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At least 235 records · Page 13Linked to original sources
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↗
PubMedDate not supplied

A theoretical framework for defining some concepts in evolution.

We present a theoretical framework for biological evolution with the intention of giving precise mathematical definitions of some concepts in evolutionary biology such as fitness, evolutionary pressure, specialization and natural selection. In this framework, such concepts are identified with well-known mathematical terms within the theory of dynamical systems. We also discuss some more general implications in evolution; for instance, the fact that our model naturally exhibits a frequency spectrum of the type 1/f for low frequencies of evolutionary events.

Algorithms↗
PubMed1976

Solution of a gene divergence problem under arbitrary stable nucleotide transition probabilities.

A nucleic acid chain L nucleotides in length, with the specific base sequence B1B2....BL, each Bi being A, G, C, or T, is defined by the L-dimensional vector B = (B1, B2, ..., BL), the kth position in the chain being occupied by the base Bk. Let pBB, be the twelve given constant nonnegative transition probabilities that in a specified position the base B is replaced by the base B' in a single step, and let P(X)BB, be the probability that the position goes from base B to B' in X steps. An exact analytical expression for P(X)BB' is derived. Assuming that each base mutates independently of the others, an exact expression is derived for the probability P(X)BB' that the initial gene sequence B goes to a sequence B' = (B'1, B'2; ..., B'L) after X = (X1, X2, ..., XL) base replacements, where Xk is the number of single step base replacements in the kth position. The resulting equations allow a more precise accounting for the effects of Darwinian natural selection in molecular evolution than does the idealized but biologically less accurate assumption that each of the four nucleotides is equally likely to mutate to and be fixed as one of the other three. Illustrative applications of the theory to some problems in biological evolution are given.

Base Sequence↗
PubMed2002

Microsporidia: biology and evolution of highly reduced intracellular parasites.

Microsporidia are a large group of microbial eukaryotes composed exclusively of obligate intracellular parasites of other eukaryotes. Almost 150 years of microsporidian research has led to a basic understanding of many aspects of microsporidian biology, especially their unique and highly specialized mode of infection, where the parasite enters its host through a projectile tube that is expelled at high velocity. Molecular biology and genomic studies on microsporidia have also drawn attention to many other unusual features, including a unique core carbon metabolism and genomes in the size range of bacteria. These seemingly simple parasites were once thought to be the most primitive eukaryotes; however, we now know from molecular phylogeny that they are highly specialized fungi. The fungal nature of microsporidia indicates that microsporidia have undergone severe selective reduction permeating every level of their biology: From cell structures to metabolism, and from genomics to gene structure, microsporidia are reduced.

Animals↗
PubMed1996

Molecular biology and evolution of resistance of toxicants.

To the prevailing biochemical/physiological classification of mechanisms of organismal resistance to toxicants, an additional molecular dimension is proposed. Predictions are developed regarding the relative prevalence of different classes of mutations and are found to compare favorably with reports from the literature. In particular, point mutations in target loci were the dominant form of resistance for both lab and field selection. Amplifications of target loci were less common than structural mutations, and more common for lab-selected than for field-selected strains. Amplification was the most common mechanism of up-regulation of metabolizing enzymes. In comparison, only one mutation involving cis-regulation and several involving trans-acting regulation were found. Mutations involving gene disruption and down-regulation were uncommon, but were found in appropriate cases, i.e., when toxicants stimulated rather than inhibited target function and when metabolizing enzymes converted toxicants into more toxic metabolites. Additional phenomena of likely but uncertain importance are genetic "succession," recombinational limitation, and negative cross-resistance. More work on these phenomena and on quantification of fitness costs of resistance is recommended.

Animal Population Groups↗
PubMed1980

A conformational rationale for the origin of the mechanism of nucleicacid-directed protein synthesis of 'living' organisms.

The physical basis for the natural evolution of a primitive decoding system is presented using the concepts of molecular interactions. Oligoribonucleotides of five residues having U at the 5'-end, a purine at the 3'-end and any combination of three bases in the middle is taken as a primitive tRNA (PIT). From conformational considerations PIT is expected to have U-turn conformation wherein, N3-H3 of base U hydrogen-bonds with phosphate, three residues ahead leaving triplet bases called primitive anticodons (PAC) into a helical conformation, and this creates a cleft between U and PAC. An amino acid can be comfortably nestled into the cleft with the amide hydrogens and carboxyl oxygen hydrogen-bonded to the last purine and the first uridine, while the side-chain can interact with the cleft side of PAC. The other side of PAC is free to base-pair with triplet codons on a longer RNA. Also two PACs can 'recognize' consecutive triplet codons, and this leads to a dynamic interaction in which the amino and carboxyl ends are brought into proximity, making the formation of peptide bond feasible. The cleft formed by different anticodon triplets, broadly speaking, shows preferences for the corresponding amino acids of the presently known codon assignment. Thus the nucleicacid-directed protein synthesis, which is a unique feature of all 'living' organisms is shown to be a natural consequence of a particular way of favourable interaction between nucleic acids and amino acids, and our model provides the missing link between the chemical evolution of small organic molecules and biological evolution through the process of mutations in nucleicacids and nucleicacid-directed protein synthesis.

Animals↗
PubMed1993

[Development of telencephalon in Agapornis roseicollis Vieillot (Psittacidae) and its relationship to the evolution of the telencephalon in vertebrates].

1. The cerebral anlage of Agapornis roseicollis was investigated in serially cut slices during the developmental stages before hatching (day 3-day 20) by light microscopical quantitative and qualitative methods. 2. During earlier stages of development, the brain anlage is divided in three dorsally and four ventrally situated, longitudinally oriented matrix zones (D1-D3, V1-V4 according to Kuhlenbeck). In this developing system, mainly the lateral part of the telencephalic wall including its dorsal extension is considered to establish special importance for the further ontogenetic development. 3. The quite simple structure of the epistriatum in Reptils occurs as the neo-hyperstriatum-complex in Birds; likewise, deriving from the neocortex primitivus in Reptils, in Mammalia this part obviously develops to the more and more expanding neocortex as can be followed from lower mammalia species up to the highly developed Primates. According to the first main criterion of Remane, the homology of these parts of the brain in different vertebrates is most evident because these brain parts occupy exactly the same position in the brain anlage of early embryonal stages. 4. In Reptils, the neocortex primitivus appears as the last during ontogenetic development. Likewise in Birds, the neohyperstriatum-complex that is homologeous to the neocortex in Mammalia, differentiates during the final stages. These facts again emphasize the homology of these structures. 5. Further evidence for homology is obtained by the observation that in Agapornides the primordium of the neo-hyperstriatumcomplex contains migrating matrix cells columns, which also in Mammalia arrange into the same manner. Moreover, the transient and heterochronuous occurrence of cell layers at the outer surface of the brain anlage reminds to the development of palaeocortex and neocortex in Reptils and Mammalia. 6. From the point of view of evolution biology, the process of the progressive evolution is considered to be based on the step by step addition of tiny new structure-function-units to the already present morphology going along with a full structural and functional integration of the added, thus to achive the new quality. This so-called "Additive Morphogenesis" was effective during millions of years, consisting of such microevolutionary processes, and finally caused the "Gestaltungswandel", the ever changing evolving variety of bodily forms (and functions) that is recapitulated during individual species ontogenesis.

Animals↗
PubMed2005

Gene products with evolutionary functions.

It is often tacitly assumed that all gene products serve the needs of life functions of the individual carrying the genome. However, a close look at the formation of genetic variations, which are the drivers of biological evolution, reveals a different view. While a majority of the products of genes, such as housekeeping genes and genes essential for each individual, when exposed to particular life conditions respond to the definition given above, other gene products clearly carry out evolutionary functions at the level of populations. Products of these evolution genes act as generators of genetic variations and/or as modulators of the frequency of genetic variation. This is most readily seen with bacterial populations. Many different mechanisms contribute to the occasional, overall formation of genetic variations. These mechanisms can be grouped into three mechanistically and qualitatively different strategies of generating genetic variations. In addition to the activities of evolution genes, specific properties of matter such as tautomery also contribute to the formation of genetic variations. The views that nature cares actively for biological evolution are documented by evidence taken mainly from microbial genetics. Essential elements of the theory of molecular evolution are discussed, as well as the relevance of this theory for higher organisms and its impact on our worldview.

Animals↗
PubMed1995

Evolution and biological significance of human retroelements.

Retroelements comprise a substantial portion of the human genome. Their large number and ubiquitous distribution has led scientists to speculate about their evolutionary origin and their biological functions. Human endogenous retroviruses and their retrotransposon relatives represent a reservoir of possibly pathogenic retroviral genes that may be activated spontaneously or by environmental conditions. They can act as insertion mutagens and activate or inactivate cellular genes, or may be involved in chromosome aberrations by recombination of related elements on different chromosomal locations. Retroviral gene products themselves may also be pathogenic and, for example, could be implicated in the development of tumors and autoimmune diseases. On the other hand, endogenous retroviral elements and nonviral retroposons are thought to have played an important role in shaping the genomes of vertebrates by intracellular transposition events and by generating hot spots of recombination. In the course of time, some of these elements have acquired cellular functions, such as, for instance, in the regulation of gene expression. Therefore, the role of human endogenous retroviruses and retroposons in biological processes is currently a subject of great interest.

Animals↗
PubMed1999

The future of the fossil record.

The fossil record provides a powerful basis for analyzing the controlling factors and impact of biological evolution over a wide range of temporal and spatial scales and in the context of an evolving Earth. An increasingly interdisciplinary paleontology has begun to formulate the next generation of questions, drawing on a wealth of new data, and on methodological advances ranging from high-resolution geochronology to simulation of morphological evolution. Key issues related to evolutionary biology include the biotic and physical factors that govern biodiversity dynamics, the developmental and ecological basis for the nonrandom introduction of evolutionary innovations in time and space, rules of biotic response to environmental perturbations, and the dynamic feedbacks between life and the Earth's surface processes. The sensitivity of evolutionary processes to rates, magnitudes, and spatial scales of change in the physical and biotic environment will be important in all these areas.

Animals↗
PubMed1986

Photoenergetics of octopus rhodopsin. Convergent evolution of biological photon counters?

The enthalpy changes associated with each of the major steps in the photoconversion of octopus rhodopsin have been measured by direct photocalorimetry. Formation of the primary photoproduct (bathorhodopsin) involves energy uptake of about 130 kJ/mol, corresponding to storage of over 50% of the exciting photon energy, and is comparable to the energy storage previously observed in bovine rhodopsin. Subsequent intermediates involve the step-wise dissipation of this energy to give the physiological end-product (acid metarhodopsin) at a level only slightly above the parent rhodopsin. No significant differences in energetics are observed between rhodopsin in microvilli membrane suspensions or detergent dispersions. Use of different buffer systems in the calorimetric experiments shows that conversion of rhodopsin to acid metarhodopsin involves no light-induced protonation change, whereas alkali metarhodopsin photoproduction occurs with the release of one proton per molecule and an additional enthalpy increase of about 50 kJ/mol. Van't Hoff analysis of the effect of temperature on the reversible metarhodopsin equilibrium gives an enthalpy for the acid----alkali transition consistent with this calorimetric result, and the proton release is confirmed by direct observation of light-induced pH changes. Acid-base titration of metarhodopsin yields an apparent pK of 9.5 for this transition, though the pH profile deviates slightly from ideal titration behaviour. We suggest that a high energy primary photoproduct is an obligatory feature of efficient biological photo-detectors, as opposed to photon energy transducers, and that the similarity at this stage between cephalopod and vertebrate rhodopsins represents either convergent evolution at the molecular level or strong conservation of a crucial functional characteristic.

Animals↗
PubMed2000

Evolution of biological information.

How do genetic systems gain information by evolutionary processes? Answering this question precisely requires a robust, quantitative measure of information. Fortunately, 50 years ago Claude Shannon defined information as a decrease in the uncertainty of a receiver. For molecular systems, uncertainty is closely related to entropy and hence has clear connections to the Second Law of Thermodynamics. These aspects of information theory have allowed the development of a straightforward and practical method of measuring information in genetic control systems. Here this method is used to observe information gain in the binding sites for an artificial 'protein' in a computer simulation of evolution. The simulation begins with zero information and, as in naturally occurring genetic systems, the information measured in the fully evolved binding sites is close to that needed to locate the sites in the genome. The transition is rapid, demonstrating that information gain can occur by punctuated equilibrium.

Base Sequence↗