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PubMed2004

Thermal force approach to molecular evolution.

Recent experiments are discussed where temperature gradients across mesoscopic pores are shown to provide essential mechanisms for autonomous molecular evolution. On the one hand, laminar thermal convection can drive DNA replication as the molecules are continuously cycled between hot and cold regions of a chamber. On the other hand, thermophoresis can accumulate charged biopolymers in similar convection settings. The experiments show that temperature differences analogous to those across porous rocks present a robust nonequilibrium boundary condition to feed the replication and accumulation of evolving molecules. It is speculated that similar nonequilibrium conditions near porous submarine hydrothermal mounds could have triggered the origin of life. In such a scenario, the encapsulation of cells with membranes would be a later development. It is expected that detailed studies of mesoscopic boundary conditions under nonequilibrium conditions will reveal new connecting pieces in the fascinating puzzle of the origins of life.

Biophysical Phenomena↗
PubMed2004

Alkalithermophiles.

Alkalithermophiles are an exciting subset of extremophilic organisms and represent extremophiles that are adapted to two extreme conditions, i.e. to a combination of alkaline and thermobiotic growth conditions. Among the anaerobic alkalithermophiles are representatives of both Bacteria and Archaea within a wide variety of physiological types and systematic groups, although a great majority belongs to the Firmicutes. Alkaliphiles have been isolated from a variety of niches including mesobiotic and neutrophilic soils and sediments. Interestingly anaerobic isolates from mesobiotic and neutrophilic niches exhibit shorter doubling times than isolates from thermobiotic niches; some anaerobic alkalithermophiles exhibit extremely fast growth rates, i.e. doubling times as short as 10 min. Their adaptation to both high pH and high temperature draws our attention not only because they are potential sources of industrially valuable enzymes but also because of their adaptive mechanisms to external environmental parameters. They could thus function as model organisms for extraterrestrial life in some environments and for theories on the origin of life. Alkalithermophiles, as far we know, do not represent the most thermophilic nor the most alkaliphilic of micro-organisms but represent the most alkaliphilic ones among the thermophiles and vice versa. We believe that the presently known species are only the tip of the iceberg and therefore that they do not represent the true boundaries under which life can thrive in respect to high temperature in alkaline environments.

Archaea↗
PubMed2004

Phenomenon of life: between equilibrium and non-linearity.

A model of ordering applicable to biological evolution is presented. It is shown that a steady state (more precisely approaching to a steady state) system of irreversible processes, under conditions of disproportionation of entropy, produces a lower-entropy product, that is, ordering. The ordering is defined as restricting of degrees of freedom: freedom of motion, interactions etc. The model differs from previous ones in that it relates the ordering to processes running not far from equilibrium, described in the linear field of non-equilibrium thermodynamics. It is shown that a system, which includes adenosine triphosphate (ATP) to adenosine diphosphate (ADP) conversion meets the demands of the physical model: it provides energy maintaining steady state conditions, and hydrolysis of ATP proceeding with consumption of water can be tightly conjugated with the most important reactions of synthesis of organic polymers (peptides, nucleotide chains etc.), which proceed with release of water. For these and other reasons ATP seems to be a key molecule of prebiotic evolution. It is argued that the elementary chemical reaction proceeding under control of an enzyme is not necessarily far from equilibrium. The experimental evidence supporting this idea, is presented. It is based on isotope data. Carbon isotope distribution in biochemical systems reveals regularity, which is inherent to steady state systems of chemical reactions, proceeding not far from equilibrium. In living organisms this feature appears at the statistical level, as many completely irreversible and non-linear processes occur in organisms. However not-far-from-equilibrium reactions are inherent to biochemical systems as a matter of principle. They are reconcilable with biochemical behavior. Extant organisms are highly evolved entities which, however, show in their basis the same features, as the simplest chemical systems must have had been involved in the origin of life. Some consequences following from the model, which may be significant for understanding the origin of life and the mechanism of biological evolution, are pointed out.

Adenosine Diphosphate↗
PubMed1984

Emergence of adaptable systems and evolution of a translation device.

An over-all organizational framework for the origin of life is outlined and attempts for realization are given. Evolution can be described as a process resulting in an increase of "knowledge" where knowledge is the number of carriers of genetic information discarded, on the average, until the evolutionary state under consideration is reached. A model for the evolution of a translation device, a crucial event in the origin of life, is described in detail. Aggregates of short polynucleotide strands in a hairpin conformation play a major role in this model. Experimental evidence for the selectivity of aggregation supports the idea of aggregates as error filters. Chromatographic separation as selection process during chemical evolution supports the model of the early translation device leading to the origin of the genetic code.

Amino Acids↗
PubMed1984

Origin and evolution of heredity-metabolism system.

The role of "theoretical physics" in the elucidation of the origin of life has been advanced by Eigen's hypercycle theory on ancient protein synthesis system and by Dyson's random drift theory on the autocatalytic formation of enzymes, although these approaches from the informational side involve many problems to be resolved. On the other hand, our C4N model calls for a stronger role of physico-chemistry in the understanding of the origin of life. Plant virus and movable genes could be the fossil vestiges of the ancient protein synthetic system, where tRNA identical to mRNA identical to gene. It is pointed out that functional differentiation of proteins closely correlates with the structure of the primitive tRNAs. Possible initial forms of the primitive tRNAs used by the earliest organisms are explicitly shown, in which the above correlation is carefully taken into account. The system of the primitive genes and the primitive enzymes in the proto-cellular membrane, say the marigranule, might simulate the earliest organism.

Base Sequence↗
PubMed1997

The nature and evolution of interstellar ices.

The evolution of icy grain mantles is governed by the environment in which they exist. This review presents an overview of the study of the molecules that make up the mantles and discusses their relevance to the origin of life. Models predict two phases of mantle growth during cloud collapse: simple polar and nonpolar molecules dominate the mantle layers at early and late times, respectively (Section 1). The effect of processing on grain mantle composition and the connection between organics in grain mantles and prebiotic chemistry is introduced. Section 2 describes how infrared spectroscopy of dense cloud sources, combined with theoretical models and laboratory data, gives us information on the composition and abundance of the ices in varying regions. The observed features and how they are used as diagnostics of mantle evolution are discussed in Section 3. This section also discusses the importance of these molecules to prebiotic chemistry. Section 4 compares grain mantle composition in different low-mass star forming regions, which best represent the solar birthplace. The final section (Section 5) summarizes the information presented, emphasizing the link between the study of interstellar dust and the origin of life.

Astronomical Phenomena↗
PubMed1997

Origin of biochemical organization.

The problems of the origin of life and biochemical evolution are analyzed in the context of the biochemical organization concept proposed earlier by the authors. The traditional view according to which the evolution of biological systems occurred from lower levels to systems of higher levels is criticized. It is suggested that the formation of the cell and biological systems of lower levels (subcellular structures, supramolecular structures, biomacromolecules) occurred in a coordinated manner. The liposome and inorganic hypotheses of the origin of life are discussed. Regosome model based on ideas of Nussinov and Mekler which combines advantages of the liposome and inorganic hypotheses has been adopted and modernized. It is suggested that the initial metabolism of protocells based itself on C2-C3-compounds. Autodevelopment of catalytic systems of protocells is discussed.

Biochemical Phenomena↗
PubMed1997

Isotopic evidence for extraterrestrial non-racemic amino acids in the Murchison meteorite.

Many amino acids contain an asymmetric centre, occurring as laevorotatory, L, or dextrorotatory, D, compounds. It is generally assumed that abiotic synthesis of amino acids on the early Earth resulted in racemic mixtures (L- and D-enantiomers in equal abundance). But the origin of life required, owing to conformational constraints, the almost exclusive selection of either L- or D-enantiomers, and the question of why living systems on the Earth consist of L-enantiomers rather than D-enantiomers is unresolved. A substantial fraction of the organic compounds on the early Earth may have been derived from comet and meteorite impacts. It has been reported previously that amino acids in the Murchison meteorite exhibit an excess of L-enantiomers, raising the possibility that a similar excess was present in the initial inventory of organic compounds on the Earth. The stable carbon isotope compositions of individual amino acids in Murchison support an extraterrestrial origin -- rather than a terrestrial overprint of biological amino acids-although reservations have persisted. Here we show that individual amino-acid enantiomers from Murchison are enriched in 15N relative to their terrestrial counterparts, so confirming an extraterrestrial source for an L-enantiomer excess in the Solar System that may predate the origin of life on the Earth.

Amino Acids↗
PubMed2003

Do viruses form lineages across different domains of life?

The scarce characterisation of the viral world has hampered our efforts to appreciate the magnitude and diversity of the viral domain. It appears that almost every species can be infected by a number of viruses. As our knowledge of viruses increases, it appears that this myriad of viruses may be organised into a reasonably low number of viral lineages including members infecting hosts belonging to different domains of life. Viruses belonging to a lineage share a common innate "self" that refers to structural and assembly principles of the virion. This hypothesis has a few consequences. All viruses are old, maybe preceding cellular life, and virus origins are polyphyletic, as opposed to the idea of a monophyletic origin of cellular life.

Adenoviridae↗
PubMed1980

Predicting coding function from nucleotide sequence or survival of "fitness" of tRNA.

The sequence of a nucleotide region of f1 bacteriophage was determined on a bonded ultrathin acrylamide gel with a discontinuous buffer system by using the dideoxy-DNA sequencing method. This sequence and one other were analyzed for maximal base pairing with tRNAs. The results allow a prediction of the direction and phase of possible coding functions. The implication of sequence constraints on mRNA codon frequency, tRNA structure, the origin of protein synthesis, and triplet reading are discussed in terms of neutral, Darwinian, and genotypic selectionist perspectives of evolution. The model of F. H. C. Crick, S. Brenner, A. Klug, and G. Pieczenik [(1976) Origins of Life 7, 389-397] for the origin of the genetic code is used to interpet contemporary adaptive and functional nucleic acid sequences.

Anticodon↗
PubMed1998

Past, present, and future life on Mars.

Although the Viking results indicated that the surface of Mars is dry and lifeless, there is direct geomorphological evidence that Mars had large amounts of liquid water on its surface in the past. From a biological perspective the existence of liquid water, by itself, motivates the question of the origin of life on Mars. One of the martian meteorites dates back to this early period and may contain evidence consistent with life. The Mars environment 3.5 to 4.0 Gyr ago was comparable to that on the Earth at this time in that both contained liquid water. Life had originated on Earth and reached a fair degree of biological sophistication by 3.5 Gyr ago. To determine if life similarly arose on Mars may require extensive robotic exploration and ultimately human exploration. Intensive exploration of Mars will require a continued presence on the Martian surface and the development of a self sustaining community in which humans can live and work for very long periods of time. A permanent Mars research station can obtain its life support requirements directly from the martian environment enabling a high degree of self-sufficiency. In the longer term, it is possible that in the future we might restore a habitable climate on Mars, returning it to the life-bearing state it may have enjoyed early in its history.

Atmosphere↗
PubMed1998

Surface-promoted replication and exponential amplification of DNA analogues.

Self-replicating chemical systems have been designed and studied to identify the minimal requirements for molecular replication, to translate the principle into synthetic supramolecular systems and to derive a better understanding of the scope and limitations of self-organization processes that are believed to be relevant to the origin of life on Earth. Current implementations make use of oligonucleotide analogues, peptides, and other molecules as templates and are based either on autocatalytic, cross-catalytic, or collectively catalytic pathways for template formation. A common problem of these systems is product inhibition, leading to parabolic instead of exponential amplification. The latter is the dynamic prerequisite for selection in the darwinian sense. We here describe an iterative, stepwise procedure for chemical replication which permits an exponential increase in the concentration of oligonucleotide analogues. The procedure employs the surface of a solid support and is called SPREAD (surface-promoted replication and exponential amplification of DNA analogues). Copies are synthesized from precursor fragments by chemical ligation on immobilized templates, and then liberated and immobilized to become new templates. The process is repeated iteratively. The role of the support is to separate complementary templates which would form stable duplexes in solution. SPREAD combines the advantages of solid-phase chemistry with chemical replication, and can be further developed for the non-enzymatic and enzymatic amplification of RNA, peptides and other templates as well as for studies of in vitro evolution and competition in artificial chemical systems. Similar processes may also have played a role in the origin of life on Earth, because the earliest replication systems may have proliferated by spreading on mineral surfaces.

Chromatography, High Pressure Liquid↗
PubMed2006

Self-assembly processes in the prebiotic environment.

An important question guiding research on the origin of life concerns the environmental conditions where molecular systems with the properties of life first appeared on the early Earth. An appropriate site would require liquid water, a source of organic compounds, a source of energy to drive polymerization reactions and a process by which the compounds were sufficiently concentrated to undergo physical and chemical interactions. One such site is a geothermal setting, in which organic compounds interact with mineral surfaces to promote self-assembly and polymerization reactions. Here, we report an initial study of two geothermal sites where mixtures of representative organic solutes (amino acids, nucleobases, a fatty acid and glycerol) and phosphate were mixed with high-temperature water in clay-lined pools. Most of the added organics and phosphate were removed from solution with half-times measured in minutes to a few hours. Analysis of the clay, primarily smectite and kaolin, showed that the organics were adsorbed to the mineral surfaces at the acidic pH of the pools, but could subsequently be released in basic solutions. These results help to constrain the range of possible environments for the origin of life. A site conducive to self-assembly of organic solutes would be an aqueous environment relatively low in ionic solutes, at an intermediate temperature range and neutral pH ranges, in which cyclic concentration of the solutes can occur by transient dry intervals.

Earth, Planet↗
PubMed1988

Gathering evidence: the case for past life on Mars.

Four billion years ago, the surface of Mars may have been conducive to the origin of life. Scientific evidence suggests that Mars had a biologically favorable atmosphere back then, with warm temperatures and abundant water during its formative years. Many scientists contend that life arose on early Mars but was subsequently wiped out. If Mars was a harbor for past life, why did it become extinct? Where should we, on future Mars missions, look for evidence of past life? Are there analogous biological systems on Earth to study and hypothesize the presence of early Martian life?

Antarctic Regions↗
PubMed1982

The atmosphere of Titan.

The discovery that Titan had an atmosphere was made by the identification of methane in the satellite's spectrum in 1944. But the abundance of this gas and the identification of other major constituents required the 1980 encounter by the Voyager 1 spacecraft. in the intervening years, traces of C2H2, C2H4, C2H6 and CH3D had been posited to interpret emission bands in Titan's IR spectrum. The Voyager infrared Spectrometer confirmed that these gases were present and added seven more. The atmosphere is now known to be composed primarily of molecular nitrogen. But the derived mean molecular weight suggests the presence of a significant amount of some heavier gas, most probably argon. It is shown that this argon must be primordial, and that one can understand the evolution of Titan's atmosphere in terms of degassing of a mixed hydrate dominated by CH4, N2 and 36Ar. This model satisfactorily explains the absence of neon and makes no special requirements on the satellite's surface temperature. The organic chemistry taking place on Titan today invites comparison with chemical evolution on the primitive Earth prior to the origin of life.

Biological Evolution↗
PubMed2003

Bridging nonliving and living matter.

Assembling non-biological materials (geomaterials) into a proto-organism constitutes a bridge between nonliving and living matter. In this article we present a simple step-by-step route to assemble a proto-organism. Many pictures have been proposed to describe this transition within the origins-of-life and artificial life communities, and more recently alternative pictures have been emerging from advances in nanoscience and biotechnology. The proposed proto-organism lends itself to both traditions and defines a new picture based on a simple idea: Given a set of required functionalities, minimize the physicochemical structures that support these functionalities, and make sure that all structures self-assemble and mutually enhance each other's existence. The result is the first concrete, rational design of a simple physicochemical system that integrates the key functionalities in a thermodynamically favorable manner as a lipid aggregate integrates proto-genes and a proto-metabolism. Under external pumping of free energy, the metabolic processes produce the required building blocks, and only specific gene sequences enhance the metabolic kinetics sufficiently for the whole system to survive. We propose an experimental implementation of the proto-organism with a discussion of our experimental results, together with relevant results produced by other experimental groups, and we specify what is still missing experimentally. Identifying the missing steps is just as important as providing the road map for the transition. We derive the kinetic and thermodynamic conditions of each of the proto-organism subsystems together with relevant theoretical and computational results about these subsystems. We present and discuss detailed 3D simulations of the lipid aggregation processes. From the reaction kinetics we derive analytical aggregate size distributions, and derive key properties of the metabolic efficiency and stability. Thermodynamics and kinetics of the ligation directed self-replication of the proto-genes is discussed, and we summarize the full life cycle of the proto-organism by comparing size, replication time, and energy with the biomass efficiency of contemporary unicells. Finally, we also compare our proto-organism picture with existing origins-of-life and protocell pictures. By assembling one possible bridge between nonliving and living matter we hope to provide a piece in the ancient puzzle about who we are and where we come from.

Artificial Intelligence↗
PubMed1997

Emerging concepts of self-organization and the living state. Special issue.

This special issue present papers that examine the concept of self-organization in the origin of life. Concepts explored include chaos and order in open systems, the origin of biochemical organization, non-cellular phases of life on clay, biodynamics necessary for the emergence of energy consumers, molecular evolution, order in self-oscillators, self-organization of semi-conductor physics, self-organizing behavior of microtubules in the cytoskeleton, biogenesis and physics, perceptive funcion, and an overview of the experimental realization of artificial intelligence.

Biophysics↗