Theoretical Biology Forum

Although most discussions on the origin and evolution of insect wings and metamorphosis have assumed that the ancestors of winged insects were terrestrial, it now seems possible that they were actually aquatic. Changing the basic assumptions affects our interpretations of the origin of metamorphosis and our understanding of insect diversity. It is argued that the ancestors of winged insects were similar to primitive mayflies, developing from aquatic larvae into terrestrial adults, and that metamorphosis originated as an inevitable consequence of an amphibiotic life cycle...

In 2007, David S. Wilson and Edward O. Wilson (27) pointed out that, Richard Dawkins had admitted that, contrary to what he had claimed in his book The Selfish Gene (1976) (7), the idea that only the gene is a fundamental unit of selection cannot be used as an argument against the notion of group selection. This elicited a sharp denial from Dawkins (30), which was followed by an explanatory reply by Wilson and Wilson (33) and another vehement denial by Dawkins (34). I analyse the prehistory of this surprisingly complex and convoluted dispute and subsequently disentangle it...

Since the ENCODE project published its final results in a series of articles in 2012, there is no consensus on what its implications are. ENCODE's central and most controversial claim was that there is essentially no junk DNA: most sections of the human genome believed to be «junk» are functional. This claim was met with many reservations. If researchers disagree about whether there is junk DNA, they have first to agree on a concept of function and how function, given a particular definition, can be discovered...

No abstract text is available yet for this article.

Based on the Recognition Concept of species, the specific-mate contact model posits that mating systems develop as combinations of two fundamental courtship strategies that we interpret here in terms of behavioural heterochrony: territorial mate-attraction evolved as an effect of peramorphosis whereas group-living mate-seeking evolved as an effect of paedomorphosis. We tested this hypothesis on primates in a phylogenetic and paleo-climatic context. Our results suggest that primate promiscuity (both males and females are mate-seekers) evolved with group-living from ancestral pair-living monogamy (both males and females are mate-attractors) in the Palaeogene, as the result of a slowdown in growth (neoteny) caused by increased environmental predictability...

No abstract text is available yet for this article.

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...

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...

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...

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...

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...

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...

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)...

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...

No abstract text is available yet for this article.

For nearly a century the main focus in biological disciplines such as molecular biology, biochemistry, genetics and evolutionary theory was cellular life as a machine like process in which mechanistic pathways regulate metabolism, genetic reading and translation into proteins and evolution by variations (random error replications) and selection. Modern biochemistry started with the cellular theory of life. Also the modern synthesis focused on cells at the starting event of life. The dominance of this paradigm lasted until ten years ago...

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...

The Third Way of Evolution was founded in 2014 to make the public aware that contemporary evolution science is not limited to the neo-Darwinian Modern Synthesis of the past century. This was important to do because evolution was challenged as incapable of explaining biological complexity by the Intelligent Design movement. Expounding biological theories like the Modern Synthesis is always subject to limited empirical evidence, fundamental concepts that inevitably change over time, and conceptual preferences that often prove to be misleading...

No abstract text is available yet for this article.

DNA methylation studies usually focus on the groups of CpG sites. Neighbouring CpG sites are analyzed together due to their group behaviour. However, this approach ignores the possible interaction between more distant CpG sites. In this work, we investigate the complete methylation correlation structure of chromosome 21. Two data sets were used for the correlation analysis, smaller data set with methylation measurements from Down syndrome patients and their family members and larger data set with healthy subjects...