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2016, Biosemiotics
Any biological species of biparental organisms necessarily includes, and is fundamentally dependent on, sign processes between individuals. In this case, the natural category of the species is based on family resemblances (in the Wittgensteinian sense), which is why a species is not a natural kind. We describe the mechanism that generates the family resemblance. An individual recognition window and biparental reproduction almost suffice as conditions to produce species naturally. This is due to assortativity of mating which is not based on certain individual traits, but on the difference between individuals. The biosemiotic model described here explains what holds a species together. It also implies that boundaries of a species are fundamentally fuzzy, and that character displacement occurs in case of sympatry. Speciation is a special case of discretisation that is an inevitable result of any communication system in work. The biosemiotic mechanism provides the conditions and communicative restrictions for the origin and persistence of diversity in the realm of living (communicative and semiotic) systems.
Biological Journal of the Linnean Society
Adaptive evolution without natural selection2014 •
A mechanism of evolution that ensures adaptive changes without the obligatory role of natural selection is described. According to this mechanism, the first event is a plastic adaptive change (change of phenotype), followed by stochastic genetic change which makes the transformation irreversible. This mechanism is similar to the organic selection mechanism as proposed by Baldwin, Lloyd Morgan and Osborn in the 1890s and later developed by Waddington, but considerably updated according to contemporary knowledge to demonstrate its independence from natural selection. Conversely, in the neo-Darwinian mechanism, the first event is random genetic change, followed by a new phenotype and natural selection or differential reproduction of genotypes. Due to the role of semiosis in the decisive first step of the mechanism described here (the ontogenic adaptation, or rearrangement of gene expression patterns and profile), it could be called a semiotic mechanism of evolution.
Biosemiotics
Semiotic Fitting and the Nativeness of Community2020 •
The concept of 'semiotic fitting' is what we provide as a model for the description and analysis of the diversity dynamics and nativeness in semiotic systems. One of its sources is the concept of 'ecological fitting' which was introduced by Daniel Janzen as the mechanism for the explanation of diversity in tropical ecosystems and which has been shown to work widely over the communities of various types. As different from the neo-Darwinian concept of fitness that describes reproductive success, 'fitting' describes functional (sign) relations and aboutness. Diversity of a semiotic system is strongly dependent on the mutual fitting of agents of which the semiotic system consists. The focus on semiotic fitting means that, in the analysis of diversity, we pay particular attention to decision making (choice), functional plasticity, recognition windows, the depth of interpretation of the agents, and the categories responsible for the structure of the semiotic system. The concept of semiotic fitting has an early analogue in Jakob von Uexküll's concept of 'Einpassung' (as different from 'Anpassung', meaning 'evolutionary adaptation'). The close concepts of 'semiotic fitness', introduced by Jesper Hoffmeyer and by Stéphanie Walsh Matthews, 'semiotic selection', introduced by Timo Maran and Karel Kleisner, and 'semiotic niche', introduced by Hoffmeyer, provide different versions of the same model. If community is constructing itself on the basis of (relational) fitting, then nativeness of the community is a product of fitting, not vice versa. Nativeness is a feature that deepens in the course of community succession. The concept of 'semiotic fitting' demonstrates the possibility to analyse the role of both indigenous and alien species or other agents in a community on the basis of a single model.
In this paper I formulate briefly the main principles of evolution of semiotic systems. The neo-Darwinian theory of evolution does not take into account the semiosic nature of the systems under study, therefore its applicability to languages and cultures (and also to biological species as communicative semiosic systems) should be rigorously questioned. The semiotic theory of evolution should include the implications from the dynamic features of semiosis and sign systems. The two major tendencies in the evolution of semiosic systems are diversification — or introduction of new mutually incompatible systems and categories — and standardization — or development of mutual compatibility. The inclusion of agency as based on semiosis provides a non-Darwinian model, yet includes the Darwinian one as a restricted special case.
Since the beginning of early evolutionary studies, in fact since Darwin himself in his most famous work, “On the Origin of Species”, biologists have been trying to answer the question of how species arise and how they can achieve the necessary reproductive barriers that are required to allow mutation and selection to operate and differentiate a neo-species from the mother species. It is an accepted tenet of evolutionary biology that species evolve into new species which are direct descendants of the original species. The closer the relationship between species is, the higher the percentage of genetic homology is. Closely related species often show extremely high levels of genetic homology (at times as high as what is measured between local populations within the same species) while differing by balanced chromosomal rearrangements. The theory of chromosomal speciation has been often proposed as a mechanism for new species emergence and the subject of this thesis is a novel approach to analysis and theoretical modeling of how it operates, and how certain categories of mutations can reinforce its effects. Translocation and chromosomal rearrangements occur in all eukaryotes with measurable and relatively fixed probabilities. Chromosomal rearrangements are one-time single events that occur in one specific individual during gametogenesis and are a common type of mutation. They can affect the Darwinian fitness of the affected individual in a significant manner if the individual is mating with non-rearranged individuals as follows. In the case of translocated individuals, gametes show reduced fertility when crossed with nonrearranged individuals. This decrease in fertility is quantified as ½ for crosses between rearranged heterozygotes and Wild Type or rearranged homozygotes, and is due to unbalanced gametes resulting from incorrect segregation during meiosis. The decrease in fertility for crosses between rearranged heterozygotes is even higher (the resulting fertility of these crosses is 5/16, making the reduction in fertility 11/16) due to the possible combinations between gametes and the resulting imbalances. Within large interbreeding populations, due to the validity of the Hardy-Weinberg law, chromosomal rearrangements are lost from the gene pool in one or very few generations due to their negatively heterotic effect on the fitness of individuals carrying these mutations (negatively heterotic meaning it negatively affects the fitness of the heterozygote). Hardy-Weinberg equilibria are also the reason that, in large populations, evolution of new characteristics is very slow (becoming increasingly slower in proportion to the size of the population, reaching theoretical zero evolutionary speed for an infinitely large freely interbreeding population). Amongst all the possible chromosomal rearrangements, some are negatively heterotic while others are neutral or potentially positively heterotic (in a limited number of cases). This thesis focuses exclusively on the negatively heterotic rearrangements, since they are the only ones that can play a leading role in speciation, and will not go into details on the other rearrangements that are expected to be present in populations as polymorphisms that play no significant role in speciation. If we examine locally isolated populations, characterized by inbreeding and, potentially, founder effects, we observe how, through stochastic processes, fixation of negatively heterotic chromosomal rearrangements can occur. It is important to note how, in order for local fixation to occur, the size of the population must be very small (fixation relies on genetic drift and stochastic factors that become extremely improbable when the number of interbreeding members of the population increases). If a chromosomal rearrangement becomes fixed in a small population, this population will be characterized by having very similar genotypes which will be to some extent different from the average allelic frequencies within the founder population. This difference will be proportional to the variance in the original population. Amongst the negatively heterotic chromosomal rearrangements (nominally Tandem Fusions, Robertsonian Fusions, Reciprocal Translocations, X-autosome translocations, and, potentially, multiple inversions) we shall focus on Reciprocal Translocations, for which a theoretical model will be presented. Once a negatively heterotic chromosomal rearrangement has become fixed in a local population, if the new population has limited and sporadic interbreeding with the founder population, the members that breed with the founding population members will have a lower fitness than those who do not do so (this has been called the “reinforcement hypothesis”). As a result of this hypothesis, it has been proposed that, over a limited number of generations, strong mating barriers will evolve. A strong candidate for the reinforcement mechanism is represented by genes that control visible factors that differentiate the new population from the old, such as secondary sexual characters, which will be favorably selected if they distinguish the new population from the founding population and increase reproductive isolation. It is therefore proposed that the new population will rapidly evolve different secondary sexual characteristics as a result of this. By modification of the Hardy Weinberg equilibrium we can model the effects of hybridization and influx of Wild Type individuals into the new population. A modified version of the Hardy-Weinberg equilibrium is presented in this thesis which includes both the effect of the translocation and the effects of the translocation coupled with the emergence of reinforcement genes. Computer models based on these matings have been developed for this thesis and will be presented. The results of the simulations show how the founding population and the new population will either merge (in which case the new population will be absorbed into the founding population and the rearrangement will disappear within very few generations) or drift apart and become completely separate, non-interbreeding (or minimally interbreeding) populations. The model also shows how, when a population fixes a chromosomal translocation, it becomes very resistant to re-invasion by the WT karyotype, and shows the capability of resisting repeat influx of up to 4.0% of the entire population per generation by WT individuals without extinction. Higher percentages, however, rapidly result in the extinction of the NS karyotype (3/10 cases in up to 4.5% random influx per generation resulted in extinction before 10.000 generations and 10/10 when the random influx is raised to up to 5%). Once reinforcement genes appear, the model shows how they rapidly become established, albeit not fixated, in the population, and generate a much stronger barrier to introgression by WT individuals. The results of these simulations show how, once a rearranged population for a negatively heterotic chromosomal rearrangement has separated itself from the original population, such as described above, it only has two possible pathways available. The first is the pathway towards becoming a new species while the second is the one leading to extinction of the rearrangement and reabsorption into the original population. Given that translocations either disappear or give rise to new species, each translocation event that can be determined to exist between two related species must represent a single speciation event. As a side note, this mechanism points to how the evolutionary significance of Sexual reproduction lies in the fact that sexual populations are capable of speciation, while asexual ones are not. Sexual reproduction thus allows for adaptation through speciation and radiation. In a nutshell, speciation exists because of sexual reproduction and vice versa. Since sexually reproducing species can radiate by chromosomal speciation into different species, the existence of sexual reproduction provides a clear evolutionary advantage that offsets the associated costs. New species can adapt and respond quicker to evolutionary pressure due to the lower numbers that allow quicker fixation of beneficial mutations compared to large populations. They are, however, more prone to the risk of extinction (i.e. it’s an “all or nothing” game, where most newly formed chromosomal species will become rapidly extinct). Paradoxically, large interbreeding populations, which would be considered an evolutionary success, pay for this success by losing the capability to speciate. In large interbreeding populations, evolution only happens in response to large disruptions (epidemics, pandemics, food shortages leading to mass mortality, etc…) or over extremely long timeframes and numbers of generations. The proposed model can be further reinforced if the translocations occur in dominant males in small populations causing a higher chance of leading to speciation. The path to speciation begins with the appearance of a F1 generation of NS/WT hybrids followed, through inbreeding, by the appearance of homozygous NS/NS individuals in the F2 generation. Stochastic factors play a large role in this stage, with the general characteristic of the probability of speciation being very low in absolute terms. The study of statistics however teaches us that, in evolutionary terms, very low probability events happen all the time. Speciation events thus are an overall rare event which happens with variable frequencies based on the characteristics of the species of origin (habitat, mobility, reproductive mechanisms, etc…). Each of these characteristics can have major effect on the number of species that evolve within closely related taxa (thus providing an explanation for taxa where speciation appears to be a very common thing and taxa which appear unchanged and composed of a very limited number of species for millions or tens of millions of years).
The terms 'life', 'species' and 'individuals' are key concepts in biology. However, theoretical and practical concerns are directly associated with definitions of these terms and their use in researchers' work. Although the practical implications of employing definition of 'species' and 'individuals' are often clear, it is surprising how most biologists work in their field of study without adhering to a specific definition of life. In everyday scientific practice, biologists rarely define life. This is somewhat understandable: the majority of biologists accept the standard definition of life without exploring it, but this represents a bad attitude. In this essay, we update the concepts of life, species, and individuals in the light of the new techniques for massive DNA sequencing collectively known as high throughput DNA sequencing (HTS). A re-evaluation of the newest approaches and traditional concepts is required, because in many scientific publications, HTS users apply concepts ambiguously (in particular that of species). However, the absence of clarity is understandable. For most of the last 250 years, from Linnaeus to the most recent researches, identification and classification have been performed applying the same process. On the contrary, through HTS, biologists have become simply identifiers, who construct boundaries around the biological entities and do not examine the taxa at length, resulting in uncertainty in most readers and displeasure in traditional taxonomists. We organised our essay to answer a basic question: can we develop new means to observe living organisms? Keywords Life Á Species Á Individual Á Biological entities Á High throughput DNA sequencing Á Next generation sequencing Á HTS Á NGS
"This book presents programmatic texts on biosemiotics, written collectively by the theoreticians in the field (Deacon, Emmeche, Favareau, Hoffmeyer, Kull, Markoš, Pattee, Stjernfelt). In addition, the book includes chapters which focus closely on semiotic case studies (Bruni, Kotov, Maran, Neuman, Turovski). According to the central thesis of biosemiotics, sign processes characterise all living systems and the very nature of life, and their diverse phenomena can be best explained via the dynamics and typology of sign relations. The authors are therefore presenting a deeper view on biological evolution, intentionality of organisms, the role of communication in the living world and the nature of sign systems — all topics which are described in this volume. This has important consequences on the methodology and epistemology of biology and study of life phenomena in general, which the authors aim to help the reader better understand."
The theory of autopoiesis claims that adaptation should be understood as a precondition, and not as a constraint, guiding the evolution of social and living systems. This premise is at first sight incompatible with the perspective of the neo-Darwinian theory of evolution. In the case of speciation (phylogenesis) the varying adaptation to the environment is here, in fact, understood as a determinant factor arranging how organisms are selected. Nevertheless, the present study tests out a perspective on evolutionary biology, which is compatible with the implications of the theory of autopoiesis and can demonstrate a productive explanatory potential for evolutionary biology. In this way, it is possible to demonstrate an approach to solving the problems being intensively discussed in (neo-Darwinian) evolutionary biology. Namely, the problems of the units to be selected in evolution, or of rendering the meaning and function of the evolutionary development of sexuality comprehensible, or of relativizing the problem of altruism in evolution. Also, explanations for the so-called Cambrian Explosion and the fundamental difference between the evolution of prokaryotic and eukaryotic forms of life can be derived. And finally, the perspective so so developed permits us to determine the relation of biotic and social evolution in a differentiated manner.
Fundamental turns in biological understanding can be interpreted as replacements of deep models that organise the biological knowledge. Three deep models distinguished here are a holistic ladder model that sees all levels of nature being complete (from Aristotle to the 18th century), a modernist tree model that emphasises progress and evolution (from Enlightenment to the recent times), and a web model that evaluates diversity (since the 20th century). The turn from the tree model to the web model in biology includes (1) a transfer from modern to postmodern approaches, (2) a shift of semiotic threshold to the border of life, and (3) building the semiotic models of living systems, i.e., the rise of biosemiotics.
2005 •
Biological Journal of The Linnean Society
The tree, the network, and the species: THE TREE, THE NETWORK, AND THE SPECIES2006 •
Theoretical Population Biology
Allee Effects Can Both Conserve and Create Spatial Heterogeneity in Population Densities1999 •
Trends in Ecology & Evolution
Evolutionary divergence in acoustic signals: causes and consequences2013 •
Труды по знаковым системам Töid märgisüsteemide …
Bioinvasion, globalization, and the contingency of cultural and biological diversity: Some ecosemiotic observations2001 •
PLoS Genetics
Interspecific Sex in Grass Smuts and the Genetic Diversity of Their Pheromone-Receptor System2011 •
International review of cell and molecular biology
Genetic mechanisms of allopolyploid speciation through hybrid genome doubling: novel insights from wheat (Triticum and Aegilops) studies2014 •
Behavioural Processes
Behavioural divergence, interfertility and speciation: A review2012 •
Trends in Ecology & Evolution
Conflictual speciation: species formation via genomic conflict2013 •
2000 •
2011 •
Molecular Ecology
Sympatric speciation in a genus of marine reef fishes2010 •