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At least 343 records · Page 19Linked to original sources
PubMed1997

Percolation on the fitness hypercube and the evolution of reproductive isolation.

We study the structure and properties of adaptive landscapes arising from the assumption that genotype fitness can only be 0 (inviable genotype) or 1 (viable genotype). An appropriate image of resulting ("holey") fitness landscapes is a (multidimensional) flat surface with many holes. We have demonstrated that in the genotype space there are clusters of viable genotypes whose members can evolve from any member by single substitutions and that there are "species" defined according to the biological species concept. Assuming that the number of genes, n, is very large while the proportion of viable genotypes among all possible genotypes, p, is very small, we have deduced many qualitative and quantitative properties of holey adaptive landscapes which may be related to the patterns of speciation. Relationship between p and n determines two qualitatively different regimes: subcritical and supercritical. The subcritical regime takes place if p is extremely small. In this case, the largest clusters of viable genotypes in the genotype space have size of order n and there are many of such size; typical members of a cluster are connected by a single ("evolutionary") path; the number of different (biological) species in the cluster has order n; the expected number of different species in the cluster within k viable substitutions from any its member is of order k. The supercritical regime takes place if p is small but not extremely small. In this case, there exists a cluster of viable genotypes (a "giant" component) that has size of order 2n/n; the giant component comes "near" every point of the genotype space; typical members of the giant component are connected by many evolutionary paths; the number of different (biological) species on the "giant" component has at least order n2; the expected number of different species on the "giant" component within k viable substitution from any its member is at least of order kn. At the boundary of two regimes all properties of adaptive landscapes undergo dramatic changes, a physical analogy of which is a phase transition. We have considered the most probable (within the present framework) scenario of biological evolution on holey landscapes assuming that it starts on a genotype from the largest connected component and proceeds along it by mutation and genetic drift. In this scenario, there is no need to cross any "adaptive valleys"; reproductive isolation between populations evolves as a side effect of accumulating different mutations. The rate of divergence is very fast: a few substitutions are sufficient to result in a new biological species. We argue that macroevolution and speciation on "rugged" fitness landscapes proceed according to the properties of the corresponding holey landscapes.

Animals↗
PubMed1980

Lipids as a principle for the identification of archaebacteria.

The 'Archaebacteria' consist of several distinct subgroups including methanogens, extreme halophiles and specific thermoacidophiles. These bacteria are distinct from other bacteria with respect to their characteristic RNA compositions, the absence of muramic acid in the cell walls and the predominance of nonsaponifiable [correction of nonsaponifable] lipids. The lipid composition of the archaebacteria consists of isoprenoid and hydroisoprenoid hydrocarbons and isopranyl glycerol ether lipids. The pathways for the biosynthesis of the lipid components are those shared by most microorganisms and demonstrate a close relationship; however, an independent line of descent is indicated by the formation of the isopranyl glycerol ether lipids. This discontinuity formulates a point for delineating the early stages of biological evolution and for dividing bacteria into two subgroups.

Archaea↗
PubMed2005

"Bioplutonism" and the evolutionary implications of beneficial genes from another biosphere.

Could exogenous genes from another biosphere have aided the evolution of life on Earth's surface over the last half-billion years? That possibility was considered by Thomas Gold in 1992, when he hypothesized that a "deep hot biosphere" (DHB) resides independently well below its cooler surface counterpart. And he suggested that "... in the long term ... there may occasionally be beneficial exchanges of genetic material between microbial life at depth and the surface life." Thus, the question: what evidence is there to support Gold's notion that exogenous genes from the DHB--let us call them "bioplutons"--ever bestowed benefits on the evolution of surface life? In pursuit of this question I drafted a null hypothesis: "Nothing beyond our own biosphere, as we know it today, renders any kind of genetic benefits to biological evolution." After objectively analyzing the evidence and arguments pro and con I failed to reject the null hypothesis, given what we know today, especially the fact that no genetic imprint from the DHB has been identified in eukaryotic genomes. But my conclusion is regarded as tentative, because the fundamentals of Gold's argument, collectively referred to herein as "bioplutonism," might be confirmed eventually with successful probes into the DHB, and with the sampling of its alleged genetic material.

Biological Evolution↗
PubMedDate not supplied

Is the "small world" effect relevant to evolution?

Mutations and selection are the driving forces of biological evolution. We model here the simplest case: an evolving population of asexual organisms. We consider two kinds of mutations: point mutations, corresponding to local displacements in the genotypic space, and all the other genotypic rearrangements, equivalent to long-range jumps. We show that a small-world effect is present in evolution: even a small fraction of quenched long-range jumps makes the results indistinguishable from those obtained by assuming all mutations equiprobable. We apply this result to the evolution of a population on a smooth fitness landscape, showing that the equilibrium distribution is a Boltzmann one, in which the fitness plays the role of an energy, and mutations that of a temperature.

Evolution, Molecular↗
PubMed1996

Are critical phenomena relevant to large-scale evolution?

Recent theoretical studies, based on the theory of self-organized critical systems, seem to suggest that the dynamical patterns of macroevolution could belong to such class of critical phenomena. Two basic approaches have been proposed: the Kauffman-Johnsen model (based on the use of coupled fitness landscapes) and the Bak-Sneppen model. Both are reviewed here. These models are oversimplified pictures of biological evolution, but the (possible) validity of them is based on the concept of universality, i.e. that apparently very different systems sharing some few common properties should also behave in a very similar way. In this paper we explore the current evidence from the fossil record, showing that some properties that are suggestive of critical dynamics would also be the result of random phenomema. Some general properties of the large-scale pattern of evolution, which should be reproduced by these models, are discussed.

Biological Evolution↗
PubMed2002

Mutation, specialization, and hypersensitivity in highly optimized tolerance.

We introduce a model of evolution in which competing organisms are represented by percolation lattice models. Fitness is based on the number of occupied sites remaining after removing a cluster connected to a randomly selected site. High-fitness individuals arising through mutation and selection must trade off density versus robustness to loss, and are characterized by cellular barrier patterns that prevent large cascading losses to common disturbances. This model shows that Highly Optimized Tolerance (HOT), which links complexity to robustness in designed systems, arises naturally through Darwinian mechanisms. Although the model is a severe abstraction of biology, it produces a surprisingly wide variety of micro- and macroevolutionary features strikingly similar to real biological evolution.

Biological Evolution↗
PubMed2003

[Equilibrium thermodynamics of quasi-closed biological systems. Cell differentiation and development of organisms].

The law of temporal hierarchies makes it possible to identify quasi-closed systems in open biological systems and to use the approaches of hierarchical quasi-equilibrium thermodynamics to establish the direction of ontogenesis and evolutionary processes. A short review of the achievements in the field of evolution biological thermodynamics and the thermodynamics of aging are presented. Cell differentiation, the development of multicell organisms, and the emergence of the structures of the higher hierarchies of the biological world are assumed to be determined by the thermodynamic direction of these processes. Cell organisms contain identical genes. Only some of them, however, function in the course of differentiation and development. Gene induction and repression during differentiation are determined by the position of newly emerging cells, whose properties depend on their functional position. These properties are determined by thermodynamic parameters of the cells' environment (thermostat), whose components and physicochemical characteristics affect gene induction and repression. A holographic (three-dimensional) design of the future organism (higher structures of the biological world) is determined by the thermodynamic demand for certain genes. The latter's operation is stimulated by their environment. One of the well-known examples that corroborates the presented model is the change of gene transcription when the nature of lipids and other metabolites contained in cells are changed. Application of the principle of stability of matter to the structures of adjacent hierarchies constitutes additional proof that quasi-equilibrium thermodynamics can be applied to the biological systems of the real world.

Biological Evolution↗
PubMedDate not supplied

[The problem of the origin of intellect and evolutionary biocybernetics].

The discussion proposed by L. M. Chailakhian in developed concerning the problem of the origin of the natural intelligence. It is stressed that studying the origin of logical thinking is very important. It is argued that the problem of the intelligence origin should be analyzed within the framework of general investigations of the evolution of biocybernetical system. This approach can constitute the powerful branch of science named evolutionary biocybernetics. The main lines of inquiry are characterized. The strategy is outlined of development of evolutionary biocybernetics: creation and development of basic mathematical models which characterize the key "intellectual inventions" of biological evolution. The examples are given of the models (the model of dominanta origin and the model of functional system in correspondence with P. K. Anokhin's ideas), which can be developed in the immediate future. The approaches are outlined to development of these models.

Biological Evolution↗
PubMed1985

Plasticity of the central nervous system--a neurosurgeon's experience of cerebral compensation and decompensation.

Cerebral plasticity constitutes one of the most decisive factors in recovery and readaptation after cerebral lesions. In contrast to the considerable progress in current studies on normal neuronal plasticity including the idea of "l'homme neuronal", the concept of plasticity postulated by Albrecht Bethe in 1929 received little attention. The author, as a neurosurgeon, has tried to describe cranial morphological plasticity, morphological and functional plasticity in infantile encephalopathies and especially in hemiatrophic lesions. It is supposed that a true morphological substrate exists due to compensatory hyperplasia of the uninvolved hemisphere. Modern neurosurgical techniques have demonstrated that the functional plastic capacity is much larger than has been supposed, even in the elderly. Some aspects of the mechanisms of compensation and decompensation of cortical and subcortical structures as well as of the central regulation systems are discussed. The full extent of the amazing recovery and functional reorganization is reached by plastic capacity, personal motivation, adequate training and sufficient time. The contribution ends with an exposition of a personal philosophy concerning psycho-somatic dualism, the body-mind problem, the future of the human brain and the ethical outlook, based on the progressive biological evolution of the basal neocortex and the immanent functional development (H. Spatz).

Adaptation, Physiological↗
PubMed2000

Antievolutionism in the Antipodes: from protesting evolution to promoting creationism in New Zealand.

Like other English-speaking peoples around the world, New Zealanders began debating Darwinism in the early 1860s, shortly after the publication of Charles Darwin's Origin of Species. Despite the opposition of some religious and political leaders - and even the odd scientist - biological evolution made deep inroads in a culture that increasingly identified itself as secular. The introduction of pro-evolution curricula and radio broadcasts provoked occasional antievolution outbursts, but creationism remained more an object of ridicule than a threat until the last decades of the twentieth century, when first American and then Australian creationists began fomenting antievolutionism among New Zealanders. Although Stephen Jay Gould assured them in 1986 that they had little to fear from so-called scientific creationism, because it was a 'peculiarly American' phenomenon, scientific creationism by the mid-1990s had captured the allegiance of an estimated five per cent of the country and proved especially attractive to Maori and Pacific Islanders. In 1992 New Zealand creationists formed their own antievolution society, Creation Science (NZ).

Australia↗
PubMed2005

Modelling the evolution of genetic regulatory networks.

An evolutionary model of genetic regulatory networks is developed, based on a model of network encoding and dynamics called the Artificial Genome (AG). This model derives a number of specific genes and their interactions from a string of (initially random) bases in an idealized manner analogous to that employed by natural DNA. The gene expression dynamics are determined by updating the gene network as if it were a simple Boolean network. The generic behaviour of the AG model is investigated in detail. In particular, we explore the characteristic network topologies generated by the model, their dynamical behaviours, and the typical variance of network connectivities and network structures. These properties are demonstrated to agree with a probabilistic analysis of the model, and the typical network structures generated by the model are shown to lie between those of random networks and scale-free networks in terms of their degree distribution. Evolutionary processes are simulated using a genetic algorithm, with selection acting on a range of properties from gene number and degree of connectivity through periodic behaviour to specific patterns of gene expression. The evolvability of increasingly complex patterns of gene expression is examined in detail. When a degree of redundancy is introduced, the average number of generations required to evolve given targets is reduced, but limits on evolution of complex gene expression patterns remain. In addition, cyclic gene expression patterns with periods that are multiples of shorter expression patterns are shown to be inherently easier to evolve than others. Constraints imposed by the template-matching nature of the AG model generate similar biases towards such expression patterns in networks in initial populations, in addition to the somewhat scale-free nature of these networks. The significance of these results on current understanding of biological evolution is discussed.

Algorithms↗
PubMed1999

Evolutionary patterns from mass originations and mass extinctions.

The Fossil Record 2 database gives a stratigraphic range of most known animal and plant families. We have used it to plot the number of families extant through time and argue for an exponential fit, rather than a logistic one, on the basis of power spectra of the residuals from the exponential. The times of origins and extinctions, when plotted for all families of marine and terrestrial organisms over the last 600 Myr, reveal different origination and extinction peaks. This suggests that patterns of biological evolution are driven by its own internal dynamics as well as responding to upsets from external causes. Spectral analysis shows that the residuals from the exponential model of the marine system are more consistent with 1/f noise suggesting that self-organized criticality phenomena may be involved.

Animals↗
PubMed1977

Life and the outer planets I. Performance of terrestrial organisms in ammonia-rich systems.

Survival and growth of organisms has been demonstrated at 298 degrees K in NH3 atmospheres, including ammonia-methane mixtures. Included are bacteria such as Clostridium perfringens, Pseudomonas aeruginosa, fungi such as Penicillium notatum and Torula utilis. Although the biological response in onion and other species of Allium is limited to germination, standard metabolic poisons were active even in 15 M aqueous NH3, at 250 degrees K. The most extreme example of compatibility between NH3-rich environments and terrestrial life was the retention of metabolic capabilities by conidia of Penicillium after 6 months at 233 degrees K in a liquid ammonia-glycerol medium. Tritiated thymidine, uridine and amino acids were incorporated by these conidia unless subjected to intense gamma-radiation. Observations spanning the past decade suggest that the analogies between H2O and NH3 as solvent media or -OH and -NH2, as functional groups are probably valid. Chemical-biological evolution similar to early terrestrial evolution could be compatible with chemical conditions presumed to exist on the outer planets and some of their satellites.

Ammonia↗
PubMed2004

Optimal traffic organization in ants under crowded conditions.

Efficient transportation, a hot topic in nonlinear science, is essential for modern societies and the survival of biological species. Biological evolution has generated a rich variety of successful solutions, which have inspired engineers to design optimized artificial systems. Foraging ants, for example, form attractive trails that support the exploitation of initially unknown food sources in almost the minimum possible time. However, can this strategy cope with bottleneck situations, when interactions cause delays that reduce the overall flow? Here, we present an experimental study of ants confronted with two alternative routes. We find that pheromone-based attraction generates one trail at low densities, whereas at a high level of crowding, another trail is established before traffic volume is affected, which guarantees that an optimal rate of food return is maintained. This bifurcation phenomenon is explained by a nonlinear modelling approach. Surprisingly, the underlying mechanism is based on inhibitory interactions. It points to capacity reserves, a limitation of the density-induced speed reduction, and a sufficient pheromone concentration for reliable trail perception. The balancing mechanism between cohesive and dispersive forces appears to be generic in natural, urban and transportation systems.

Animals↗
PubMed1985

The prokaryote-eukaryote interface.

Over the past 30 years the study of the sequences of proteins and nucleic acids has produced almost incredible amounts of information, new concepts, and new avenues of research. The beginning was slow: the first peptide hormones sequenced in the early 1950's, the first cytochrome c (horse) in 1961, the first bacterial ferredoxin in 1964, and the first transfer RNA (yeast alanine tRNA) in 1965. In the past 6 years, the rate of data accumulation has accelerated tremendously, primarily due to technological advances in nucleic acid sequencing techniques. For investigators of biological evolution, the sequence data and the new information on genetic mechanisms would prove to be the best evidence for elucidating relationships among the genomes of living organisms and for deducing phylogenetic history. In particular, they needed evidence to decide between the two hypotheses for the origin of eukaryotic cells. Now, less than 20 years since Margulis renewed the investigation of this problem, comparisons of protein and nucleic acid sequences, especially of the small subunit ribosomal RNAs, have answered this question in favor of the endosymbiotic origin of eukaryotic cells. After briefly discussing some of the concepts that helped resolve this controversy and the problems involved in using sequence data for evolutionary studies, we describe a few examples of useful evolutionary trees.

Amino Acid Sequence↗
PubMed1993

Optimization by hierarchical mutant production.

Inspired by the successful description of the first steps of molecular evolution by the quasispecies theory and the successful application of quasispecies-like algorithms to optimization problems, we propose a hierarchically organized algorithm. This new algorithm is able to solve a spin glass and a travelling salesman problem using only point mutations. Furthermore, it performs better under comparable circumstances than the ordinary quasispecies algorithm. Depending on the structure of the fitness landscape of the examined problem under consideration the hierarchically organized algorithm proves to be much more suitable than a simple quasispecies algorithm, especially in clustered landscapes. Tuning the error rates reveals the critical minimum copy fidelity necessary to guarantee optimization. We propose to incorporate hierarchical concepts into optimization algorithms inspired by biological evolution, such a genetic algorithms.

Algorithms↗
PubMed1992

[The general functional characteristics of endogenous regulatory oligopeptides].

A number of physicochemical factors of the endogenous regulatory oligopeptides are considered to be the basis of their general functional properties as indicated by the phenomena of cascade regulation, morphogenesis, behaviour and biological evolution. Functional characteristics and chemical features of classical transmitters and, probably, other endogenous substances allow to consider them as the integrity of endogenous molecular regulators.

Animals↗