Theoretical Biology Forum最新文献

The idea of The Selfish Gene, first published in 1976, grew out of the Modern Synthesis of evolutionary biology formulated by Julian Huxley in 1942, and more specifically from George Williams' Adaptation and Natu - ral Selection in 1966. It presents a severely narrowed down version of Huxley's synthesis, which developed in the 1960s following the formulation of the Cen tral Dogma of molecular biology by Francis Crick. The idea rests on three assumptions: the isolation of the genome from any influences by the soma and its development in interaction with the environment (the Weis - mann Barrier), one-way causation from DNA to proteins (The Central Dogma), and the autoreplication of DNA (Schrödinger's aperiodic crystal). All three of these assumptions have now been shown to be incorrect. The 'replicator' (DNA) is not independent of the 'vehicle', the organism itself, so that The Selfish Gene can no longer be regarded as a valid scientific hypothesis.

The theory of organic evolution is incomplete until it can explain life's meaningmaking capacity and its role in the evolutionary processes, i.e. until semiosis is included. The extended synthesis theory of evolution has made a decisive step towards such an integrative theory, yet the explicit inclusion of semiotics of life is still to come. Here, we describe the steps made towards the semiotics-based theory of evolution, as the next stage after evo-devo and eco-evo-devo approaches. This includes demonstration of independent roles that natural selection, plastic adjustment, and interpretative choice have in adaptive evolution, and the distinction between adaptive and neutral modifications in genetic, plastic and interpretative mechanisms. Real meaning-making takes place only due to organism's interpretative processes. It should be complemented with a description of the ways by which knowledge (defined as products of semiotic learning), or rather the constraints of semiosis, can be inherited. This will complete the inclusion of semiosis into the extended mechanism of evolution.

The case has been made that the-gene-centric approach to biology, which has prevailed over the past ~100 years, should be replaced by a fundamental framework based on the cell being a far from equilibrium complex dissipative system, regulated and governed by its phenotype (1, 2), the metaphor for which is a brain. This independent attractor (IA) model is a radical departure from the conventional view based on Wilhelm Johannsen's genotype-conception which has prevailed since 1910. In this prevailing paradigm the gene and the genotype are fundamental in accounting for inheritance, evolution, development, and morphogenesis: the phenotype, upon which natural selection is deemed to act, plays little or no role in these crucial aspects of biology. Here I discuss how the process of evolution might be viewed under the IA model. Based on empirical evidence, evolution can be seen as a two-part process, one part based on thermodynamics and resulting in increased resilience to perturbation of the cellular phenotype (conditioning), and the other part, based on agency exhibited by the evolving organisms. A crucial open question is: should we view the realisation of the phenotype as a matter for biochemistry, or physics.

We may induce from a longue durée examination of Anglo-American History of Biology that the impulse to reject reduc - tionism persists and will continue to percolate cyclically. This impulse I deem "bioexceptionalism": an intuition, stance, attitude, or activating metaphor that the study of living beings requires explanations in addition to exclusively bottom-up causal explanations and the research programs constructed upon that bottom-up philosophical foundation by non-organismal biologists, biochemists, and biophysicists - the explanations, in other words, that Wadding - ton (1977) humorously termed the "Conventional Wisdom of the Dominant Group, or cowdung." Bioexceptionalism might indicate an ontological assertion, like vitalism. Yet most often in the last century, it has been defined by a variety of methodological or even sociological positions. On three occasions in the interval from the late nineteenth century to the present, a small but significant group of practicing biologists and allies in other research disciplines in the UK and US adopted a species of bioexceptionalism, rejecting the dominant explanatory philosophy of reductionistic mechanism. Yet they also rejected the vitalist alternative. We can refer to their subset of bioexceptionalism as a "Third-Way" approach, though participants at the time called it by a variety of names, including "organicism." Today's appeals to a Third-Way are but the latest eruption of this older dissensus and retain at least heuristic value apart from any explanatory success.

Multilevel interpretations of development and evolution take to heart the contextual nature of both those processes, and so necessarily assume top-down causation occurs, right down to the physics level. In this article we revisit the Principle of Biological Relativity proposed by Noble in 2012, where all emergent levels of organisation are equally causally valid. While this is true in general for physical interactions between levels, we argue that in the case of conscious organisms making rational choices, there is indeed a preferred causal origin - namely the overall embracing influence of meaning and values. This is the opposite of what is suggested by a reductionist viewpoint, where it is the bottom-most physical level that is stated to be causally preferred (by some physicists), or the genetic level (by some evolutionary theorists). Charles Darwin was therefore correct to distinguish between Artificial (conscious) Selection, where values enter, and Natural Selection. The Modern Synthesis was wrong to exclude Darwin's distinction.

It is logical to define "Life" prior to uncovering the mechanisms that allow changes, e.g. short (development) and long (evolution). In retrospect, however, the opposite happened. Darwin, Wallace, Lamarck, and other pioneers who lived when modern science was in its infancy, formulated their ideas on evolution asking "how new species come into existence", and not "How does 'Life' evolve?". It led to revolutionary concepts of Common Descent and Natural Selection. It took until the advent of communication sciences in the 20th century that the computer/ digital vocabulary was gradually embraced by many disciplines, as well as in daily language. Concurrently, substantial progress was also realized in the majority of the exact sciences and in the humanities. Therefore the question - asked in 2014 - whether the classical neo-Darwinism-based evolutionary theory needs a rethink was then justified and appropriate (too early for some, too late for others). This paper, summarizes the gradual development of my ideas why a switch in paradigm, from "The cell is the basic building block structure and function of all living compartments" to "a sender-receiver alternative" offers a novel and better perspective. Indeed, it introduces a new communicationbased potent concept and approach for analyzing various as yet undervalued aspects in the evolution of "Life". Of particular importance is the view that any act of communication is a problem-solving act because all messages are coded and need to be decoded before they can yield a response.

A major theoretical issue in evolutionary biology over the past two decades has concerned the rise of complexity over time in the natural world, and a search has been underway for "a Grand Unified Theory" - as biologist Daniel McShea characterized it - that is consistent with Darwin's great vision. As it happens, such a theory already exists. It was first proposed many years ago in The Synergism Hypothesis: A Theory of Progressive Evolution, and it involves an economic (or perhaps bioeconomic) theory of complexity. Simply stated, cooperative interactions of various kinds, however they may occur, can produce novel combined effects - synergies - with functional advantages that may, in turn, become direct causes of natural selection. In other words, the Synergism Hypothesis is a theory about the unique combined effects produced by the relationships between things. I refer to it as Holistic Darwinism; it is entirely con - sistent with natural selection theory, properly understood. Because the Synergism Hypothesis was first proposed during a time when the genecentric, neo-Darwinist paradigm was domi nant in evolutionary biology, it was largely overlooked. But times have changed. Biologist Richard Michod has concluded that "cooperation is now seen as the primary creative force behind ever greater levels of complexity and organization in all of biology." And Martin Nowak has called cooperation "the master architect of evolution." Here I will revisit this theory in the light of the many theoretical developments and research findings in recent years that are supportive of it, including the role of symbiogenesis in evolution, the phenomenon of hybridization, lateral gene transfer in prokaryotes, "developmental plasticity" (evo-devo), epigenetic inheritance, the role of behaviour (and teleonomy) in evolution, and gene-culture coevolution. The Synergism Hypothesis is especially relevant to the evolution of humankind.

An enduring problem concerning the evolution of RNA viruses stems from the fact that their long-term rates of evolution (substitutions/ site/year) are lower than those calculated by comparing sequences of isolates collected over short time periods or within a single host (shortterm or intra-host evolution). This inconsistency has been attributed to several reasons, including deviations from the assumption of a molecularclock (constancy of mutational inputs as a function of time) and variations in viral multiplication rates, among others. We previously proposed a non-phylogenetic method for extracting information contained in mRNAs, that cannot be identified from examination of primary sequences alone, and that we called «archaeological» information. In this new approach, mRNAs are of interest as molecules, not for their primary sequence or encoded proteins but for encrypted information established in a remote past. In the present article, we propose that an archaeological approach may also contribute to explain higher short-term than long-term evolution rates in RNA viruses, in this case, by using the archaeological concept of palimpsest. The palimpsest is a record of historical changes, but it is not a successively ordered or a complete record, rather it is the product of two opposing activities, one of writing and rewriting and the other of erasing. In RNA virus quasispecies, the gain or loss of mutations is reflected in changes in the submolar frequency of myriads of variants in the population. The fact that mutation elimination is not always complete, turns viral quasispecies into complex palimpsests of viral variants or sub-populations thereof. Here we relate two main different temporalities of the quasispecies palimpsest (short- and long-term) to the stability of mutations in response to changes related to three components of the virus: the virions, the infected cell and the host cell lineage. Host cell lineage-related viral memory would be mostly irre versible as they are adaptive products to host cell changes. In contrast, memories related to the environment of the virion or responsive to the environment of the infected cell, which is shortterm mutational input, is less constrained provided the alteration in the ancestral information carried by the RNA is only transient. The two intermixed memory components result in two differently contributing mutation rates whose influence in the final result depends on whether the timescales used to take the sequences for comparison are short or long term.

While the modern synthesis has at its core the claim that evolution can be entirely explained by the natural selection of random variations, neither "random" nor "variation" is adequately defined. Neo-Darwinists explicitly deny that they use random with the meaning of haphazard, but it is what they assume in their work; if they did not, they could not justify their total concentration on selection and neglect of variations. They conflate variations in the genotype with those in the phenotype. This might be justifiable if the connection between the two were simple and straightforward, but it is not. Like Darwin, neo-Darwinists are committed to the belief that evolution is always gradual. Also like Darwin, they justify this on theoretical rather than empirical grounds and despite acknowledging that the evidence does not support them. The paradox could be resolved by relaxing the commitment to gradualism, but only at the cost of significant consequences for the paradigm.