The frame of non-canonical theory of heredity: from genes to epigenes

Particular theory of heredity that exceeds the limits of mendelian genetics is suggested. The model based on five sufficiently obvious assumptions (accepted as axioms) As consequence of these axioms the strict statements concerningfunctional heredity memory were formulated in mathematical terms. Molecular-genetic realization of the memory cells appears as new class of heredity units--epigenes. In the epigenes part f hereditary information is contained, encoded and transmitted beyond the primary structure of DNA molecules of genome. Epigenes capable to conserve sequences of genes functional states in the course of ontogenesis and provide transmission of information contained in this states throw consequent generations. It was shown that epigenes differ from genes at least by encoding method of heredity information. There are three functional-equivalent classes of really existing epigenes mechanisms: dynamic, modificational and transpositional; and there is one hypothetical class--invertional. It was shown that a lot of experimental data concerning epigenetic mechanism of heredity is in accord with theoretical conclusions concerning epigenes existence. Moreover, we constructed an artificial epigenes by genetic engineering methods. The existence of epigenes means that obtaining complete genome sequence, its physical and genetic maps, as well as distinguishing the rules of genes function encoding by its primary structure do not provide complete decoding of hereditary information. The role of epigenes in ontogenesis and phylogenesis was examined. It was shown that even elementary epigenetic systems could determine key ontogenesis events. Epigenetic system could serve as the basis of non-darwinian evolutionary strategies by means of "memorization of rather unsuccessfully steps of evolution" and conservation of alternative variants of ontogenesis. Teleonomic hypothesis on functional heredity memory was formulated. This theory provides explanation of phenomena of acquired features inheritance and molecular mechanisms of stress-induced evolution.     

Molecular genetics and epigenetics in the morphogenesis mechanisms

The progress of molecular genetics principally changed the views on heredity and, in the long run, wrecked the synthetic theory of evolution, designed for the microevolutionary processes in populations only. Molecular genetics as a whole is sufficient for analyzing evolutionary processes in viruses and prokaryotes. But in multicellular organisms, with the advent of more complicated morphogenesis, epigenetic processes took effect. Appealing exclusively to the integrity of the organism in ontogeny is insufficient for the understanding of these processes; further studies of the molecular basis for this integrity are required. The discovery of homeobox genes was an important step on this path. The theory of evolution should include not only the molecular processes but also the laws of ecosystem and biosphere processes, which study requires handling many problems of ecology, parasitology, palaeontology, and geology. All these fields together comprise an enormous area of knowledge for which the development of a unified theory is scarcely possible.     

A possible role of genetic translation ambiguity in evolution

A hypothesis has been suggested that the variability of translation machinery is one of the key factors of evolutionary transformations of genetic material. It considers a module principle of the evolution theory based on the concepts of duplication and divergence of genetic material, which is required for origination of new genes and proteins with new functions. The duplication results in the appearance of pseudogenes, functionally inactive, but serving a material for creating new functions. The possible mechanisms changing the translation machinery have been considered, which may lead to the sporadic pseudogene activation "supplying" natural selection with mutational changes accumulated by pseudogenes to assess their adaptive value. This takes into account not only potential possibilities of mutational variability of the translation machinery, but also the possibility of protein prioritization: a prion mechanism of inheritance is also considered which is intensively studied nowadays.     

An optimizing principle of natural selection in evolutionary population genetics

This paper brings together two themes in evolutionary population genetics theory. The first concerns Fisher's Fundamental Theorem of Natural Selection: a recent interpretation of this theorem claims that it is an exact result, relating to the so-called "partial" increase in mean fitness. The second theme concerns the desire to find an optimality principle in genetic evolution. Such a principle is found here: of all gene frequency changes which lead to the same partial increase in mean fitness as the natural selection gene frequency changes, the natural selection values minimize a generalized distance measure between parent and daughter generation gene frequency values.     

Problem of organism integrity and its perspectives

The organism integrity in onto-and phylogenesis is considered as an initial element of biosphere integrity and its evolution at the eukaryotic level. The Schmalhausen’s concept of organism integrity is discussed in the context of his original strategy of evolutionary synthesis and his works on stabilizing selection. The perspectives of investigations on the problem of integrity and development of the principle of dynamic stability in contemporary evolutionary biology as integrating factors are discussed.     

The genome‐centric concept: resynthesis of evolutionary theory

Modern biology has been heavily influenced by the gene‐centric concept. Paradoxically, this very concept – on which bioresearch is based – is challenged by the success of gene‐based research in terms of explaining evolutionary theory. To overcome this major roadblock, it is essential to establish new theories, to not only solve the key puzzles presented by the gene‐centric concept, but also to provide a conceptual framework that allows the field to grow. This paper discusses a number of paradoxes and illustrates how they can be addressed by the genome‐centric concept in order to further resynthesize evolutionary theory. In particular, methodological breakthroughs that analyze genome evolution are discussed. The multiple interactions among different levels of a complex system provide the key to understanding the relationship between self‐organization and natural selection. Darwinian natural selection applies to the biological level due to its unique genetic and heterogeneous features, but does not simply or directly apply to either the lower non‐living level or higher intellectual society level. At the complex bio‐system level, the genome context (the entire package of genes and their genomic physical relationship or genomic topology), not the individual genes, defines the system and serves as the principle selection platform for evolution.     

Co-evolution of partners and the integrity of symbiotic systems

Symbioses are very suitable models for studying the integrity of biosystems which characterizes their structural/functional organization enabling the partners to respond adequately to the environmental changes. Analysis of different forms of plant-microbe and animal-microbe symbiosis suggests that a qualitative increase of its integrity occurs under the facultative and ecologically obligatory interactions and is culminated under the genetically obligatory interactions. By use of mathematical models, we demonstrate that the functional integrity of N2-fixing legume-rhizobia symbiosis (concordance of changes in partners' genotypic frequencies induced by environmental fluctuations) correlates to its ecological efficiency which increases under force of natural selection. It results in the tight partners' regulatory feedbacks leading to their genetic integration manifested in the establishment of "symbiogenome". The genetic integrity of symbiosis determines its high evolutionary potential based on: a) epigenetic inheritance of symbiotic traits by hosts which may occur in the form of vertical transmission of either microsymbionts themselves or genes obtained from them; b) interspecies altruism interactions related to the positive partners' feedbacks which determine the ecological efficiency of mutualistic interactions. Realization of this potential results in the deep genetic integration of initially independent partners including their fusions into the novel integral organisms.     

Classification of organisms and structuralism in biology

Structuralism in biology is the oldest trend oriented to the search for natural "laws of forms" comparable with laws of growth of crystal, was revived at the end of 20th century on the basis of structuralist thought in socio-humanitarian sciences. The development of principal ideas of the linguistic structuralism in some aspects is similar to that of biological systematics, especially concerning the relationships between "system" and "evolution". However, apart from this general similarity, biological structuralism is strongly focused on familiar problems of the origin of diversity in nature. In their striving for the renovation of existing views, biological structuralists oppose the neo-darwinism emphasizing the existence of "law of forms", that are independent on heredity and genetic "determinism". The trend to develop so-called "rational taxonomy" is also characteristic of biological structuralism but this attempt failed being connected neither with Darwin's historicism nor with Plato's typology.     

The sociobiological perspectives in the study of human evolution

The idea of a new multilevel approach to an understanding of regularities of evolution and its consequences for the study of human evolution is analysed. Three levels of evolutionary process are defined: (1) genetic level-the basic one. Memory of this level is coded, fixed, collected and translated by means of chemical structures (mainly of nucleic acids). The super-organismic system is the population. Classic natural selection functioned on this level. (2) The epigenetic level had originated with the origin of multicellular organisms and is relatively self-dependent. Regularities of this level allow the organisms to vary their phenotypes within the limits of reaction norms corresponding to the actual environment. The superorganismic system is the “family group”. Sexual selection functioned on this level and influenced the genetic one indirectly. (3) The behavioural level had originated on the high stage of evolution with the origin of species that are able to adapt themselves by behaviour. Their own means of coding, fixation, collection and translation of information have originated from symbolic signals (sounds, smells, postures, gestures, etc.) used for communication (signal or social heredity). The super-organismic system is society. Group selection functioned on this level. Sociobiology as a science is defined as “the systematic study of the biological basis of all forms of social behaviour, including sexual and parental behaviour; in all kinds of organisms including man” (Wilson, 1978, p. 10), and has become the necessary tool for the study of human evolution beginning from its origin. To kill an error is as good a service as, and sometimes even better than, the establishment of a new truth or fact.Charles Darwin     

基于生物适应进化原理论证生物进化的动力

文章从现有主流生物进化理论存在的问题入手, 以生物适应进化原理为认识基础, 讨论生物进化的动力, 以求对生物进化机制有一个新的认识。在薛定谔“生命赖负熵生存”观点的指导下, 提出了“负熵流”包括能量流、物质流和信息流, 以及负熵流是生命生存和发育的动力的观点。作者在原有生物适应进化原理基础上, 修改完善并提出了“DNA、RNA和蛋白质在环境作用下的生物适应进化调控系统”理论, 并根据系统发育是个体发育的“积分”的观点, 推论得出生物与环境的负熵差引起的负熵流也是生命进化的动力, 对生物进化机制作出了新的理解。基于这样的生物进化机制的认识, 提出了“进化是一个子系统在其上一等级系统中, 将自身全部或部分信息遗传给下一代子系统, 并在其适应上一等级系统过程中, 产生一些新质, 终止一些旧质, 从而在其上一等级系统中得以延续的变化过程”的概念, 并探讨了一些与进化有关的其他争议问题。     

Rethinking the theoretical foundation of sociobiology

Current sociobiology is in theoretical disarray, with a diversity of frameworks that are poorly related to each other Part of the problem is a reluctance to revisit the pivotal events that took place during the 1960s, including the rejection of group selection and the development of alternative theoretical frameworks to explain the evolution of cooperative and altruistic behaviors. In this article, we take a "back to basics" approach, explaining what group selection is, why its rejection was regarded as so important, and how it has been revived based on a more careful formulation and subsequent research. Multilevel selection theory (including group selection) provides an elegant theoretical foundation for sociobiology in the future, once its turbulent past is appropriately understood.     

A Possible Role of Translation Ambiguity in Gene Evolution (A Hypothesis)

A hypothesis is put forward that the variability of translation machinery is one of the key factors of evolutionary transformations of genetic material. It considers the module principle of the evolution theory based on the concepts of duplication and divergence of genetic material, which is required for origination of new genes and proteins with new functions. The duplication results in the appearance of pseudogenes, functionally inactive, but serving a material for creating new functions. The possible mechanisms changing the translation machinery have been considered, which may lead to sporadic pseudogene activation supplying natural selection with mutational changes accumulated by pseudogenes to assess their adaptive value. This takes into account not only potential possibilities of mutational variability of the translation machinery, but also the possibility of protein prionization: also considered is a prion mechanism of inheritance, which is intensely studied nowadays.     

In the Beginning was a Mutualism - On the Origin of Translation

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.     

A systems-analytical approach to macro-evolutionary phenomena.

Two sets of evolutionary phenomena find no explanation through current theory. For the static phenomena (such as homology, homonomy, systematic weight, and "Type") there is no causal base, although these principles are responsible for all phenomena of predictable order in the living world. The dynamic phenomena (such as homodynamy, coadaptation, parallel evolution, orthogenesis, Cartesian transformation, typostrophy, hetermorphosis, systemic mutation, and spontaneous atavism) have no causal explanation, although they are responsible for all directed phenomena in macroevolution. These phenomena share one unifying principle which can be explained by a system theory of evolution based on, but extending, the current synthetic theory. This system theory envisages feedback conditions between genotype and phenotype by which the chances of successful adaptation increase if the genetic units, by insertion of superimposed genes, copy the functional dependencies of those phene structures for which they code. This positive feedback of the adaptive speed (or probability) within a single adaptive direction is compensated by negative feedback in most of the alternative directions. The negative feedback operates as selection not be environmental but by systemic conditions developed by the organization of the organism. The consequences are an imitatively organized system of gene interractions, the rehabilitation of classical systematics, the reality of the "natural system," and, in general, the resolution of the contradiction between neodarwinists and their critics, between reductionists and holists, between "a priori" and "a posteriori" views, between idealism and materialism, and between the notions of freedom and of purpose in evolution.     

Is Life Law-Like?

Genes are generally assumed to be primary biological causes of biological phenotypes and their evolution. In just over a century, a research agenda that has built on Mendel's experiments and on Darwin's theory of natural selection as a law of nature has had unprecedented scientific success in isolating and characterizing many aspects of genetic causation. We revel in these successes, and yet the story is not quite so simple. The complex cooperative nature of genetic architecture and its evolution include teasingly tractable components, but much remains elusive. The proliferation of data generated in our "omics" age raises the question of whether we even have (or need) a unified theory or "law" of life, or even clear standards of inference by which to answer the question. If not, this not only has implications for the widely promulgated belief that we will soon be able to predict phenotypes like disease risk from genes, but also speaks to the limitations in the underlying science itself. Much of life seems to be characterized by ad hoc, ephemeral, contextual probabilism without proper underlying distributions. To the extent that this is true, causal effects are not asymptotically predictable, and new ways of understanding life may be required.     

Meiosis in perspective.

Our understanding of meiosis springs from two suggestions made by Weismann in 1887. One was that meiosis would be found to compensate for fertilization in the life cycles of both sexes and all organisms. The other was that the development of sexual reproduction in evolution depended on the value of meiosis in exposing the results of genetic recombination to natural selection. In confirming these propositions we were bound to discover that the properties of meiosis appear both as the causes and the consequences of evolution: it is the hinge on which turns the evolution of breeding method, reproductive habit, life cycle and hereditary structure, that is the genetic system, in all sexually reproducing species of organism. We have had three main fields of attack on our problem. First, there was the natural variation of meiosis including that of two-track hereditary within the species: here, animals took the lead. Secondly, there was the experimental field - both with genetic controls such as polyploidy and the sterilizing mutations of mitosis as well as meiosis, and with physical and chemical controls: here, the higher plants and micro-organisms have given us our great opportunities. Thirdly, we have the widening field where physicochemical knowledge and genetic control converge and collaborate. In all this work we have to be aware that meiosis works with chromosomes which always have the two functions of accomplishing evolution and of implementing its results in heredity. In consequence, the adaptation of meiosis is perpetually imperfect.     

Weak selection and protein evolution

The "nearly neutral" theory of molecular evolution proposes that many features of genomes arise from the interaction of three weak evolutionary forces: mutation, genetic drift, and natural selection acting at its limit of efficacy. Such forces generally have little impact on allele frequencies within populations from generation to generation but can have substantial effects on long-term evolution. The evolutionary dynamics of weakly selected mutations are highly sensitive to population size, and near neutrality was initially proposed as an adjustment to the neutral theory to account for general patterns in available protein and DNA variation data. Here, we review the motivation for the nearly neutral theory, discuss the structure of the model and its predictions, and evaluate current empirical support for interactions among weak evolutionary forces in protein evolution. Near neutrality may be a prevalent mode of evolution across a range of functional categories of mutations and taxa. However, multiple evolutionary mechanisms (including adaptive evolution, linked selection, changes in fitness-effect distributions, and weak selection) can often explain the same patterns of genome variation. Strong parameter sensitivity remains a limitation of the nearly neutral model, and we discuss concave fitness functions as a plausible underlying basis for weak selection.     

SOCIAL SELECTION AND THE EVOLUTION OF ANIMAL SIGNALS

Social selection is presented here as a parallel theory to sexual selection and is defined as a selective force that occurs when individuals change their own social behaviors, responding to signals sent by conspecifics in a way to influence the other individuals' fitness. I analyze the joint evolution of a social signal and behavioral responsiveness to the signal by a quantitative-genetic model. The equilibria of average phenotypes maintained by a balance of social selection and natural selection and their stability are examined for two alternative assumptions on behavioral responsiveness, neutral and adaptive. When behavioral responsiveness is neutral on fitness, a rapid evolution by runaway selection occurs only with enough genetic covariance between the signal and responsiveness. The condition for rapid evolution also depends on natural selection and the number of interacting individuals. When signals convey some information on signalers (e.g., fighting ability), behavioral responsiveness is adaptive such that a receiver's fitness is also influenced by the signal. Here there is a single point of equilibrium. The equilibrium point and its stability do not depend on the genetic correlation. The condition needed for evolution is that the signal is beneficial for receivers, which results from reliability of the signal. Frequency-dependent selection on responsiveness has almost no influence on the equilibrium and the rate of evolution.