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An experimental system is described, which opens up a novel pathway towards a molecular understanding of the origin of life. The systemic conditions for the evolution of biological macromolecules are investigated in detail.
A theoretical methodology for the systematic study of the interstellar molecules is proposed. Some examples, dealing with formaldehyde excited states, formyl radical and ion, reactivity of the excited states of formic acid, methyl cyanide and methyl acetylene, as well as the reaction patho of formaldehyde photodecomposition are presented. Quantum chemical methods appear to be a powerful tool to study the structure and behaviour of molecules related with interstellar space and the Origin of Life.
The problem of chiral purity in living organisms is still one of the prominent difficulties in the study of the origins of life. In particular the parity non-conservation known to occur in weak interactions could not be related to this lack of symmetry: these physical forces, though universal, are very weak and up to now no amplification process had been proposed. In 1991, A. Salam remarked that, due to the attractive character of the parity violating force in electro-weak interactions, a phase transition at low temperature should exist, leading eventually to enantiomeric purity. We undertook then a series of experimental tests, looking for a sizeable change in the optical activity of cystine molecules. We found no evidence for the phase transition down to 0.01 K. The interpretation of these negative results will be discussed, and future experiments proposed.
The iron oxide hydroxide minerals goethite and akaganéite were likely constituents of the sediments present in, for instance, geothermal regions of the primitive earth. They may have adsorbed organics and catalyzed the condensation processes which led to the origins of life. The binding to and reactions of nucleotides and oligonucleotides with these minerals was investigated. The adsorption of adenosine, 5'-AMP, 3'-AMP, 5'-UMP, and 5'-CMP to these minerals was studied. Adenosine did not bind to goethite and akaganéite. The adsorption isotherms for the binding of the nucleotides revealed that they all had close to the same affinity for the mineral. Binding to goethite was about four times stronger than to akaganéite. There was little difference in the adsorption of each nucleotide suggesting the binding was between the negative charge on the phosphate group and the positive charges on the mineral surface. The absence of binding of adenosine is consistent with this explanation. Binding decreases as the pH increases due to the titration of the positive (acidic) centers on the minerals. Two times as many moles of polynucleotides were bound to these minerals as compared to the mononucleotides. Watson-Crick hydrogen bonding of adenosine and 5'-AMP to poly(U) complexes with goethite and akaganéite was observed. There was no interaction of uridine with the poly(U)-goethite complex as expected if Watson-Crick hydrogen bonding is taking place. Neither goethite nor akaganéite catalyzed the oligomerization of the phosphorimidazolide of adenosine (ImpA). The template directed synthesis of oligomers of 5'-GMP on the poly(C) bound to goethite was observed. Higher molecular weight oligomers were observed when the poly(C) was bound to goethite than was found in the absence of the mineral.
In the present review we analyze the available literature on the distribution of dust in the Universe, methods of its observation and determination of the chemical composition, and the roles for terrestrial prebiotic chemistry. The most plausible natural sources of dust on the Earth in the prebiotic era are sedimentation of interplanetary dust, meteoritic and cometary impacts, volcanic eruptions, and soil microparticulates; the interplanetary medium being among the most powerful supplier of the dust matter. Two fundamental roles of dust particles for the origins of life are considered: (1) catalytic formation of prebiotic compounds; and (2) delivery of organic matter to the Earth by space dust particles. Due to the fact that there is only approximate information on the chemical composition and properties of interstellar, circumstellar, and major part of interplanetary dust, even the simulating experiments are difficult to perform. Until these gaps are filled, it seems reasonable to focus efforts of the scientists dealing with dust-driven catalytic formation of prebiotically important compounds on the volcanic and meteoritic/cometary impact environments.
The origin and molecular evolution of viruses in this issue is dealt with at two levels: (1) tracing the past evolutionary pathways of viruses belonging to RNA virus families, retroviruses, and small and large DNA viruses; (2) tracing current changes in the RNA and DNA viral genomes that lead to the evolution of new virus mutants. In this interim summary, a time scale for the evolutionary processes is given, based on the accumulated published knowledge concerning the postulated origins of life on planet Earth, and the hypothesis that living cells with RNA genomes may have emerged (the "RNA world hypothesis") that then developed into cells with DNA genomes in eukaryotic and prokaryotic cells (1-3). The ideas about the evolution of RNA and DNA viruses from ancient cellular RNA and DNA molecules over a period of 3.5 billion years are discussed. It may be possible that by studying virus genes and molecular processes in virus-infected cells, and their involvement in the shaping of the genomes of bacteria, yeast, plants, insects, mammals, and humans, it will be possible to understand the importance of viruses in past evolution and to predict their possible impact on current and future evolutionary trends in biology.
The results of the Viking Biology experiments are best explained by non-biological phenomena: The interaction of the reagents with the materials comprising the regolith. Conditions of water activity, temperature, availability of carbon sources and others in most regions of the planet are too extreme for survival and growth of any known Earth microorganisms. Although the possibility persists that some very unusual form of life is somewhere on that planet the evidence is best interpreted as negative. Even though there is no evidence for current life on Mars, whether or not life ever originated there is not known.
No element is found to be commonly required if it has an abundance of less than about 2 nM in the ocean, 20 mumoles/kg in the earth's crust, or 200 mumoles/100 moles Si in the cosmos. More than 40 elements are above these limits, but only 18 of them are commonly required (6 of these being dispensed with by some organism). It is postulated that all of the required elements fall under one of four hypotheses: H-I--a unique requirement dating from the origin of life; H-II--a unique requirement, acquired later; H-III--a primordial requirement which was satisfied by a number of elements, evolutionary adaptation being made to the most abundant member; H-IV--same as III, but a later acquisition. It is suggested that H, K (vs. Na), Mg (vs. Ca), C, N, O, P, S and Fe fall under H-I. Special requirements such as for B, Se and I fall under H-II. In H-III are K vs. Rb, Mg vs. Be(?), S vs. Se, Clvs. Br, H vs F(?), and Zn and Mn vs. various metals. In H-IV probably fall Ca vs. Sr, Na vs. Li (?), Mo vs. V, and Si vs. Ge. The most abundant heavy metal in the ocean is Zn, which may account for its utilization; other required heavy metals have special utility as electron carriers.
The effect of adsorbed ions and pH on the adsorption of several purine and pyrimidine nucleotides on montmorillonite was studied. The cations used to prepare homoionic montmorillonite was Na+, Mn2+, Fe3+, Co2+, Ni+, Cu2+, and Zn2+. The nucleotides studied were 5'-,3'-, and 2'-AMP, and 5'-CMP in the pH range 2 through 12. The results show that preferential adsorption amongst nucleotides and similar molecules is dependent upon pH and the nature of the substituted metal cation in the clay. At neutral pH, it was observed that 5'-AMP was more strongly adsorbed than 2'AMP, 3'-AMP, and 5'-CMP. Cu2+ and Zn2+ clays showed enhanced adsorption of 5'-AMP compared to the other cation clays studied in the pH range 4-8. Below pH 4, the adsorption is attributed to cation and anion exchange adsorption mechanisms: above pH 4, anion exchange may also occur, but the adsorption (when it occurs) likely depends on a complexation mechanism occurring between metal cation in the clay exchange site the biomolecule. It is thus proposed that homoionic clays may have played a significant role in the concentration mechanism of biomonomers in the prebiotic environment, a prerequisite step necessary for the formation of biopolymers in the remaining steps leading to the origin of life.
The interactions of Ni(II) cation with a representative suite of purine bases and the respective nucleosides and nucleotides have been studied by ultraviolet difference spectroscopy. Apparent association constants, Kapp, were determined for each system at pH 7.0, using computer linear regression coupled with an iteration technique. The specificity of binding of Ni2+ for the purine nucleotides studied at pH 7.0 was 5'-GMP greater than 5'-IMP greater than 5'-AMP; a similar ordering was also found for the respective nucleosides and bases. In this study binding was not observed for the suite of pyramidines used, although a Ni2+ - cytidine complex has been observed (Fiskin and Beer, 1965). It was also found that Ni2+ bound more strongly to the purine 5'-nucleotides than to the respective nucleosides and bases. These trends are explained in terms of metal-ligand bonds and available bonding positions on the ligands. A role for metal-ion-nucleotide types of complexes is suggested in the processes that might have given rise to the origin of life.
The prebiotic synthesis of organic compounds using a spark discharge on various simulated primitive earth atmospheres at 25 degrees C has been studied. Methane mixtures contained H2 + CH4 + H2O + N2 + NH3 with H2/CH4 molar ratios from 0 to 4 and pNH3 = 0.1 torr. A similar set of experiments without added NH3 was performed. The yields of amino acids (1.2 to 4.7% based on the carbon) are approximately independent of the H2/CH4 ratio and whether NH3 was present, and a wide variety of amino acids are obtained. Mixtures of H2 + CO + H2O + N2 and H2 + CO2 + H2O + N2, with and without added NH3, all gave about 2% yields of amino acids at H2/CO and H2/CO2 ratios of 2 to 4. For a H2/CO2 ratio of 0, the yield of amino acids is extremely low (10(-3)%). Glycine is almost the only amino acid produced from CO and CO2 model atmospheres. These results show that the maximum yield is about the same for the three carbon sources at high H2/carbon ratios, but that CH4 is superior at low H2/carbon ratios. In addition, CH4 gives a much greater variety of amino acids than either CO or CO2. If it is assumed that an abundance of amino acids more complex than glycine was required for the origin of life, then these results indicate the requirement for CH4 in the primitive atmosphere.
Bis-phosphoimidazolides of an analogue of adenosine (in which ribose is replaced by an acyclic chain) and of two related analogues of guanosine undergo oligomerization in the presence of complementary polynucleotide templates. Data on the template- and nontemplate-directed reactions are presented, and the possible relevance to origins of life is discussed.
The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained? A number of speculative studies have been carried out that have reached the conclusion that the Krebs cycle evolved from pathways for amino acid biosynthesis, but many important questions remain open: Why and how did the full pathway emerge from there? Are other alternative routes for the same purpose possible? Are they better or worse? Have they had any opportunity to be developed in cellular metabolism evolution? We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of this metabolic pathway as it occurs in living cells is the best chemical solution: It has the least possible number of steps and it also has the greatest ATP yielding. Study of the evolutionary possibilities of each one-taking the available material to build new pathways-demonstrates that the emergence of the Krebs cycle has been a typical case of opportunism in molecular evolution. Our analysis proves, therefore, that the role of opportunism in evolution has converted a problem of several possible chemical solutions into a single-solution problem, with the actual Krebs cycle demonstrated to be the best possible chemical design. Our results also allow us to derive the rules under which metabolic pathways emerged during the origin of life.
Statistical studies of gene populations on the purine/pyrimidine alphabet have shown that the mean occurrence probability of the i-motif YRY(N)iYRY (R = purine, Y = pyrimidine, N = R or Y) is not uniform by varying i in the range, but presents a maximum at i = 6 in the following populations: protein coding genes of eukaryotes, prokaryotes, chloroplasts and mitochondria, and also viral introns, ribosomal RNA genes and transfer RNA genes (Arquès and Michel, 1987b, J. theor. Biol. 128, 457-461). From the "universality" of this observation, we suggested that the oligonucleotide YRY(N)6 is a primitive one and that it has a central function in DNA sequence evolution (Arquès and Michel, 1987b, J. theor. Biol. 128, 457-461). Following this idea, we introduce a concept of a model of DNA sequence evolution which will be validated according to a schema presented in three parts. In the first part, using the last version of the gene database, the YRY(N)6YRY preferential occurrence (maximum at i = 6) is confirmed for the populations mentioned above and is extended to some newly analysed populations: chloroplast introns, chloroplast 5' regions, mitochondrial 5' regions and small nuclear RNA genes. On the other hand, the YRY(N)6YRY preferential occurrence and periodicities are used in order to classify 18 gene populations. In the second part, we will demonstrate that several statistical features characterizing different gene populations (in particular the YRY(N)6YRY preferential occurrence and the periodicities) can be retrieved from a simple Markov model based on the mixing of the two oligonucleotides YRY(N)6 and YRY(N)3 and based on the percentages of RYR and YRY in the unspecified trinucleotides (N)3 of YRY(N)6 and YRY(N)3. Several properties are identified and prove in particular that the oligonucleotide mixing is an independent process and that several different features are functions of a unique parameter. In the third part, the return of the model to the reality shows a strong correlation between reality and simulation concerning the presence of a large alternating purine/pyrimidine stretches and of periodicities. It also contributes to a greater understanding of biological reality, e.g. the presence or the absence of large alternating purine/pyrimidine stretches can be explained as being a simple consequence of the mixing of two particular oligonucleotides. Finally, we believe that such an approach is the first step toward a unified model of DNA sequence evolution allowing the molecular understanding of both the origin of life and the actual biological reality.
The aim of the paper is to review critically the notion of autopoiesis as presented by Maturana and Varela. In particular, recognizing that there are difficulties in obtaining a complete and clear picture from the primary literature, an effort is made to present a coherent view-also based on many years of personal contact with Francisco Varela. The paper begins with a few historical notes to highlight the cultural background from which the notion of autopoiesis arose. The basic principles of autopoiesis as a theory of cellular life are then described, emphasizing also what autopoiesis is not: not an abstract theory, not a concept of artificial life, not a theory about the origin of life-but rather a pragmatic blueprint of life based on cellular life. It shown how this view leads to a conceptually clear definition of minimal life and to a logical link with related notions, such as self-organization, emergence, biological autonomy, auto-referentiality, and interactions with the environment. The perturbations brought about by the environment are seen as changes selected and triggered by the inner organization of the living. These selective coupling interactions impart meaning to the minimal life and are thus defined by Maturana and Varela with the arguable term of "cognition". This particular view on the mutual interactions between living organism and environment leads these authors to the notion of "enaction", and to the surprising view that autopoiesis and cognition are two complementary, and in a way equivalent, aspects of life. It is then shown how cognition, so defined, permits us to build a bridge between biology and cognitive science. Autopoiesis also allows one to conceive chemical models of minimal cellular life that can be implemented experimentally. The corresponding work on "chemical autopoiesis" is then reviewed. The surprising impact of autopoiesis in the social sciences ("social autopoiesis") is also briefly discussed. This review also comments on why the theory of autopoiesis had, and still has, a difficult time being accepted into the mainstream of life-science research. Finally, it is pointed out that the new interest in system biology and complexity theories may lead to a reappraisal of autopoiesis and related notions, as outlined also by other authors, such as Tibor Ganti and Stuart Kauffmann.
Following is a synthetic review on the minimal living cell, defined as an artificial or a semi-artificial cell having the minimal and sufficient number of components to be considered alive. We describe concepts and experiments based on these constructions, and we point out that an operational definition of minimal cell does not define a single species, but rather a broad family of interrelated cell-like structures. The relevance of these researches, considering that the minimal cell should also correspond to the early simple cell in the origin of life and early evolution, is also explained. In addition, we present detailed data in relation to minimal genome, with observations cited by several authors who agree on setting the theoretical full-fledged minimal genome to a figure between 200 and 300 genes. However, further theoretical assumptions may significantly reduce this number (i.e. by eliminating ribosomal proteins and by limiting DNA and RNA polymerases to only a few, less specific molecular species). Generally, the experimental approach to minimal cells consists in utilizing liposomes as cell models and in filling them with genes/enzymes corresponding to minimal cellular functions. To date, a few research groups have successfully induced the expression of single proteins, such as the green fluorescence protein, inside liposomes. Here, different approaches are described and compared. Present constructs are still rather far from the minimal cell, and experimental as well as theoretical difficulties opposing further reduction of complexity are discussed. While most of these minimal cell constructions may represent relatively poor imitations of a modern full-fledged cell, further studies will begin precisely from these constructs. In conclusion, we give a brief outline of the next possible steps on the road map to the minimal cell.
The definition of the node of the last universal common ancestor (LUCA) is justified in a topology of the unrooted universal tree. This definition allows previous analyses based on paralogous proteins to be extended to orthologous ones. In particular, the use of a thermophily index (based on the amino acids' propensity to enter the [hyper] thermophile proteins more frequently) and its correlation with the optimal growth temperature of the various organisms allow inferences to be made on the habitat in which the LUCA lived. The reconstruction of ancestral sequences by means of the maximum likelihood method and their attribution to the set of mesophilic or hyperthermophilic sequences have led to the following conclusions: the LUCA was a hyperthermophile "organism," as were the ancestors of the Archaea and Bacteria domains, while the ancestor of the Eukarya domain was a mesophile. These conclusions are independent of the presence of hyperthermophile bacteria in the sample of sequences used in the analysis and are therefore independent of whether or not these are the first lines of divergence in the Bacteria domain, as observed in the topology of the universal tree of ribosomal RNA. These conclusions are thus more easily understood under the hypothesis that the origin of life took place at a high temperature.
Zoochory is the most common mode of seed dispersal for the majority of plant species in the tropics. Based on the assumption of tight plant-animal interactions several hypotheses have been developed to investigate the origin of life history traits of plant diaspores and their dispersers, such as species-specific co-evolution, the low/high investment model (low investment in single fruits but massive fruiting to attract many different frugivores versus high investment in single fruits and fruit production for extended periods to provide food for few frugivores), and the evolution of syndromes which represent plant adaptations to disperser groups (e.g. birds, mammals, mixed). To test these hypotheses the dispersal strategies of 34 tree species were determined in the littoral forest of Sainte Luce (SE-Madagascar) with the help of fruit traps and tree watches. The impact of fruit consumers on the seeds was determined based on detailed behavioral observations. Phenological, morphological and biochemical fruit traits from tree species were measured to look for co-variation with different types of dispersal. No indication for species-specific co-evolution could be found nor any support for the low/high investment model. However dispersal syndromes could be distinguished as diaspores dispersed by birds, mammals or both groups (mixed) differ in the size of their fruits and seeds, fruit shape, and seed number, but not in biochemical traits. Five large-seeded tree species seem to depend critically on the largest lemur, Eulemur fulvus collaris, for seed dispersal. However, this does not represent a case of tight species-specific co-evolution. Rather it seems to be the consequence of the extinction of the larger frugivorous birds and lemurs which might also have fed on these large fruits. Nevertheless these interactions are of crucial importance to conserve the integrity of the forest.