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Nonequilibrium thermodynamics and different axioms of evolution.

Proponents of two axioms of biological evolutionary theory have attempted to find justification by reference to nonequilibrium thermodynamics. One states that biological systems and their evolutionary diversification are physically improbable states and transitions, resulting from a selective process; the other asserts that there is an historically constrained inherent directionality in evolutionary dynamics, independent of natural selection, which exerts a self-organizing influence. The first, the Axiom of Improbability, is shown to be nonhistorical and thus, for a theory of change through time, acausal. Its perception of the improbability of living states is at least partially an artifact of closed system thinking. The second, the Axiom of Historically Determined Inherent Directionality, is supported evidentially and has an explicit historical component. Historically constrained dynamic populations are inherently nonequilibrium systems. It is argued that living, evolving systems, when considered to be historically constrained nonequilibrium systems, do not appear improbable at all. Thus, the two axioms are not compatible. Instead, the Axiom of Improbability is considered to result from an unjustified attempt to extend the contingent proximal actions of natural selection into the area of historical, causal explanations. It is thus denied axiomatic status, and the effects of natural selection are subsumed as an additional level of constraint in an evolutionary theory derived from the Axiom of Historically Determined Inherent Directionality.

Biological Evolution↗

The posterior probability distribution of alignments and its application to parameter estimation of evolutionary trees and to optimization of multiple alignments.

How to sample alignments from their posterior probability distribution given two strings is shown. This is extended to sampling alignments of more than two strings. The result is first applied to the estimation of the edges of a given evolutionary tree over several strings. Second, when used in conjunction with simulated annealing, it gives a stochastic search method for an optimal multiple alignment.

Algorithms↗

Reconstruction of ancestral sequences by the inferential method, a tool for protein engineering studies.

This paper describes the inferential method, an approach for reconstructing protein and nucleotide sequences of ancestral species, starting from known, homologous, contemporary sequences. The method requires knowledge of the topology of the phylogenetic tree, whose nodes are the species to whom the reconstructed sequences belong. The method has been tested by computer simulation of speciation and nucleotide substitutions, starting from a single ancestral sequence, and by subsequent reconstruction of nodal sequences. Results have shown that reconstructions obtained by the inferential method are affected by limited error frequencies, which (1) are proportional to the squares of nucleotide substitution rates and of internodal distances, and (2) are little influenced by non-uniformity of transformation rates of nucleotides. Furthermore, good agreement of the results has been obtained by comparing protein-sequence reconstructions carried out with the inferential method with those obtained using the maximum parsimony method in two different cases: e.g., a reconstruction of simulated sequences and a reconstruction of mammalian ribonuclease sequences.

Amino Acid Sequence↗

On the recombinational origin of protein-sequence-subunit structure.

Since 1929 the concept that proteins are built from subunits of certain standard size (Svedberg 1929) has been revisited several times, each time with a new demonstration that, indeed, there are certain preferred protein sizes. According to recent estimates the overrepresented sizes are close to multiples of 125 amino acid (aa) residues for eukaryotes and 150 residues for prokaryotes. To explain these preferences, a hypothesis is suggested, and quantitatively developed, on the recombinational nature of this regularity. The protein-coding sequences are assumed to evolve at some early stage via recombinational events--insertions of DNA circles of a certain optimal size. The contour lengths of the protein-coding DNA circles had to be simultaneously divisible by three and, to minimize torsional constraint, by the DNA helical repeat. With these two conditions satisfied, the calculated contour lengths of the DNA circles, 250-500 base pairs (bp), turn out to correspond well to known optimal DNA circularization sizes and to the predicted range of the protein sequence subunit sizes: 80-170 aa residues, which covers experimentally observed values. The subunit size is found to be strongly influenced by the helical repeat of DNA. The sizes 125 and 150 aa are derived when the corresponding helical repeats of DNA are set within fractions of promilles from the 10.54 bp/turn value. This fits to the experimentally estimated mean for natural mixed DNA sequences, 10.53-10.57 bp/turn.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

When are two qualitative taxonomic characters compatible?

A proof is given of a procedure that has previously appeared claiming to determine when two amino acid positions on a protein could both possibly be divergent taxonomic characters. An algorithm for executing this procedure is described.

Amino Acid Sequence↗

Optimization by stimulating molecular evolution.

Based on the analogy between mathematical optimization and molecular evolution and on Eigen's quasi-species model of molecular evolution, an evolutionary algorithm for combinatorial optimization has been developed. This algorithm consists of a versatile variation scheme and an innovative decision rule, the essence of which lies in a radical revision of the conventional philosophy of optimization: A number of configurations of variables with better values, instead of only a single best configuration, are selected as starting points for the next iteration. As a result the search proceeds in parallel along a number of routes and is unlikely to get trapped in local optima. An important innovation of the algorithm is introduction of a constraint to let the starting points always keep a certain distance from each other so that the search is able to cover a larger region of space effectively. The main advantage of the algorithm is that it has more chances to find the global optimum and as many local optima as possible in a single run. This has been demonstrated in preliminary computational experiments.

Algorithms↗

Role of interstellar molecules in prebiological evolution.

Three generations of organic molecules in space are considered: interstellar molecules, molescules synthesised in protosolar cloud and molecules synthesised on the Earth. It is shown that there is no possibilities for amino acid polymers to be synthesised under interstellar cloud conditions. Molecules of the second generation were disintegrated during the Earth accumulation period. The problem of the origin of life is connected with the evolution of molecules of the third generation.

Amino Acids↗

Self-sequencing of amino acids and origins of polyfunctional protocells.

The primal role of the origins of proteins in molecular evolution is discussed. On the basis of this premise, the significance of the experimentally established self-sequencing of amino acids under simulated geological conditions is explained as due to the fact that the products are highly nonrandom and accordingly contain many kinds of information. When such thermal proteins are aggregated into laboratory protocells, an action that occurs readily, the resultant protocells also contain many kinds of information. Residue-by-residue order, enzymic activities, and lipid quality accordingly occur within each preparation of proteinoid (thermal protein). In this paper are reviewed briefly the phenomenon of self-sequencing of amino acids, its relationship to evolutionary processes, other significance of such self-ordering, and the experimental evidence for original polyfunctional protocells.

Amino Acid Sequence↗

Ritual female genital surgery among Bedouin in Israel.

Ritual female genital operations are common in many parts of the world, with varying degrees of mutilation from clitoridectomy and removal of the labia to removal of the clitoral prepuce. Interviews of 21 Bedouin women in southern Israel revealed the practice to be normative in several tribes. However, physical examination of 37 young women from those tribes at a gynecological clinic revealed only small scars on the labia in each woman. Bedouin in southern Israel may offer a model of evolution of female circumcision into a nonmutilative ritual incision.

Adolescent↗

A hypothesis: reciprocal information transfer between oligoribonucleotides and oligopeptides in prebiotic molecular evolution.

We wish to propose a mechanism for reciprocal information transfer in prebiotic molecular evolution, based on heterologous pairing complex formation between oligoribonucleotides and oligopeptides. In this proposed pairing complex, the bases of the oligoribonucleotide and the side chains of the oligopeptide may form three types of complementary Watson-Crick-type hydrogen bonds. The structural basis for the pairing is the close correspondence of the distances between the side chains in the two molecules. Both the inter-nucleotide spacing of the RNA and the inter-side-chain spacing of the peptide are approximately 3.4 A. The proposed pairing mode would allow both specific and nonspecific interactions required for reciprocal information transfer. Thus, it represents a simple and versatile coding system that could have had significant implications in prebiotic molecular selection and evolution. In addition, we propose several testable experimental approaches based on the pairing mode of oligoribonucleotides and oligopeptides to verify our hypothesis.

Amino Acid Sequence↗

Formation of the thioester, N,S-diacetylcysteine, from acetaldehyde and N,N'diacetylcystine in aqueous solution with ultraviolet light.

The thioester, N,S-diacetylcysteine, is formed during the illumination of phosphate buffered (pH 7.0) aqueous solutions of acetaldehyde and N,N'-diacetylcystine with ultraviolet light. The yield of N,S-diacetylcysteine relative to N-acetylcysteine and unidentified products progressively increases as ultraviolet light below 239 nm, 253 nm and 281 nm is cut off with optical filters. When ultraviolet light below 320 nm is removed with an optical filter, there is no detectable reaction. Illumination of 0.025 M N,N'-diacetylcystine with 0.5 M and 1.0 M acetaldehyde with filtered ultraviolet light gives, respectively, 20% and 80% yields of N,S-diacetylcysteine. In the reaction with 1.0 M acetaldehyde, N-acetylcysteine forms early in the reaction and later decreases with its conversion to N,S-diacetylcysteine. The prebiotic significance of these reactions is discussed.

Acetaldehyde↗

Was there a universal tRNA before specialized tRNAs came into existence?

It is generally true that evolving systems begin simply and become more complex in the evolutionary process. For those who try to understand the origin of a biochemical system, what is required is the development of an idea as to what simpler system preceeded the present one. Here we present an hypothesis that a universal tRNA molecule, capable of reading many codons may have preceeded the appearance of individual tRNAs. Evidence seems to suggest that this molecule may have been derived from a common ancestor of the contemporary 5S rRNAs and tRNAs.

Biological Evolution↗

Beta-decay, bremsstrahlen, and the origin of molecular chirality.

A brief review is presented of the Vester-Ulbricht beta-decay Bremsstrahlen hypothesis for the origin of optical activity, and of subsequent experiments designed to test it. Certain of our experiments along these lines, begun in 1974 and involving the irradiation of racemic and optically active amino acids in a 61.7 KCi 90Sr-90Y Bremsstrahlen source, have now been completed and are described. After 10.89 years of irradiation with a total Bremsstrahlen dose of 2.5 X 10(9) rads, crystalline DL-leucine, norleucine, and norvaline suffered 47.2, 33.6, and 27.4% radiolysis, respectively, but showed no evidence whatsoever of asymmetric degradation. D- and L-Leucine underwent about 48% radiolysis and showed 2.4-2.9% radioracemization. Other samples in solution were too severely degraded to analyze. Probable intrinsic reasons for the failure of the Vester-Ulbricht mechanism to afford asymmetric radiolysis in the present and related experiments involving beta-decay Bremsstrahlen are enumerated.

Amino Acids↗

Interrelatedness of 5S RNA sequences investigated by correspondence analysis.

Correspondence analysis (a form of multivariate statistics) applied to 74 5S ribosomal RNA sequences indicates that the sequences are interrelated in a systematic, nonrandom fashion. Aligned sequences are represented as vectors in a 5N-dimensional space, where N is the number of base positions in the 5S RNA molecule. Mutually orthogonal directions (called factor axes) along which intersequence variance is greatest are defined in this hyperspace. Projection of the sequences onto planes defined by these factorial directions reveals clustering of species that is suggestive of phylogenetic relationships. For each factorial direction, correspondence analysis points to regions of "importance," i.e., those base positions at which the systematic changes occur that define that particular direction. In effect, the technique provides a rapid determination of group-specific signatures. In several instances, similarities between sequences are indicated that have only recently been inferred from visual base-to-base comparisons. These results suggest that correspondence analysis may provide a valuable starting point from which to uncover the patterns of change underlying the evolution of a macromolecule, such as 5S RNA.

Analysis of Variance↗

The stereoselectivity of alcohol dehydrogenases: a stereochemical imperative?

The stereoselectivity of NAD+-dependent alcohol dehydrogenases (transfering either the pro-R or pro-S hydrogen of NADH) correlates with the thermodynamic stability of their substrates, and appears to reflect evolutionary pressure to adjust in the active site the conformation of NADH so as to match the cofactor's reducing power to the oxidizability of the substrate. A requirement that the free energies of protein-bound intermediates be matched suggests a new approach for understanding catalysis and evolution in enzymes.

Alcohol Oxidoreductases↗