based on four main experimental observations: (i) Surfactant aggregation can lead to cell-like compartimentation (vesicles). (ii) Surfactant assemblies can provide local reaction conditions that are very different from the bulk medium, which may lead to a dramatic change in the rate of chemical reactions and to a change in reaction product distributions. (iii) The surface properties of surfactant assemblies that may be liquid- or solid-like, charged or neutral, and the elasticity and packing density of surfactant assemblies depend on the chemical structure of the surfactants, on the presence of other molecules, and on the overall environmental conditions (e. g. temperature). This wide range of surface characteristics of surfactant assemblies may allow a control of surface-bound chemical reactions not only by the charge or hydrophobicity of the surface but also by its "softness". (iv) Chiral polymolecular assemblies (helices) may form from chiral surfactants. There are many examples that illustrate the different roles and potential roles of surfactant assemblies in different research areas outside of the field of the origin(s) of life, most importantly in investigations of contemporary living systems, in nanotechnology applications, and in the development of drug delivery systems. Concepts and ideas behind many of these applications may have relevance also in connection to the different unsolved problems in understanding the origin(s) of life.

Did life begin on the beach?

Water is one of the prerequisites of life. Further requirements are the existence of a system of interacting organic molecules capable of capturing and converting the supply of external energy and elaborating the replicating function that is needed for propagation. None of this would be possible without the existence of some means of concentrating, selecting, and then containing these mutually interacting substances in proximity to one another, i.e., a primitive cell. Starting from this hypothesis we propose a model for the development of life on Earth. Our model embodies the following new features: (1) rapid cycles of catalysis and transport of material, (2) desegregation (separation by tidal action and degradation by catalysis) as well as segregation (by chromatography on tidal beaches), (3) cross-catalysis instead of auto-catalysis, as well as (4) compartmentalization, although the latter idea is of course not new. But our "lipid first" model, in contrast to earlier "peptide first" or "RNA first" models, provides for the compartments needed to act as a cradle for the subsequent development of information- rich molecules like peptides and RNA. If anything, the earliest information-rich molecules were probably membrane-spanning peptides/proteins.

Mineral radioactivity in sands as a mechanism for fixation of organic carbon on the early Earth

Irradiation of organic molecules by mineral radioactivity is a feasible alternative to cosmic irradiation to precipitate solid organic carbon-rich matter on the early Earth. Radioactive (uranium- and thorium-rich) minerals have been concentrated at the Earth's surface, and accumulated accretionary coatings of carbon due to irradiation, since early Archean times. The organic accretion process could have occurred at the surface or in the sub-surface, and is independent of a terrestrial or extraterrestrial source for the carbon.

Cations as mediators of the adsorption of nucleic acids on clay surfaces in prebiotic environments

Monovalent ([Na+] > 10 mM) and divalent ([Ca2+], [Mg2+] > 1.0 mM) cations induced the precipitation of nucleic acid molecules. In the presence of clay minerals (montmorillonite and kaolinite), there was adsorption instead of precipitation. The cation concentration needed for adsorption depended on both the valence of the cations and the chemical nature of the nucleic acid molecules. Double-stranded nucleic acids needed higher cation concentrations than single-stranded ones to be adsorbed to the same extent on clay. Divalent cations were more efficient than monovalent ones in mediating adsorption. Adsorption to the clay occurred only when both nucleic acids and cations were present. However, once the complexes were formed, the cations could not be removed from the system by washing, indicating that they are directly involved in the association between nucleic acids and mineral surfaces. These observations indicate that cations take part directly in the formation of nucleic acid-clay complexes, acting as a 'bridge' between the negative charges on the mineral surface and those of the phosphate groups of the genetic polymer. The relatively low cation concentrations needed for adsorption and the ubiquitous presence of clay minerals in the environment suggest that the adsorption of nucleic acids on mineral surfaces could have taken place in prebiotic habitats. This may have played an important role in the formation and preservation of nucleic acids and/or their precursor polymers.

Sticking coefficient-orchestrated selection in a kinetic model for the first origin

The mathematical formalism of the steady-state Poisson equation is applied to a variant of Freeman Dyson's "Toy Model" for a first origin. Our kinetic approach allows for an examination of the requisite conditions under which metabolism is quantized into discrete eigenstates (e.g. Dyson's disordered, saddle point, and metabolically active toy cell states). The surface reaction machinery additionally allows for more realistic modeling, whence the crucial role of sticking coefficients (catalyst precursors) as prebiotic selectors emerges. In our interior source model, a steady influx of vent nutrients fuels the intracellular synthesis of (impermeable) monomers within a rock-encradled cavity. Random adsorptions and desorptions occur at inactive "cell" wall sites (where the inert monomers remain impermeable until their eventual return to the intracellular metabolite pool). Occasionally, metabolizing reactions also occur due to endogeneous source monomers adsorbing at their "active" sites. Dyson's mean field approach is used to simplify the species-specific sticking coefficients at empty active (substrate) sites to functions of the fraction x of sites occupied by (catalytically) active monomers. In short, our work suggests that disorder-order transition models based on random drift between discrete metabolic eigenstates (Dyson's Toy Model) do not, in general, extend to more realistic metabolisms. From a perspective based on quasi-random feedback kinetics, the contraindication for discretization (spontaneous generation) in non-autocatalytic metabolisms is consistent with the emergence of ordered metabolism under hydrothermal driving forces, a provisio the occurrence of each period of vent dormancy coincides with a discrete zero-source (dormant) metabolic state. Cell drift to higher order is induced by the random reactions which happen to enhance the substrate specificity (chemical selectivity) of the sticking coefficients for active monomers. The result is stronger sink effects for metabolizing species, whence active adsorptions are promoted in favor of inactive adsorptions at substrate sites. Positive feedback plays a crucial role in preserving ("propagating") order in the cell wall reaction kinetics and is held in check by negative feedback inhibition of excessive cell growth. Finally, the eventual desorption of randomly growing dysfunctional proteins is postulated as a deterrent to deterioration catastrophes.

The habitat and nature of early life

Earth is over 4,500 million years old. Massive bombardment of the planet took place for the first 500-700 million years, and the largest impacts would have been capable of sterilizing the planet. Probably until 4,000 million years ago or later, occasional impacts might have heated the ocean over 100 degrees C. Life on Earth dates from before about 3,800 million years ago, and is likely to have gone through one or more hot-ocean 'bottlenecks'. Only hyperthermophiles (organisms optimally living in water at 80-110 degrees C) would have survived. It is possible that early life diversified near hydrothermal vents, but hypotheses that life first occupied other pre-bottleneck habitats are tenable (including transfer from Mars on ejecta from impacts there). Early hyperthermophile life, probably near hydrothermal systems, may have been non-photosynthetic, and many housekeeping proteins and biochemical processes may have an original hydrothermal heritage. The development of anoxygenic and then oxygenic photosynthesis would have allowed life to escape the hydrothermal setting. By about 3,500 million years ago, most of the principal biochemical pathways that sustain the modern biosphere had evolved, and were global in scope.