Chemistry of potentially prebiological natural products

Evolutionary Abilities of Minimalistic Physicochemical Models of Life Processes

The ability of living organisms to persist, grow, evolve and invade environments seemingly challenges physical laws. Emerging Autonomous Systems representing autocatalytic cycles constituted of energized components in a state of Dynamic Kinetic Stability feature some of these properties. These simple theoretical models can grow, can be transferred but need an initiation to emerge and can collapse. Moreover, they can undergo kinetic selection in a way consistent with Darwinian behaviour, though they lack the ability to undergo change. The mere existence of these systems and their open-ended growth potential are proposed to constitute a transmissible factor of a non-coded kind. The onset and selection of epigenetic factors may therefore have preceded that of genetic polymers. Here is addressed the question of how these systems may arise from the diversity exhibited by abiotic organic matter, sometimes associated with intractable mixtures, which may actually be useful in providing initiators. The Darwinian description of evolution may therefore be merged without critical discontinuity within an origin scenario. Accordingly, such a theory would rests solely on physicochemical laws beginning with the potential of emerging autonomous systems to compete and invade the space dimension, and to further develop along other available dimensions including variability and, possibly, cognition.

On the Emergence of Autonomous Chemical Systems through Dissipation Kinetics

This work addresses the kinetic requirements for compensating the entropic cost of self-organization and natural selection, thereby revealing a fundamental principle in biology. Metabolic and evolutionary features of life cannot therefore be separated from an origin of life perspective. Growth, self-organization, evolution and dissipation processes need to be metabolically coupled and fueled by low-entropy energy harvested from the environment. The evolutionary process requires a reproduction cycle involving out-of-equilibrium intermediates and kinetic barriers that prevent the reproductive cycle from proceeding in reverse. Model analysis leads to the unexpectedly simple relationship that the system should be fed energy with a potential exceeding a value related to the ratio of the generation time to the transition state lifetime, thereby enabling a process mimicking natural selection to take place. Reproducing life's main features, in particular its Darwinian behavior, therefore requires satisfying constraints that relate to time and energy. Irreversible reaction cycles made only of unstable entities reproduce some of these essential features, thereby offering a physical/chemical basis for the possible emergence of autonomy. Such Emerging Autonomous Systems (EASs) are found to be capable of maintaining and reproducing their kind through the transmission of a stable kinetic state, thereby offering a physical/chemical basis for what could be deemed an epigenetic process.

A self-sustaining serpentinization mega-engine feeds the fougerite nanoengines implicated in the emergence of guided metabolism

The demonstration by Ivan Barnes et al. that the serpentinization of fresh Alpine-type ultramafic rocks results in the exhalation of hot alkaline fluids is foundational to the submarine alkaline vent theory (AVT) for life's emergence to its 'improbable' thermodynamic state. In AVT, such alkaline fluids ≤ 150°C, bearing H2 > CH4 > HS--generated and driven convectively by a serpentinizing exothermic mega-engine operating in the ultramafic crust-exhale into the iron-rich, CO2> > > NO3--bearing Hadean ocean to result in hydrothermal precipitate mounds comprising macromolecular ferroferric-carbonate oxyhydroxide and minor sulfide. As the nanocrystalline minerals fougerite/green rust and mackinawite (FeS), they compose the spontaneously precipitated inorganic membranes that keep the highly contrasting solutions apart, thereby maintaining redox and pH disequilibria. They do so in the form of fine chimneys and chemical gardens. The same disequilibria drive the reduction of CO2 to HCOO- or CO, and the oxidation of CH4 to a methyl group-the two products reacting to form acetate in a sequence antedating the 'energy-producing' acetyl coenzyme-A pathway. Fougerite is a 2D-layered mineral in which the hydrous interlayers themselves harbor 2D solutions, in effect constricted to ~ 1D by preferentially directed electron hopping/tunneling, and proton Gröthuss 'bucket-brigading' when subject to charge. As a redox-driven nanoengine or peristaltic pump, fougerite forces the ordered reduction of nitrate to ammonium, the amination of pyruvate and oxalate to alanine and glycine, and their condensation to short peptides. In turn, these peptides have the flexibility to sequester the founding inorganic iron oxyhydroxide, sulfide, and pyrophosphate clusters, to produce metal- and phosphate-dosed organic films and cells. As the feed to the hydrothermal mound fails, the only equivalent sustenance on offer to the first autotrophs is the still mildly serpentinizing upper crust beneath. While the conditions here are very much less bountiful, they do offer the similar feed and disequilibria the survivors are accustomed to. Sometime during this transition, a replicating non-ribosomal guidance system is discovered to provide the rules to take on the incrementally changing surroundings. The details of how these replicating apparatuses emerged are the hard problem, but by doing so the progenote archaea and bacteria could begin to colonize what would become the deep biosphere. Indeed, that the anaerobic nitrate-respiring methanotrophic archaea and the deep-branching Acetothermia presently comprise a portion of that microbiome occupying serpentinizing rocks offers circumstantial support for this notion. However, the inescapable, if jarring conclusion is drawn that, absent fougerite/green rust, there would be no structured channelway to life.

Perspectives on parity violation in chiral molecules: theory, spectroscopic experiment and biomolecular homochirality

The reflection (or ‘mirror’) symmetry of space is among the fundamental symmetries of physics. It is connected to the conservation law for the quantum number parity and a fundamental ‘non-observable’ property of space (as defined by an absolute ‘left-handed’ or ‘right-handed’ coordinate system). The discovery of the violation of this symmetry – the non-conservation of parity or ‘parity violation’ – in 1956/1957 had an important influence on the further development of physics. In chemistry the mirror symmetry of space is connected to the existence of enantiomers as isomers of chiral (‘handed’) molecules. These isomers would relate to each other as idealized left or right hand or as image and mirror image and would be energetically exactly equivalent with perfect space inversion symmetry. Parity violation results in an extremely small ‘parity violating’ energy difference between the ground states of the enantiomers which can be theoretically calculated to be about 100 aeV to 1 feV (equivalent to 10⁻¹¹ to 10⁻¹⁰ J mol⁻¹), depending on the molecule, but which has not yet been detected experimentally. Its detection remains one of the great challenges of current physical–chemical stereochemistry, with implications also for fundamental problems in physics. In biochemistry and molecular biology one finds a related fundamental question unanswered for more than 100 years: the evolution of ‘homochirality’, which is the practically exclusive preference of one chiral, enantiomeric form as building blocks in the biopolymers of all known forms of life (the l-amino acids in proteins and d-sugars in DNA, not the reverse d-amino acids or l-sugars). In astrobiology the spectroscopic detection of homochirality could be used as strong evidence for the existence of extraterrestrial life, if any. After a brief conceptual and historical introduction we review the development, current status, and progress along these three lines of research: theory, spectroscopic experiment and the outlook towards an understanding of the evolution of biomolecular homochirality.

The reflection (or ‘mirror’) symmetry of space is among the fundamental symmetries of physics. It is connected to the conservation law for the quantum number purity and its violation and has a fundamental relation to stereochemistry and molecular chirality.

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”).

The furanosidic scaffold of d-ribose: a milestone for cell life

The recruitment of the furanosidic scaffold of ribose as the crucial step for nucleotides and then for nucleic acids synthesis is presented. Based on the view that the selection of molecules to be used for relevant metabolic purposes must favor structurally well-defined molecules, the inadequacy of ribose as a preferential precursor for nucleotides synthesis is discussed. The low reliability of ribose in its furanosidic hemiacetal form must have played ab initio against the choice of d-ribose for the generation of d-ribose-5-phosphate, the fundamental precursor of the ribose moiety of nucleotides. The latter, which is instead generated through the 'pentose phosphate pathway' is strictly linked to the affordable and reliable pyranosidic structure of d-glucose.

Observation of the Unbiased Conformers of Putative DNA-Scaffold Ribosugars

The constitution, configuration, and flexibility of the core sugars of DNA molecules alter their function in diverse roles. Conformational itineraries of the ribofuranosides (fs) have long been known to finely determine rates of processing, yet we also know that, strikingly, semifunctional DNAs containing pyranosides (ps) or other configurations can be created, suggesting sufficient but incompletely understood plasticity. The multiple conformers involved in such processes are necessarily influenced by context and environment: solvent, hosts, ligands. Notably, however, to date the unbiased, "naked" conformers have not been experimentally determined. Here, the inherent conformational biases of DNA scaffold deoxyribosides in unsolvated and solvated forms have now been defined using gas-phase microwave and solution-phase NMR spectroscopies coupled with computational analyses and exploitation of critical differences between natural-abundance isotopologues. Serial determination of precise, individual spectra for conformers of these 25 isotopologues in alpha (α-d) and beta (β-d); pyrano (p) and furano (f) methyl 2-deoxy-d-ribosides gave not only unprecedented atomic-level resolution structures of associated conformers but also their quantitative populations. Together these experiments revealed that typical ²E and ³E conformations of the sugar found in complex DNA structures are not inherently populated. Moreover, while both OH-5' and OH-3' are constrained by intramolecular hydrogen bonding in the unnatural αf scaffold, OH-3' is "born free" in the "naked" lowest lying energy conformer of natural βf. Consequently, upon solvation, unnatural αf is strikingly less perturbable (retaining ²T₁ conformation in vacuo and water) than natural βf. Unnatural αp and βp ribosides also display low conformational perturbability. These first experimental data on inherent, unbiased conformers therefore suggest that it is the background of conformational flexibility of βf that may have led to its emergence out of multiple possibilities as the sugar scaffold for "life's code" and suggest a mechanism by which the resulting freedom of OH-3' (and hence accessibility as a nucleophile) in βf may drive preferential processing and complex structure formation, such as replicative propagation of DNA from 5'-to-3'.

On the conditions for mimicking natural selection in chemical systems

The emergence of natural selection, requiring that reproducing entities present variations that may be inherited and passed on, was arguably the most important breakthrough in the self-organization of life. In this Perspective, the assumptions governing biological reproduction are confronted with physico-chemical principles that control the evolution of material systems. In biology, the reproduction of living organisms is never considered to be reversible, whereas microscopic reversibility is an essential principle in the physical description of matter. Here, we show that this discrepancy places constraints on the possibility of finding kinetic processes in the chemical world that are equivalent to natural selection in the biological one. Chemical replicators can behave in a similar fashion to living entities, provided that the reproduction cycle proceeds in a unidirectional way. For this to be the case, kinetic barriers must hinder the reverse process. The system must, thus, be held far from equilibrium and fed with a non-degraded (low-entropy) form of energy. The ensuing constraints must be factored in when proposing scenarios that account for the origin of life at the molecular level.

How Prebiotic Chemistry and Early Life Chose Phosphate

The very specific thermodynamic instability and kinetic stability of phosphate esters and anhydrides impart them invaluable properties in living organisms in which highly efficient enzyme catalysts compensate for their low intrinsic reactivity. Considering their role in protein biosynthesis, these properties raise a paradox about early stages: How could these species be selected in the absence of enzymes? This review is aimed at demonstrating that considering mixed anhydrides or other species more reactive than esters and anhydrides can help in solving the paradox. The consequences of this approach for chemical evolution and early stages of life are analysed.

How and why kinetics, thermodynamics, and chemistry induce the logic of biological evolution

Thermodynamic stability, as expressed by the Second Law, generally constitutes the driving force for chemical assembly processes. Yet, somehow, within the living world most self-organisation processes appear to challenge this fundamental rule. Even though the Second Law remains an inescapable constraint, under energy-fuelled, far-from-equilibrium conditions, populations of chemical systems capable of exponential growth can manifest another kind of stability, dynamic kinetic stability (DKS). It is this stability kind based on time/persistence, rather than on free energy, that offers a basis for understanding the evolutionary process. Furthermore, a threshold distance from equilibrium, leading to irreversibility in the reproduction cycle, is needed to switch the directive for evolution from thermodynamic to DKS. The present report develops these lines of thought and argues against the validity of a thermodynamic approach in which the maximisation of the rate of energy dissipation/entropy production is considered to direct the evolutionary process. More generally, our analysis reaffirms the predominant role of kinetics in the self-organisation of life, which, in turn, allows an assessment of semi-quantitative constraints on systems and environments from which life could evolve.

Physicochemical Requirements Inferred for Chemical Self-Organization Hardly Support an Emergence of Life in the Deep Oceans of Icy Moons

An approach to the origin of life, focused on the property of entities capable of reproducing themselves far from equilibrium, has been developed recently. Independently, the possibility of the emergence of life in the hydrothermal systems possibly present in the deep oceans below the frozen crust of some of the moons of Jupiter and Saturn has been raised. The present report is aimed at investigating the mutual compatibility of these alternative views. In this approach, the habitability concept deduced from the limits of life on Earth is considered to be inappropriate with regard to emerging life due to the requirement for an energy source of sufficient potential (equivalent to the potential of visible light). For these icy moons, no driving force would have been present to assist the process of emergence, which would then have had to rely exclusively on highly improbable events, thereby making the presence of life unlikely on these Solar System bodies, that is, unless additional processes are introduced for feeding chemical systems undergoing a transition toward life and the early living organisms.

KEY WORDS

Icy moon-Bioenergetics-Chemical evolution-Habitability-Origin of life. Astrobiology 16, 328-334.

Towards an evolutionary theory of the origin of life based on kinetics and thermodynamics

A sudden transition in a system from an inanimate state to the living state—defined on the basis of present day living organisms—would constitute a highly unlikely event hardly predictable from physical laws. From this uncontroversial idea, a self-consistent representation of the origin of life process is built up, which is based on the possibility of a series of intermediate stages. This approach requires a particular kind of stability for these stages—dynamic kinetic stability (DKS)—which is not usually observed in regular chemistry, and which is reflected in the persistence of entities capable of self-reproduction. The necessary connection of this kinetic behaviour with far-from-equilibrium thermodynamic conditions is emphasized and this leads to an evolutionary view for the origin of life in which multiplying entities must be associated with the dissipation of free energy. Any kind of entity involved in this process has to pay the energetic cost of irreversibility, but, by doing so, the contingent emergence of new functions is made feasible. The consequences of these views on the studies of processes by which life can emerge are inferred.

Formaldehyde-a key monad of the biomolecular system

Experiments will be presented and reviewed to support the hypothesis that the intrinsic reactivity of formaldehyde may lead to the formation of a rather comprehensive set of defined biomolecules, including D-glucose, thus fostering concepts of evolution considering the existence of a premetabolic system as a primordial step in the generation of life.

Life's Order, Complexity, Organization, and Its Thermodynamic-Holistic Imperatives

In memoriam Jeffrey S. Wicken (1942-2002)-the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken's legacy. (i) Connecting life's origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic 'charging' of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called 'microspheres' is more realistic as a kinetic transition model of primal biogenesis than 'hypercycle replication' theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic 'microspheres'. On the 'continuist vs. miraculist' schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic 'continuist' views and agenda.

Etiology of potentially primordial biomolecular structures: from vitamin B12 to the nucleic acids and an inquiry into the chemistry of life's origin: a retrospective

"We'll never be able to know" is a truism that leads to resignation with respect to any experimental effort to search for the chemistry of life's origin. But such resignation runs radically counter to the challenge imposed upon chemistry as a natural science. Notwithstanding the prognosis according to which the shortest path to understanding the metamorphosis of the chemical into the biological is by way of experimental modeling of "artificial chemical life", the scientific search for the route nature adopted in creating the life we know will arguably never truly end. It is, after all, part of the search for our own origin.

Energy sources, self-organization, and the origin of life

The emergence and early developments of life are considered from the point of view that contingent events that inevitably marked evolution were accompanied by deterministic driving forces governing the selection between different alternatives. Accordingly, potential energy sources are considered for their propensity to induce self-organization within the scope of the chemical approach to the origin of life. Requirements in terms of quality of energy locate thermal or photochemical activation in the atmosphere as highly likely processes for the formation of activated low-molecular weight organic compounds prone to induce biomolecular self-organization through their ability to deliver quanta of energy matching the needs of early biochemical pathways or the reproduction of self-replicating entities. These lines of reasoning suggest the existence of a direct connection between the free energy content of intermediates of early pathways and the quanta of energy delivered by available sources of energy.

Position-dependent effects on stability in tricyclo-DNA modified oligonucleotide duplexes

A series of oligodeoxyribonucleotides and oligoribonucleotides containing single and multiple tricyclo(tc)-nucleosides in various arrangements were prepared and the thermal and thermodynamic transition profiles of duplexes with complementary DNA and RNA evaluated. Tc-residues aligned in a non-continuous fashion in an RNA strand significantly decrease affinity to complementary RNA and DNA, mostly as a consequence of a loss of pairing enthalpy ΔH. Arranging the tc-residues in a continuous fashion rescues T(m) and leads to higher DNA and RNA affinity. Substitution of oligodeoxyribonucleotides in the same way causes much less differences in T(m) when paired to complementary DNA and leads to substantial increases in T(m) when paired to complementary RNA. CD-spectroscopic investigations in combination with molecular dynamics simulations of duplexes with single modifications show that tc-residues in the RNA backbone distinctly influence the conformation of the neighboring nucleotides forcing them into higher energy conformations, while tc-residues in the DNA backbone seem to have negligible influence on the nearest neighbor conformations. These results rationalize the observed affinity differences and are of relevance for the design of tc-DNA containing oligonucleotides for applications in antisense or RNAi therapy.

Elementary reactions and their role in gas-phase prebiotic chemistry

The formation of complex organic molecules in a reactor filled with gaseous mixtures possibly reproducing the primitive terrestrial atmosphere and ocean demonstrated more than 50 years ago that inorganic synthesis of prebiotic molecules is possible, provided that some form of energy is provided to the system. After that groundbreaking experiment, gas-phase prebiotic molecules have been observed in a wide variety of extraterrestrial objects (including interstellar clouds, comets and planetary atmospheres) where the physical conditions vary widely. A thorough characterization of the chemical evolution of those objects relies on a multi-disciplinary approach: 1) observations allow us to identify the molecules and their number densities as they are nowadays; 2) the chemistry which lies behind their formation starting from atoms and simple molecules is accounted for by complex reaction networks; 3) for a realistic modeling of such networks, a number of experimental parameters are needed and, therefore, the relevant molecular processes should be fully characterized in laboratory experiments. A survey of the available literature reveals, however, that much information is still lacking if it is true that only a small percentage of the elementary reactions considered in the models have been characterized in laboratory experiments. New experimental approaches to characterize the relevant elementary reactions in laboratory are presented and the implications of the results are discussed.

A new theoretical model for the origin of amino acid homochirality

Amino acid homochirality, as a unique behavior of life, could have originated synchronously with the genetic code. In this paper, phosphoryl amino-acid-5'-nucleosides with P-N bond are postulated to be a chiral origin model in prebiotic molecular evolution. The enthalpy change in the intramolecular interaction between the nucleotide base and the amino-acid side-chain determines the stability of the particular complex, resulting in a preferred conformation associated with the chirality of amino acids. Based on the theoretical model, our experiments and calculations show that the chiral selection of the earliest amino acids for L-enantiomers seems to be a strict stereochemical/physicochemical determinism. As other amino acids developed biosynthetically from the earliest amino acids, we infer that the chirality of the later amino acids was inherited from the precursor amino acids. This idea probably goes far back in history, but it is hoped that it will be a guide for further experiments in this area.

Microwave Spectrum, Structure, and Quantum Chemical Studies of a Compound of Potential Astrochemical and Astrobiological Interest: Z-3-Amino-2-propenenitrile

Z-3-Amino-2-propenenitrile, H2NCH=CHCN, a compound of astrochemical and astrobiological interest, has been studied by Stark and Fourier transform microwave spectroscopy along with eight of its isotopologues; the synthesis of five of these are reported. The spectra of the ground vibrational state and of three vibrationally excited states belonging to the two lowest normal modes were assigned for the parent species, whereas the ground states were assigned for the isotopologues. The frequency of the lowest in-plane bending fundamental vibration was determined to be 152(20) cm(-1) and the frequency of the lowest out-of-plane fundamental mode was found to be 176(20) cm(-1) by relative intensity measurements. A delicate problem is whether this compound is planar or slightly nonplanar. It was found that the rotational constants of the nine species cannot be used to conclude definitely whether the molecule is planar or not. The experimental dipole moment is mu(a) = 16.45(12), mu(b) = 2.86(6), mu(c) = 0 (assumed), and mu(tot.) = 16.70(12) x 10(-30) C m [5.01(4) D]. The quadrupole coupling constants of the two nitrogen nuclei are chi(aa) = -1.4917(21) and chi(cc) = 1.5644(24) MHz for the nitrogen atom of the cyano group and chi(aa) = 1.7262(18) and chi(cc) = -4.0591(17) MHz for the nitrogen atom of the amino group. Extensive quantum-chemical calculations have been performed, and the results obtained from these calculations have been compared with the experimental values. The equilibrium structures of vinylamine, vinyl cyanide, and Z-3-amino-2-propenenitrile have been calculated. These calculations have established that the equilibrium structure of the title compound is definitely nonplanar. However, the MP2/VQZ energy difference between the planar and nonplanar forms is small, only -423 J/mol. Z-Amino-2-propenenitrile and E-3-amino-2-propenenitrile are formed simply by mixing ammonia and cyanoacetylene at room temperature. A plausible reaction path has been modeled. G3 calculations indicate that the enthalpy (298.15 K, 1 atm) of the transition state is about 130 kJ/mol higher than the sum of the enthalpies of the reactants ammonia and cyanoacetylene. This energy difference is comparatively high, which indicates that both E- and Z-3-aminopropenenitrile are not likely to be formed in the gas phase in cold interstellar clouds via a collision between ammonia and cyanoacetylene. An alternative reaction between protonated cyanoacetylene (H-C[triple bond]C-C[triple bond]NH+) and ammonia is predicted to have a much lower activation energy than the reaction between the neutral molecules. Although protonated E- and Z-3-aminopropenenitrile in principle may be formed this way, it is more likely that a collision between NH3 and H-C[triple bond]C-C[triple bond]NH+ leads to NH4+ and H-C[triple bond]C-C[triple bond]N.

Universality in intermediary metabolism

We analyze the stoichiometry, energetics, and reaction concentration dependence of the reductive tricarboxylic acid (rTCA) cycle as a universal and possibly primordial metabolic core. The rTCA reaction sequence is a network-autocatalytic cycle along the relaxation pathway for redox couples in nonequilibrium reducing environments, which provides starting organic compounds for the synthesis of all major classes of biomolecules. The concentration dependence of its reactions suggests it as a precellular bulk process. We propose that rTCA is statistically favored among competing redox relaxation pathways under early-earth conditions and that this feature drove its emergence and also accounts for its evolutionary robustness and universality. The ability to enhance the rate of core reactions creates an energetic basis for selection of subsequent layers of biological complexity.

The roads to and from the RNA world

The historical existence of the RNA world, in which early life used RNA for both genetic information and catalytic ability, is widely accepted. However, there has been little discussion of whether protein synthesis arose before DNA or what preceded the RNA world (i.e. the pre-RNA world). We outline arguments of what route life may have taken out of the RNA world: whether DNA or protein followed. Metabolic arguments favor the possibility that RNA genomes preceded the use of DNA as the informational macromolecule. However, the opposite can also be argued based on the enhanced stability, reactivity, and solubility of 2-deoxyribose as compared to ribose. The possibility that DNA may have come before RNA is discussed, although it is a less parsimonious explanation than DNA following RNA.

Open problems in artificial life

This article lists fourteen open problems in artificial life, each of which is a grand challenge requiring a major advance on a fundamental issue for its solution. Each problem is briefly explained, and, where deemed helpful, some promising paths to its solution are indicated.

Chemical etiology of nucleic acid structure: comparing pentopyranosyl-(2'-->4') oligonucleotides with RNA

All four members of the family of pentopyranosyl-(2'-->4') oligonucleotide systems that contain beta-ribo-, beta-xylo-, alpha-lyxo-, or alpha-arabinopyranosyl units as repeating sugar building blocks are found to be much stronger Watson-Crick base-pairing systems than RNA. The alpha-arabinopyranosyl system is the strongest of all and in fact belongs to the strongest oligonucleotide base-pairing systems known. Whatever the chemical determinants by which nature selected RNA as a genetic system, maximization of base-pairing strengths within the domain of pentose-derived oligonucleotide systems was not the critical selection criterion.

Residue-based control of helix shape in beta-peptide oligomers

Proteins and RNA are unique among known polymers in their ability to adopt compact and well-defined folding patterns. These two biopolymers can perform complex chemical operations such as catalysis and highly selective recognition, and these functions are linked to folding in that the creation of an active site requires proper juxtaposition of reactive groups. So the development of new types of polymeric backbones with well-defined and predictable folding propensities ('foldamers') might lead to molecules with useful functions. The first step in foldamer development is to identify synthetic oligomers with specific secondary structural preferences. Whereas alpha-amino acids can adopt the well-known alpha-helical motif of proteins, it was shown recently that beta-peptides constructed from carefully chosen beta-amino acids can adopt a different, stable helical conformation defined by interwoven 14-membered-ring hydrogen bonds (a 14-helix; Fig. 1a). Here we report that beta-amino acids can also be used to design beta-peptides with a very different secondary structure, a 12-helix (Fig. 1a). This demonstrates that by altering the nature of beta-peptide residues, one can exert rational control over the secondary structure.

Life on Mars: a clue to life on Earth?

A martian meteorite has recently been claimed to show evidence of life and certainly shows the presence of organic matter. What might we learn about how life on Earth developed from studies of Mars?

Why exobiology on Mars?

Processing of organic molecules by liquid water was probably an essential requirement towards the emergence of terrestrial primitive life. According to Oparin's hypothesis, organic building blocks required for early life were produced from simple organic molecules formed in a primitive reducing atmosphere. Geochemists favour now a less reducing atmosphere dominated by carbon dioxide. In such an atmosphere, very few building blocks are formed. Import of extraterrestrial organic molecules may represent an alternative supply. Experimental support for such an alternative scenario is examined in comets, meteorites and micrometeorites. The early histories of Mars and Earth clearly show similarities. Liquid water was once stable on the surface of Mars attesting the presence of an atmosphere capable of decelerating C-rich micro-meteorites. Therefore, primitive life may have developed on Mars, as well. Liquid water disappeared from the surface of Mars very early, about 3.8 Ga ago. The Viking missions did not find, at the surface of the Martian soil, any organic molecules or clear-cut evidence for microbial activities such as photosynthesis, respiration or nutrition. The results can be explained referring to an active photochemistry of Martian soil driven by the high influx of solar UV. These experiments do not exclude the existence of organic molecules and fossils of micro-organisms which developed on early Mars until liquid water disappeared. Mars may store below its surface some well preserved clues of a still hypothetical primitive life.

Mineral induced formation of sugar phosphates

Glycolaldehyde phosphate, sorbed from highly dilute, weakly alkaline solution into the interlayer of common expanding sheet structure metal hydroxide minerals, condenses extensively to racemic aldotetrose-2,4-diphosphates and aldohexose-2,4,6-triphosphates. The reaction proceeds mainly through racemic erythrose-2,4-phosphate, and terminates with a large fraction of racemic altrose-2,4,6-phosphate. In the absence of an inductive mineral phase, no detectable homogeneous reaction takes place in the concentration- and pH range used. The reactant glycolaldehyde phosphate is practically completely sorbed within an hour from solutions with concentrations as low as 50 micrometers; the half-time for conversion to hexose phosphates is of the order of two days at room temperature and pH 9.5. Total production of sugar phosphates in the mineral interlayer is largely independent of the glycolaldehyde phosphate concentration in the external solution, but is determined by the total amount of GAP offered for sorption up to the capacity of the mineral. In the presence of equimolar amounts of rac-glyceraldehyde-2-phosphate, but under otherwise similar conditions, aldopentose-2,4,-diphosphates also form, but only as a small fraction of the hexose-2,4,6-phosphates.