Biochemical evolution II: origin of life in tubular microstructures on weathered feldspar surfaces

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.

Endowing universal CAR T-cell with immune-evasive properties using TALEN-gene editing

Universal CAR T-cell therapies are poised to revolutionize cancer treatment and to improve patient outcomes. However, realizing these advantages in an allogeneic setting requires universal CAR T-cells that can kill target tumor cells, avoid depletion by the host immune system, and proliferate without attacking host tissues. Here, we describe the development of a novel immune-evasive universal CAR T-cells scaffold using precise TALEN-mediated gene editing and DNA matrices vectorized by recombinant adeno-associated virus 6. We simultaneously disrupt and repurpose the endogenous TRAC and B2M loci to generate TCRαβ- and HLA-ABC-deficient T-cells expressing the CAR construct and the NK-inhibitor named HLA-E. This highly efficient gene editing process enables the engineered T-cells to evade NK cell and alloresponsive T-cell attacks and extend their persistence and antitumor activity in the presence of cytotoxic levels of NK cell in vivo and in vitro, respectively. This scaffold could enable the broad use of universal CAR T-cells in allogeneic settings and holds great promise for clinical applications.

New Signatures of Bio-Molecular Complexity in the Hypervelocity Impact Ejecta of Icy Moon Analogues

Impact delivery of prebiotic compounds to the early Earth from an impacting comet is considered to be one of the possible ways by which prebiotic molecules arrived on the Earth. Given the ubiquity of impact features observed on all planetary bodies, bolide impacts may be a common source of organics on other planetary bodies both in our own and other solar systems. Biomolecules such as amino acids have been detected on comets and are known to be synthesized due to impact-induced shock processing. Here we report the results of a set of hypervelocity impact experiments where we shocked icy mixtures of amino acids mimicking the icy surface of planetary bodies with high-speed projectiles using a two-stage light gas gun and analyzed the ejecta material after impact. Electron microscopic observations of the ejecta have shown the presence of macroscale structures with long polypeptide chains revealed from LCMS analysis. These results suggest a pathway in which impact on cometary ices containing building blocks of life can lead to the synthesis of material architectures that could have played a role in the emergence of life on the Earth and which may be applied to other planetary bodies as well.

Greenalite Nanoparticles in Alkaline Vent Plumes as Templates for the Origin of Life

Mineral templates are thought to have played keys roles in the emergence of life. Drawing on recent findings from 3.45-2.45 billion-year-old iron-rich hydrothermal sedimentary rocks, we hypothesize that greenalite (Fe3Si2O5(OH)4) was a readily available mineral in hydrothermal environments, where it may have acted as a template and catalyst in polymerization, vesicle formation and encapsulation, and protocell replication. We argue that venting of dissolved Fe2+ and SiO2(aq) into the anoxic Hadean ocean favored the precipitation of nanometer-sized particles of greenalite in hydrothermal plumes, producing a continuous flow of free-floating clay templates that traversed the ocean. The mixing of acidic, metal-bearing hydrothermal plumes from volcanic ridge systems with more alkaline, organic-bearing plumes generated by serpentinization of ultramafic rocks brought together essential building blocks for life in solutions conducive to greenalite precipitation. We suggest that the extreme disorder in the greenalite crystal lattice, producing structural modulations resembling parallel corrugations (∼22 Å wide) on particle edges, promoted the assembly and alignment of linear RNA-type molecules (∼20 Å diameter). In alkaline solutions, greenalite nanoparticles could have accelerated the growth of membrane vesicles, while their encapsulation allowed RNA-type molecules to continue to form on the mineral templates, potentially enhancing the growth and division of primitive cell membranes. Once self-replicating RNA evolved, the mineral template became redundant, and protocells were free to replicate and roam the ocean realm.

How to Build a Biological Machine Using Engineering Materials and Methods

We present work in 3D printing electric motors from basic materials as the key to building a self-replicating machine to colonise the Moon. First, we explore the nature of the biological realm to ascertain its essence, particularly in relation to the origin of life when the inanimate became animate. We take an expansive view of this to ascertain parallels between the biological and the manufactured worlds. Life must have emerged from the available raw material on Earth and, similarly, a self-replicating machine must exploit and leverage the available resources on the Moon. We then examine these lessons to explore the construction of a self-replicating machine using a universal constructor. It is through the universal constructor that the actuator emerges as critical. We propose that 3D printing constitutes an analogue of the biological ribosome and that 3D printing may constitute a universal construction mechanism. Following a description of our progress in 3D printing motors, we suggest that this engineering effort can inform biology, that motors are a key facet of living organisms and illustrate the importance of motors in biology viewed from the perspective of engineering (in the Feynman spirit of “what I cannot create, I cannot understand”).

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'.

Observing the formation of ice and organic crystals in active sites

Heterogeneous nucleation is vital to a wide range of areas as diverse as ice nucleation on atmospheric aerosols and the fabrication of high-performance thin films. There is excellent evidence that surface topography is a key factor in directing crystallization in real systems; however, the mechanisms by which nanoscale pits and pores promote nucleation remain unclear. Here, we use natural cleavage defects on Muscovite mica to investigate the activity of topographical features in the nucleation from vapor of ice and various organic crystals. Direct observation of crystallization within surface pockets using optical microscopy and also interferometry demonstrates that these sharply acute features provide extremely effective nucleation sites and allows us to determine the mechanism by which this occurs. A confined phase is first seen to form along the apex of the wedge and then grows out of the pocket opening to generate a bulk crystal after a threshold saturation has been achieved. Ice nucleation proceeds in a comparable manner, although our resolution is insufficient to directly observe a condensate before the growth of a bulk crystal. These results provide insight into the mechanism of crystal deposition from vapor on real surfaces, where this will ultimately enable us to use topography to control crystal deposition on surfaces. They are also particularly relevant to our understanding of processes such as cirrus cloud formation, where such topographical features are likely candidates for the "active sites" that make clay particles effective nucleants for ice in the atmosphere.

Microbes, Mineral Evolution, and the Rise of Microcontinents-Origin and Coevolution of Life with Early Earth

Earth is the most mineralogically diverse planet in our solar system, the direct consequence of a coevolving geosphere and biosphere. We consider the possibility that a microbial biosphere originated and thrived in the early Hadean-Archean Earth subseafloor environment, with fundamental consequences for the complex evolution and habitability of our planet. In this hypothesis paper, we explore possible venues for the origin of life and the direct consequences of microbially mediated, low-temperature hydrothermal alteration of the early oceanic lithosphere. We hypothesize that subsurface fluid-rock-microbe interactions resulted in more efficient hydration of the early oceanic crust, which in turn promoted bulk melting to produce the first evolved fragments of felsic crust. These evolved magmas most likely included sialic or tonalitic sheets, felsic volcaniclastics, and minor rhyolitic intrusions emplaced in an Iceland-type extensional setting as the earliest microcontinents. With the further development of proto-tectonic processes, these buoyant felsic crustal fragments formed the nucleus of intra-oceanic tonalite-trondhjemite-granitoid (TTG) island arcs. Thus microbes, by facilitating extensive hydrothermal alteration of the earliest oceanic crust through bioalteration, promoted mineral diversification and may have been early architects of surface environments and microcontinents on young Earth. We explore how the possible onset of subseafloor fluid-rock-microbe interactions on early Earth accelerated metavolcanic clay mineral formation, crustal melting, and subsequent metamorphic mineral evolution. We also consider environmental factors supporting this earliest step in geosphere-biosphere coevolution and the implications for habitability and mineral evolution on other rocky planets, such as Mars.

A Prebiotic Chemistry Experiment on the Adsorption of Nucleic Acids Bases onto a Natural Zeolite

There are currently few mechanisms that can explain how nucleic acid bases were synthesized, concentrated from dilute solutions, and/or protected against degradation by UV radiation or hydrolysis on the prebiotic Earth. A natural zeolite exhibited the potential to adsorb adenine, cytosine, thymine, and uracil over a range of pH, with greater adsorption of adenine and cytosine at acidic pH. Adsorption of all nucleic acid bases was decreased in artificial seawater compared to water, likely due to cation complexation. Furthermore, adsorption of adenine appeared to protect natural zeolite from thermal degradation. The C=O groups from thymine, cytosine and uracil appeared to assist the dissolution of the mineral while the NH2 group from adenine had no effect. As shown by FT-IR spectroscopy, adenine interacted with a natural zeolite through the NH2 group, and cytosine through the C=O group. A pseudo-second-order model best described the kinetics of adenine adsorption, which occurred faster in artificial seawaters.

Metabolically Coupled Replicator Systems: Overview of an RNA-world model concept of prebiotic evolution on mineral surfaces

Metabolically Coupled Replicator Systems (MCRS) are a family of models implementing a simple, physico-chemically and ecologically feasible scenario for the first steps of chemical evolution towards life. Evolution in an abiotically produced RNA-population sets in as soon as any one of the RNA molecules become autocatalytic by engaging in template directed self-replication from activated monomers, and starts increasing exponentially. Competition for the finite external supply of monomers ignites selection favouring RNA molecules with catalytic activity helping self-replication by any possible means. One way of providing such autocatalytic help is to become a replicase ribozyme. An additional way is through increasing monomer supply by contributing to monomer synthesis from external resources, i.e., by evolving metabolic enzyme activity. Retroevolution may build up an increasingly autotrophic, cooperating community of metabolic ribozymes running an increasingly complicated and ever more efficient metabolism. Maintaining such a cooperating community of metabolic replicators raises two serious ecological problems: one is keeping the system coexistent in spite of the different replicabilities of the cooperating replicators; the other is constraining parasitism, i.e., keeping "cheaters" in check. Surface-bound MCRS provide an automatic solution to both problems: coexistence and parasite resistance are the consequences of assuming the local nature of metabolic interactions. In this review we present an overview of results published in previous articles, showing that these effects are, indeed, robust in different MCRS implementations, by considering different environmental setups and realistic chemical details in a few different models. We argue that the MCRS model framework naturally offers a suitable starting point for the future modelling of membrane evolution and extending the theory to cover the emergence of the first protocell in a self-consistent manner. The coevolution of metabolic, genetic and membrane functions is hypothesized to follow the progressive sequestration scenario, the conceptual blueprint for the earliest steps of protocell evolution.

Reactions and surface interactions of saccharides in cement slurries

Glucose, maltodextrin, and sucrose exhibit significant differences in their alkaline reaction properties and interactions in aluminate/silicate cement slurries that result in diverse hydration behaviors of cements. Using 1D solution- and solid-state (13)C nuclear magnetic resonance (NMR), the structures of these closely related saccharides are identified in aqueous cement slurry solutions and as adsorbed on inorganic oxide cement surfaces during the early stages of hydration. Solid-state 1D (29)Si and 2D (27)Al{(1)H} and (13)C{(1)H} NMR techniques, including the use of very high magnetic fields (18.8 T), allow the characterization of the hydrating silicate and aluminate surfaces, where interactions with adsorbed organic species influence hydration. These measurements establish the molecular features of the different saccharides that account for their different adsorption behaviors in hydrating cements. Specifically, sucrose is stable in alkaline cement slurries and exhibits selective adsorption at hydrating silicate surfaces but not at aluminate surfaces in cements. In contrast, glucose degrades into linear saccharinic or other carboxylic acids that adsorb relatively weakly and nonselectively on nonhydrated and hydrated cement particle surfaces. Maltodextrin exhibits intermediate reaction and sorption properties because of its oligomeric glucosidic structure that yields linear carboxylic acids and stable ring-containing degradation products that are similar to those of the glucose degradation products and sucrose, respectively. Such different reaction and adsorption behaviors provide insight into the factors responsible for the large differences in the rates at which aluminate and silicate cement species hydrate in the presence of otherwise closely related saccharides.

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.

Adsorption of adenine and thymine on zeolites: FT-IR and EPR spectroscopy and X-ray diffractometry and SEM studies

The interactions of adenine and thymine with and adsorption on zeolites were studied using different techniques. There were two main findings. First, as shown by X-ray diffractometry, thymine increased the decomposition of the zeolites (Y, ZSM-5) while adenine prevented it. Second, zeolite Y adsorbed almost the same amount of adenine and thymine, thus both nucleic acid bases could be protected from hydrolysis and UV radiation and could be available for molecular evolution. The X-ray diffractometry and SEM showed that artificial seawater almost dissolved zeolite A. The adsorption of adenine on ZSM-5 zeolite was higher than that of thymine (Student-Newman-Keuls test-SNK p<0.05). Adenine was also more greatly adsorbed on ZSM-5 zeolite, when compared to other zeolites (SNK p<0.05). However the adsorption of thymine on different zeolites was not statistically different (SNK p>0.05). The adsorption of adenine and thymine on zeolites did not depend on pore size or Si/Al ratio and it was not explained only by electrostatic forces; rather van der Waals interactions should also be considered.

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 amino acids (ALA, CYS, HIS, MET) on zeolites: fourier transform infrared and Raman spectroscopy investigations

Minerals adsorb more amino acids with charged R-groups than amino acids with uncharged R-groups. Thus, the peptides that form from the condensation of amino acids on the surface of minerals should be composed of amino acid residues that are more charged than uncharged. However, most of the amino acids (74%) in today's proteins have an uncharged R-group. One mechanism with which to solve this paradox is the use of organophilic minerals such as zeolites. Over the range of pH (pH 2.66-4.50) used in these experiments, the R-group of histidine (His) is positively charged and neutral for alanine (Ala), cysteine (Cys), and methionine (Met). In acidic hydrothermal environments, the pH could be even lower than those used in this study. For the pH range studied, the zeolites were negatively charged, and the overall charge of all amino acids was positive. The conditions used here approximate those of prebiotic Earth. The most important finding of this work is that the relative concentrations of each amino acid (X=His, Met, Cys) to alanine (X/Ala) are close to 1.00. This is an important result with regard to prebiotic chemistry because it could be a solution for the paradox stated above. Pore size did not affect the adsorption of Cys and Met on zeolites, and the Si/Al ratio did not affect the adsorption of Cys, His, and Met. ZSM-5 could be used for the purification of Cys from other amino acids (Student-Newman-Keuls test, p<0.05), and mordenite could be used for separation of amino acids from each other (Student-Newman-Keuls test, p<0.05). As shown by Fourier transform infrared (FT-IR) spectra, Ala interacts with zeolites through the [Formula: see text] group, and methionine-zeolite interactions involve the COO, [Formula: see text], and CH(3) groups. FT-IR spectra show that the interaction between the zeolites and His is weak. Cys showed higher adsorption on all zeolites; however, the hydrophobic Van der Waals interaction between zeolites and Cys is too weak to produce any structural changes in the Cys groups (amine, carboxylic, sulfhydryl, etc.); thus, the FT-IR and Raman spectra are the same as those of solid Cys.

A late methanogen origin for molybdenum-dependent nitrogenase

Mounting evidence indicates the presence of a near complete biological nitrogen cycle in redox-stratified oceans during the late Archean to early Proterozoic (c. 2.5-2.0 Ga). It has been suggested that the iron (Fe)- or vanadium (V)-dependent nitrogenase rather than molybdenum (Mo)-dependent form was responsible for dinitrogen fixation during this time because oceans were depleted in Mo and rich in Fe. We evaluated this hypothesis by examining the phylogenetic relationships of proteins that are required for the biosynthesis of the active site cofactor of Mo-nitrogenase in relation to structural proteins required for Fe-, V- and Mo-nitrogenase. The results are highly suggestive that among extant nitrogen-fixing organisms for which genomic information exists, Mo-nitrogenase is unlikely to have been associated with the Last Universal Common Ancestor. Rather, the origin of Mo-nitrogenase can be traced to an ancestor of the anaerobic and hydrogenotrophic methanogens with acquisition in the bacterial domain via lateral gene transfer involving an anaerobic member of the Firmicutes. A comparison of substitution rates estimated for proteins required for the biosynthesis of the nitrogenase active site cofactor and for a set of paralogous proteins required for the biosynthesis of bacteriochlorophyll suggests that Nif emerged from a nitrogenase-like ancestor approximately 1.5-2.2 Ga. An origin and ensuing proliferation of Mo-nitrogenase under anoxic conditions would likely have occurred in an environment where anaerobic methanogens and Firmicutes coexisted and where Mo was at least episodically available, such as in a redox-stratified Proterozoic ocean basin.

Possible origin of life between mica sheets

The mica hypothesis is a new hypothesis about how life might have originated. The mica hypothesis provides simple solutions to many basic questions about the origins of life. In the mica hypothesis, the spaces between mica sheets functioned as the earliest cells. These 'cells' between mica sheets are filled with potassium ions, and they provide an environment in which: polymer entropy is low; cyclic wetting and drying can occur; molecules can evolve in isolated spaces and also migrate and ligate to form larger molecules. The mica hypothesis also proposes that mechanical energy (work) is a major energy source that could have been used on many length scales to form covalent bonds, to alter polymer conformations, and to bleb daughter cells off protocells. The mica hypothesis is consistent with many other origins hypotheses, including the RNA, lipid, and metabolic 'worlds'. Therefore the mica hypothesis has the potential to unify origins hypotheses, such that different molecular components and systems could simultaneously evolve in the spaces between mica sheets.

The Fe-rich clay microsystems in basalt-komatiite lavas: importance of Fe-smectites for pre-biotic molecule catalysis during the Hadean eon

During the Hadean to early Archean period (4.5-3.5 Ga), the surface of the Earth's crust was predominantly composed of basalt and komatiite lavas. The conditions imposed by the chemical composition of these rocks favoured the crystallization of Fe-Mg clays rather than that of Al-rich ones (montmorillonite). Fe-Mg clays were formed inside chemical microsystems through sea weathering or hydrothermal alteration, and for the most part, through post-magmatic processes. Indeed, at the end of the cooling stage, Fe-Mg clays precipitated directly from the residual liquid which concentrated in the voids remaining in the crystal framework of the mafic-ultramafic lavas. Nontronite-celadonite and chlorite-saponite covered all the solid surfaces (crystals, glass) and are associated with tiny pyroxene and apatite crystals forming the so-called "mesostasis". The mesostasis was scattered in the lava body as micro-settings tens of micrometres wide. Thus, every square metre of basalt or komatiite rocks was punctuated by myriads of clay-rich patches, each of them potentially behaving as a single chemical reactor which could concentrate the organics diluted in the ocean water. Considering the high catalytic potentiality of clays, and particularly those of the Fe-rich ones (electron exchangers), it is probable that large parts of the surface of the young Earth participated in the synthesis of prebiotic molecules during the Hadean to early Archean period through innumerable clay-rich micro-settings in the massive parts and the altered surfaces of komatiite and basaltic lavas. This leads us to suggest that Fe,Mg-clays should be preferred to Al-rich ones (montmorillonite) to conduct experiments for the synthesis and the polymerisation of prebiotic molecules.

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.

High local concentration: a fundamental strategy of life

Local increase in concentration is a basic principle of transcriptional control. Closer inspection reveals that it is a major force governing all interactions within and between proteins and DNA. Local increase in concentration acts on all levels of organization of living matter. The structures and functions of two central molecules of life-the linear polymers DNA and protein-are particularly illuminating examples. Local increase in concentration leads to cooperative or competitive interactions between molecules. It is an important principle of life.

Neutral vs zwitterionic glycine forms at the water/silica interface: structure, energies, and vibrational features from B3LYP periodic simulations

B3LYP periodic calculations with a triple-xi-polarized Gaussian basis set have been used to study adsorption of glycine on a hydroxylated silica surface (2.2 OH/nm2) model derived from the (001) surface of edingtonite. The simulation envisages glycine adsorbed either as a gas-phase molecule or when microsolvated by up to five H20 molecules. Both neutral and zwitterionic forms of glycine have been considered and their structural, energetic, and spectroscopic vibrational features compared internally and with experiments. As a gas phase glycine sticks in its neutral form at the silica surface, the zwitterion being highly unstable and with transition-state character. When glycine is microsolvated at the silica interface, two H20 molecules render the zwitterion population comparable to that of the neutral form whereas with four H2O molecules the neutral glycine population is wiped out in favor of the zwitterion. With four H20 molecules the most stable structure shows no direct contact between glycine and the silica surface, H20 acting as a mediator via H-bond interactions. The B3LYP energies and structural data were also supported by comparing the scaled harmonic vibrational features with literature FTIR data of glycine adsorbed on an amorphous silica surface either from the gas phase or in water solution.

Adsorption and polymerization of amino acids on mineral surfaces: a review

The present paper offers a review of recent (post-1980) work on amino acid adsorption and thermal reactivity on oxide and sulfide minerals. This review is performed in the general frame of evaluating Bernal's hypothesis of prebiotic polymerization in the adsorbed state, but written from a surface scientist's point of view. After a general discussion of the thermodynamics of the problem and exactly what effects surfaces should have to make adsorbed-state polymerization a viable scenario, we examine some practical difficulties in experimental design and their bearing on the conclusions that can be drawn from extant works, including the relevance of the various available characterization techniques. We then present the state of the art concerning the mechanisms of the interactions of amino acids with mineral surfaces, including results from prebiotic chemistry-oriented studies, but also from several different fields of application, and discuss the likely consequences for adsorption selectivities. Finally, we briefly summarize the data concerning thermally activated amide bond formation of adsorbed amino acids without activating agents. The reality of the phenomenon is established beyond any doubt, but our understanding of its mechanism and therefore of its prebiotic potential is very fragmentary. The review concludes with a discussion of future work needed to fill the most conspicuous gaps in our knowledge of amino acids/mineral surfaces systems and their reactivity.

The rate of 2,2-dichloropropane transformation in mineral micropores: implications of sorptive preservation for fate and transport of organic contaminants in the subsurface

Nanometer scale pores are ubiquitous in porous geologic media (soils and sediments). Sorption of organic contaminants in micropores (< or = 2 nm) can inhibittheir hydrolytic transformation due to the limited availability of reactive water within hydrophobic micropore spaces. As a test case, we studied the dehydrohalogenation of 2,2-dichloropropane (2,2-DCP) sorbed in the micropores of several model mineral solids. In the micropores of a hydrophobic dealuminated Y zeolite, CBV-780, 2,2-DCP dehydrohalogenation proceeded significantly slower than in bulk aqueous solution and eventually stopped. This was attributed to the depletion of reactive water molecules in the micropore spaces. The 2,2-DCP sorbed in the micropores of more hydrophilic solids (aquifer sediment, aquifer sand, and silica gel) also transformed slower than in aqueous solution, and the reaction no longer followed first-order kinetics. Results of transport modeling support that reactive contaminants sorbed in microporous minerals can be preserved over geological time scales under conditions that limit desorption. This study shows that hydrophobic micropores in geological media may act as an important sink for anthropogenic organic contaminants in the subsurface, and that sorption in micropores may significantly increase the persistence of the sorbed contaminants.

On the interactions of alkyl 2-hydroxycarboxylic acids with alkoxysilanes: selective esterification of simple 2-hydroxycarboxylic acids

The interactions of a range of monocarboxylic acids with tetramethoxysilane Si(OMe)(4) (TMOS), in methanol (MeOH), have been investigated by using (1)H, (13)C and (29)Si solution-phase NMR spectroscopy and electrospray mass spectrometry (ESMS). Si(OMe)(4) acts as a catalyst/reagent in the selective methylation of 2-hydroxycarboxylic acids (2HOAs) in MeOH at room temperature: glycolic acid, lactic acid and 2-hydroxybutyric acid are esterified more than a hundred times faster in MeOH and Si(OMe)(4) than in MeOH alone. No acceleration of methylation is observed for carboxylic acids lacking the 2-hydroxy group. Methylation of the 2HOAs is associated with the condensation of individual siloxane units to form oligomers. A mechanism is proposed in which 2HOAs attach to silicon via the alkoxy group, then subsequently via the carboxyl group in an intramolecular rearrangement to form an unstable and reactive cyclic intermediate. This intermediate may lead to accelerated methylation of the carboxylic acid via nucleophilic attack of MeOH at the carbonyl group, while a separate reaction pathway leads to condensation of silanols and/or alkoxysilanes leading to oligosiloxanes. The mechanism has implications for the use of 2HOAs as templates in sol-gel silica preparation.

The origin and emergence of life under impact bombardment

Craters formed by asteroids and comets offer a number of possibilities as sites for prebiotic chemistry, and they invite a literal application of Darwin's 'warm little pond'. Some of these attributes, such as prolonged circulation of heated water, are found in deep-ocean hydrothermal vent systems, previously proposed as sites for prebiotic chemistry. However, impact craters host important characteristics in a single location, which include the formation of diverse metal sulphides, clays and zeolites as secondary hydrothermal minerals (which can act as templates or catalysts for prebiotic syntheses), fracturing of rock during impact (creating a large surface area for reactions), the delivery of iron in the case of the impact of iron-containing meteorites (which might itself act as a substrate for prebiotic reactions), diverse impact energies resulting in different rates of hydrothermal cooling and thus organic syntheses, and the indiscriminate nature of impacts into every available lithology-generating large numbers of 'experiments' in the origin of life. Following the evolution of life, craters provide cryptoendolithic and chasmoendolithic habitats, particularly in non-sedimentary lithologies, where limited pore space would otherwise restrict colonization. In impact melt sheets, shattered, mixed rocks ultimately provided diverse geochemical gradients, which in present-day craters support the growth of microbial communities.

Looking for the primordial genetic honeycomb

All life forms on Earth share the same biological program based on the DNA/RNA genomes and proteins. The genetic information, recorded in the nucleotide sequence of the DNA and RNA molecule, supplies the language of life which is transferred through the different generations, thus ensuring the perpetuation of genetic information on Earth. The presence of a genetic system is absolutely essential to life. Thus, the appearance in an ancestral era of a nucleic acid-like polymer able to undergo Darwinian evolution indicates the beginning of life on our planet. The building of primordial genetic molecules, whatever they were, required the presence of a protected environment, allowing the synthesis and concentration of precursors (nucleotides), their joining into larger molecules (polynucleotides), the protection of forming polymers against degradation (i.e. by cosmic and UV radiation), thus ensuring their persistence in a changing environment, and the expression of the "biological" potential of the molecule (its capacity to self-replicate and evolve). Determining how these steps occurred and how the primordial genetic molecules originated on Earth is a very difficult problem that still must be resolved. It has long been proposed that surface chemistry, i.e. on clay minerals, could have played a crucial role in the prebiotic formation of molecules basic to life. In the present work, we discuss results obtained in different fields that strengthen the hypothesis of a clay-surface-mediated origin of genetic material.

With a grain of salt: what halite has to offer to discussions on the origin of life

This experimental study investigated how the dynamics of the crystallization of the evaporite mineral halite could affect the accumulation and preservation of organic macromolecules present in the crystallizing solution. Halite was grown under controlled conditions in the presence of polymer nanoparticles that acted as an analog to protocellular material. Optical microscopy, atomic force microscopy, and laser scanning confocal fluorescence microscopy were used to trace the localization of the nanoparticles during and after growth of halite crystals. The present study revealed that the organic nanoparticles were not regularly incorporated within the halite, but were very concentrated on its surfaces. Their distribution was controlled dominantly by the morphologic surface features of the mineral rather than by specific molecular interactions with an atomic plane of the mineral. This means that the distribution of organic molecules was controlled by surfaces like those of halite's evaporitic growth forms. The experiments with halite also demonstrated that a mineral need not continuously incorporate organic molecules during its crystallization to preserve those molecules: After rejection by (non-incorporation into) the crystallizing halite, the organic nanoparticles increased in concentration in the evaporating brine. They ultimately either adsorbed in rectilinear patterns onto the hopper-enhanced surfaces and along discontinuities within the crystals, or they were encapsulated within fluid inclusions. Of additional importance in origin-of-life considerations is the fact that halite in the natural environment rapidly can change its role from that of a protective repository (in the absence of water) to that of a source of organic particles (as soon as water is present) when the mineral dissolves.

Interaction of glycine with isolated hydroxyl groups at the silica surface: first principles B3LYP periodic simulation

The adsorption of a glycine molecule on a model silica surface terminated by an isolated hydroxyl group has been studied ab initio using a double-zeta polarized Gaussian basis set, the hybrid B3LYP functional, and a full periodic treatment of the silica surface/glycine system. The hydroxylated silica surface has been simulated using either a 2D slab or a single polymer strand cut out from the (001) surface of an all-silica edingtonite. A number of B3LYP-optimized structures have been found by docking glycine on the silica surface exploiting all possible hydrogen bond patterns. Whereas glycine is generally adsorbed in its neutral form, two structures show glycine adsorbed as a zwitterion, the surface playing the role of a "solid solvent" whereas intrastrand hydrogen bond cooperativity stabilizes the zwitterions. The adsorbed zwitterionic structures are no longer formed at a lower glycine coverage as simulated by enlarging the unit cell so as to break intrastrand hydrogen bonds, showing the importance of H-bond cooperativity in stabilizing the zwitterionic forms. Each structure has been characterized by computing its harmonic vibrational spectrum at the Gamma point, which also allowed us to calculate the free energy of adsorption. The experimental infrared features of chemical-vapor-deposited glycine on a silica surface are in agreement with those computed for glycine adsorbed in its neutral form and engaging three hydrogen bonds with the surface silanols, two of them involving the C=O bond and one originating from the glycine OH group. The NH(2) group plays only a minor role as a weak hydrogen bond donor.

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.

A surface-mediated origin of the RNA world: biogenic activities of clay-adsorbed RNA molecules

The involvement of clay surfaces in the origin of the first genetic molecules on Earth has long been suggested. However, the formation of these polymers was not sufficient by itself to initiate the evolutionary process leading to the appearance of life. These macromolecules had to persist in primeval habitats so that their biological potentiality could be expressed. In this study, we assess the possibility of development of the RNA world on a clay substrate by investigating the capacity of different RNA molecules adsorbed/bound on the clay minerals montmorillonite (M) and kaolinite (K) to persist in the presence of a degrading agent (RNase-A), to interact specifically with complementary RNA strands, and to transmit the information contained in their nucleotide sequences. The RNase-A degradation of clay-adsorbed 23S rRNA from Escherichia coli was significantly slower (75-80%) than that observed for free rRNA, and the complete digestion of nucleic acid in the presence of clay was obtained in 2 vs. 1 h. Clay-adsorbed Poly[A] homopolymer was able to recognize the complementary Poly[U] homopolymer present in the surrounding water solution and to establish a specific interaction (association) with it, possibly leading to the formation of double strands. Reverse transcription and amplification (RT-PCR) amplification of free and clay-adsorbed 16S indicated that the presence of clay particles partially reduced the efficiency and processivity of reverse transcriptase but did not inhibit its activity, demonstrating that clay-adsorbed RNA is still available for enzymatic replication. These findings indicate that primordial genetic molecules adsorbed on clay minerals would have been protected against degrading agents present in the environment and would have been in the right conditions to undergo evolutionary processes.

Life before RNA

The hypothesis that life originated and evolved from linear informational molecules capable of facilitating their own catalytic replication is deeply entrenched. However, widespread acceptance of this paradigm seems oblivious to a lack of direct experimental support. Here, we outline the fundamental objections to the de novo appearance of linear, self-replicating polymers and examine an alternative hypothesis of template-directed coding of peptide catalysts by adsorbed purine bases. The bases (which encode biological information in modern nucleic acids) spontaneously self-organize into two-dimensional molecular solids adsorbed to the uncharged surfaces of crystalline minerals; their molecular arrangement is specified by hydrogen bonding rules between adjacent molecules and can possess the aperiodic complexity to encode putative protobiological information. The persistence of such information through self-reproduction, together with the capacity of adsorbed bases to exhibit enantiomorphism and effect amino acid discrimination, would seem to provide the necessary machinery for a primitive genetic coding mechanism.

Origins of life: a route to nanotechnology

The origins of life and nanotechnology are two seemingly disparate areas of scientific investigation. However, the fundamental questions of life's beginnings and the applied construction of a Drexlerian nanotechnology both share a similar problem; how did and how can self-reproducing molecular machines originate? Here we draw attention to the coincidence between nanotechnology and origins research with particular attention paid to the spontaneous adsorption and scanning tunneling microscopy investigation of purine and pyrimidine bases self-organized into monolayers, adsorbed to the surfaces of crystalline solids. These molecules which encode biological information in nucleic acids, can form supramolecular architectures exhibiting enantiomorphism with the complexity to store and encode putative protobiological information. We conclude that the application of nanotechnology to the investigation of life's origins, and vice versa, could provide a viable route to an evolution-driven synthetic life.

Differential adsorption of nucleic acid bases: Relevance to the origin of life

The adsorption of organic molecules onto the surfaces of inorganic solids has long been considered a process relevant to the origin of life. We have determined the equilibrium adsorption isotherms for the nucleic acid purine and pyrimidine bases dissolved in water on the surface of crystalline graphite. The markedly different adsorption behavior of the bases describes an elutropic series: guanine > adenine > hypoxanthine > thymine > cytosine > uracil. We propose that such differential properties were relevant to the prebiotic chemistry of the bases and may have influenced the composition of the primordial genetic architecture.

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

Catalysis at organophilic silica-rich surfaces of zeolites and feldspars might generate replicating biopolymers from simple chemicals supplied by meteorites, volcanic gases, and other geological sources. Crystal-chemical modeling yielded packings for amino acids neatly encapsulated in 10-ring channels of the molecular sieve silicalite-ZSM-5-(mutinaite). Calculation of binding and activation energies for catalytic assembly into polymers is progressing for a chemical composition with one catalytic Al-OH site per 25 neutral Si tetrahedral sites. Internal channel intersections and external terminations provide special stereochemical features suitable for complex organic species. Polymer migration along nano/micrometer channels of ancient weathered feldspars, plus exploitation of phosphorus and various transition metals in entrapped apatite and other microminerals, might have generated complexes of replicating catalytic biomolecules, leading to primitive cellular organisms. The first cell wall might have been an internal mineral surface, from which the cell developed a protective biological cap emerging into a nutrient-rich "soup." Ultimately, the biological cap might have expanded into a complete cell wall, allowing mobility and colonization of energy-rich challenging environments. Electron microscopy of honeycomb channels inside weathered feldspars of the Shap granite (northwest England) has revealed modern bacteria, perhaps indicative of Archean ones. All known early rocks were metamorphosed too highly during geologic time to permit simple survival of large-pore zeolites, honeycombed feldspar, and encapsulated species. Possible microscopic clues to the proposed mineral adsorbents/catalysts are discussed for planning of systematic study of black cherts from weakly metamorphosed Archaean sediments.