New thoughts on the evolution of hormone-receptor systems

A possible pathway of the evolution of hormone-receptor systems has been discussed in light of the genomic potential hypothesis. Unlike the Darwinian system which is based on uninvestigatable chance events, the genomic potential hypothesis offers predictions based upon chemical determinism (boundary determinism). Accordingly, the production of highly specific protein-protein interactions between receptors and hormones, for example, are based upon the development of interacting components before the primordial chemistry was segregated by membranes. It is proposed that in addition to the primary structure (coding activity) a higher level of information exists in the genome which caused genomic products to function in a complementary fashion in living systems. The first steps in that direction have already been taken via experiments on sense and antisense peptides which may have specific relationships to each other. It is clear that I have not given an answer but I hope that I have touched upon certain aspects of a problem that can be illuminated better by a new and different approach to evolution. The hormone-receptor development was probably a powerful formative force in the development of macroorganisms, and its baffling complexity can only begin to find an explanation on the basis of structure/function relationships of the encoding material and its products.(ABSTRACT TRUNCATED AT 250 WORDS)     

Randomness and multilevel interactions in biology

The dynamic instability of living systems and the “superposition” of different forms of randomness are viewed, in this paper, as components of the contingently changing, or even increasing, organization of life through ontogenesis or evolution. To this purpose, we first survey how classical and quantum physics define randomness differently. We then discuss why this requires, in our view, an enriched understanding of the effects of their concurrent presence in biological systems’ dynamics. Biological randomness is then presented not only as an essential component of the heterogeneous determination and intrinsic unpredictability proper to life phenomena, due to the nesting of, and interaction between many levels of organization, but also as a key component of its structural stability. We will note as well that increasing organization, while increasing “order”, induces growing disorder, not only by energy dispersal effects, but also by increasing variability and differentiation. Finally, we discuss the cooperation between diverse components in biological networks; this cooperation implies the presence of constraints due to the particular nature of bio-entanglement and bio-resonance, two notions to be reviewed and defined in the paper.     

The randomness of life: A philosophical approach inspired by the Enlightenment

Did the Enlightenment anticipate modern reflections about the role of chance within cells or in living beings? No, especially if one pays attention to the very different scientific context of that periods and takes care to distrust the concept of "precursors". Nonetheless, several thinkers of the Enlightenment, scientists or philosophers, have constructed an opposition between the random and order that shares some links with modern concerns. More precisely, philosophers like Diderot and some physicians, chemists or naturalists, have articulated the necessity and contingency in opposition to the idea of an absolute natural order and to any preformed "germ" explaining the development of animals. But I will argue that this subtle concept also diverges from the idea of a universal determinism developed by Laplace. There is a way to deal with natural necessity and the universal interdependence of phenomena without excluding the random, going beyond the classical - though posterior to the eighteenth century - opposition between determinism and indeterminism. Particularly with Diderot, the Enlightenment presents an epistemology of the random loosely attached to the natural sciences, producing a philosophical reflection that can be linked with some modern issues of biology. I examine two examples: the criticism of the explanation of order by order, and the thesis that probability can tell us something about natural productions through the idea of randomized "expression," e.g., stochastic expression of genes for modern molecular biology and expressions of natural forms for Diderot.     

Necessity of chance: biological roulettes and biodiversity

Chance plays an important role in the dynamics of biodiversity. It is largely responsible for the spontaneous processes leading to biological diversification. The mechanisms behind chance belong to two categories: on the one hand, those outside of biological systems, and thus belonging to their environment, on the other hand, those endogenous to these systems. These last mechanisms are present at all levels of the hierarchical organization of the living world, from genes to ecosystems. We propose calling them 'biological roulettes'. Like roulettes in casinos, they could be deterministic processes functioning in chaotic domains and producing results that look as though they had been generated by random processes. The spontaneous appearance and natural selection of these roulettes have led to living systems potentially adapted to new environmental conditions not encountered before. They may even have permitted some of them to survive major upheavals. Moreover, palaeontological data show that the rate of biological diversification accelerates and that living systems become more and more complex over time. That may also increase their resilience. It can be also the consequence of the appearance and the selection of 'biological roulettes' and of chance they generate. They are at the same time products and engines of the evolution. Without them, life would have disappeared from the Earth a long time ago. Thus, they are of primary importance.     

Chance, Necessity, and Mode of Production: A Marxist Critique of Cultural Evolutionism

Cultural evolutionism and historical materialism are two fundamentally divergent theories of evolution. The nonrecognition by cultural evolutionists of Marx's distinction between "social formation" and "mode of production" has led them to interpret his thesis of the determination of superstructures by economic base as "techno-economic change begets new levels of general evolution." In fact, Marx's actual thesis was aimed at explaining the interrelationships between superstructures and economy within a previously established mode of production. As a consequence, Marx's analysis of how a new mode is "given" has been consistently ignored. Marx poses the problem of the origins of capitalism, not in terms of economic determinism, much less technological fatalism, but in terms of chance and necessity. In this paper, I attempt to draw the theoretical implications of such an approach in respect to general cultural evolution . [Marxism and cultural evolutionism; mode of production; economic determinism criticized; capitalism, rise of; cultural evolution, chance in]     

Temporal changes in therophytic communities across the boundary of disturbed-intact ecosystems

External control processes cause continual compositional and structural readjustments of Mediterranean pasture ecosystems. Such control processes include herbivore grazing, meteorological fluctuations and traditional management activities, which determine the stable environment where the succession occurs. Traditional management in this ecosystem frequently involves periodic ploughing or controlled fires.Experimental disturbances were applied to pastures of different maturity. Recovery was studied by relating information gathered for each disturbed system to successional age. The boundary between original systems of differing ages and the newly created systems was studied to compare the space-time evolution of therophytic communities. Permanent transects perpendicular to the disturbance boundaries and containing many small plots were sampled during consecutive years.Sampling plots located on both sides of the boundaries were classified into communities, in order to detect the space-time pasture evolution in successive years. Annual conditional probabilities were calculated for transitions between the recognised communities. During succession different strategies were detected in response to meteorological variations. In pioneer successional stages, substitutions of one community by another in the same space seem to be random. However, greater determinism was detected in more mature pastures, where, in addition, communities' abundance does not respond to meteorological change.Nomenclature follows T. G. Tutin et al. 1964–1980. Flora Europaea. Cambridge University Press, Cambridge.     

Morphological Diversity and the Roles of Contingency,Chance and Determinism in African Cichlid Radiations

Background

Deterministic evolution, phylogenetic contingency and evolutionary chance each can influence patterns of morphological diversification during adaptive radiation. In comparative studies of replicate radiations, convergence in a common morphospace implicates determinism, whereas non-convergence suggests the importance of contingency or chance.

Methodology/Principal Findings

The endemic cichlid fish assemblages of the three African great lakes have evolved similar sets of ecomorphs but show evidence of non-convergence when compared in a common morphospace, suggesting the importance of contingency and/or chance. We then analyzed the morphological diversity of each assemblage independently and compared their axes of diversification in the unconstrained global morphospace. We find that despite differences in phylogenetic composition, invasion history, and ecological setting, the three assemblages are diversifying along parallel axes through morphospace and have nearly identical variance-covariance structures among morphological elements.

Conclusions/Significance

By demonstrating that replicate adaptive radiations are diverging along parallel axes, we have shown that non-convergence in the common morphospace is associated with convergence in the global morphospace. Applying these complimentary analyses to future comparative studies will improve our understanding of the relationship between morphological convergence and non-convergence, and the roles of contingency, chance and determinism in driving morphological diversification.     

Evolution as resistance to entropy. I. Mechanisms of species homeostasis

The idea is discussed that the common output of any evolution is creation of the entities that are increasingly resistant to further evolution. The moving force of evolution is entropy, the tendency to disorder. This general aspiration for chaos is a cause of the mortality of organisms and species, however, being prerequisite for any movement, it creates (by chance) novelties, which may occur (by chance) more resistant to further decay and thus survive. The surviving of those who survive is the most general principle of evolution discovered by Darwin for particular case of biological evolution. The second law of thermodynamics states that our Universe is perishing but its ontology is such that it creates resistance to destruction. The evolution is a history of this resistance. Not only those who die do not survive but also those who evolve. The entities that change (evolve) rapidly disappear rapidly and by this reason they are not observed among both the fossils and now-living organisms. We know only about long-living species. All the existing organisms are endowed with an ability to resist other changing. The following main achievements of the species homeostasis are discussed: high fidelity of DNA replication and effective mechanisms of DNA repair; diploidy; normalizing selection; truncated selection; heterozygote superiority; ability to change phenotype adaptively without changing genotype; parental care and the K-strategy of reproduction; behavior that provides independence of the environment. The global resistance of the living systems to entropy is provided the state that all the essential in biology is determined not by physical-chemical interactions but could semantic rules. A conception of "potential zygotic information" that determines the rules of ontogenesis is proposed. A zygote does not contain this information in explicit form. It is created de novo step by step during ontogenesis and it could not be decoded beforehand. The experimental data on the adaptive mutagenesis and the relevant hypothesis are discussed. It is concluded that the special mechanisms for speeding-up of evolution as created by evolution are impossible conceptually.     

Randomness + determinism = progresses: Why random processes could be favored by evolution

Biologists are somehow pioneers on the idea that progress can be driven by randomness: randomness is one of the main engine of evolution; small variations induced by randomness coupled with natural selection allows the species to self-adapt to their moving environment. Studies from the last 40 years in computer science suggest that randomness is in fact able of doing much more and revealed unexpected possibilities which might appear impossible at first. Furthermore, it turns out that these discoveries are faster, cheaper and above all exponentially thriftier than their deterministic alternatives. This means that random explorations would almost surely generate a stochastic process way before any equivalent deterministic counterpart is found. It follows that most likely these processes are favored by evolution and should thus be known to anyone dealing with systems (alive or not) having access to random sources. This article presents some of these counter-intuitive results as a possible source of inspiration for studying systems fed with randomness.     

Die biosoziale Evolution

Summary The term biosocial evolution refers to mutual relations between different organisms and specially to functional systems composed of individuals belonging to a species (colonial organisms, social insectsetc.), or to two or more different species (ecosystems).The main features of the biosocial evolutioni.e. historical development of the functional systems of biosocial order are: 1. functional differentiation of the individual components of corresponding systems, 2. coordination of the differentiated functions and as a result, 3. the intergration of this systems as functional wholes.The tropical rain forest is to be considered as one of the most advanced terrestrial ecosystems, caracterized by its extreme differentiation, high level of its integration and violent reactions to main forces.The functional differentiation of the components of ecosystems is considered as a manifestation of the development of their individual traits as members of this system.The mechanisms of both phylogenetical and biosocial evolution as well as some other questions related to the problem (rhythms and celerity of evolution, determinism, immediate causesetc.) are briefly discussed in the text.     

Sound improves visual discrimination learning in avian predators

Aposematic insects use warning colours to deter predators, but many also produce odours or sounds when attacked by a predator. One possible role for these additional components is that they promote the association between the warning colour and the non-profitability it signals, thus reducing the chance of future attacks from visually hunting predators. This experiment explicitly tests this idea by looking at the effects of sound on a visual discrimination task. Young domestic chicks were trained to look for food rewards under coloured paper cones scattered in an experimental arena. In a subsequent visual discrimination task, they learned to discriminate between rewarded and non-rewarded hats on the basis of colour. Half the chicks performed this task in silence, whilst the other half had a tone played when they attacked non-rewarded hats. The presence of the tone improved the speed of colour discrimination learning. This demonstrates that there could be a selective advantage for aposematic coloured insects to emit sounds when attacked, since avian predators will learn to avoid their coloration more quickly. The role of psychological interactions between signal components in receivers is discussed in relation to the evolution of multimodal displays.     

Historical contingency and ecological determinism interact to prime speciation in sticklebacks, Gasterosteus

Historical contingency and determinism are often cast as opposing paradigms under which evolutionary diversification operates. It may be, however, that both factors act together to promote evolutionary divergence, although there are few examples of such interaction in nature. We tested phylogenetic predictions of an explicit historical model of divergence (double invasions of freshwater by marine ancestors) in sympatric species of three-spined sticklebacks (Gasterosteus aculeatus) where determinism has been implicated as an important factor driving evolutionary novelty. Microsatellite DNA variation at six loci revealed relatively low genetic variation in freshwater populations, supporting the hypothesis that they were derived by colonization of freshwater by more diverse marine ancestors. Phylogenetic and genetic distance analyses suggested that pairs of sympatric species have evolved multiple times, further implicating determinism as a factor in speciation. Our data also supported predictions based on the hypothesis that the evolution of sympatric species was contingent upon 'double invasions' of postglacial lakes by ancestral marine sticklebacks. Sympatric sticklebacks, therefore, provide an example of adaptive radiation by determinism contingent upon historical conditions promoting unique ecological interactions, and illustrate how contingency and determinism may interact to generate geographical variation in species diversity     

Unusual biophysics of intrinsically disordered proteins

Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the “turned-out” response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the “edge of chaos” systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue entitled: The emerging dynamic view of proteins: Protein plasticity in allostery, evolution and self-assembly.     

From Here to Eternity—The Theory and Practice of a Really Long Experiment

In February 1988, Richard Lenski set up 12 replicate populations of a single genotype of Escherichia coli in a simple nutrient medium. He has been following their evolution ever since. Here, Lenski answers provocative questions from Jeremy Fox about his iconic "Long-Term Evolution Experiment" (LTEE). The LTEE is a remarkable case study of the interplay of determinism and chance in evolution—and in the conduct of science.     

Next-generation sequencing: A new avenue to understand viral RNA–protein interactions

The genomes of RNA viruses present an astonishing source of both sequence and structural diversity. From intracellular viral RNA-host interfaces to interactions between the RNA genome and structural proteins in virus particles themselves, almost the entire viral lifecycle is accompanied by a myriad of RNA–protein interactions that are required to fulfill their replicative potential. It is therefore important to characterize such rich and dynamic collections of viral RNA–protein interactions to understand virus evolution and their adaptation to their hosts and environment. Recent advances in next-generation sequencing technologies have allowed the characterization of viral RNA–protein interactions, including both transient and conserved interactions, where molecular and structural approaches have fallen short. In this review, we will provide a methodological overview of the high-throughput techniques used to study viral RNA–protein interactions, their biochemical mechanisms, and how they evolved from classical methods as well as one another. We will discuss how different techniques have fueled virus research to characterize how viral RNA and proteins interact, both locally and on a global scale. Finally, we will present examples on how these techniques influence the studies of clinically important pathogens such as HIV-1 and SARS-CoV-2.     

Species interactions alter evolutionary responses to a novel environment

Studies of evolutionary responses to novel environments typically consider single species or perhaps pairs of interacting species. However, all organisms co-occur with many other species, resulting in evolutionary dynamics that might not match those predicted using single species approaches. Recent theories predict that species interactions in diverse systems can influence how component species evolve in response to environmental change. In turn, evolution might have consequences for ecosystem functioning. We used experimental communities of five bacterial species to show that species interactions have a major impact on adaptation to a novel environment in the laboratory. Species in communities diverged in their use of resources compared with the same species in monocultures and evolved to use waste products generated by other species. This generally led to a trade-off between adaptation to the abiotic and biotic components of the environment, such that species evolving in communities had lower growth rates when assayed in the absence of other species. Based on growth assays and on nuclear magnetic resonance (NMR) spectroscopy of resource use, all species evolved more in communities than they did in monocultures. The evolutionary changes had significant repercussions for the functioning of these experimental ecosystems: communities reassembled from isolates that had evolved in polyculture were more productive than those reassembled from isolates that had evolved in monoculture. Our results show that the way in which species adapt to new environments depends critically on the biotic environment of co-occurring species. Moreover, predicting how functioning of complex ecosystems will respond to an environmental change requires knowing how species interactions will evolve.     

Natural selection as an emergent process: instructional implications

Student reasoning about cases of natural selection is often plagued by errors that stem from miscategorising selection as a direct, causal process, misunderstanding the role of randomness, and from the intuitive ideas of intentionality, teleology and essentialism. The common thread throughout many of these reasoning errors is a failure to apply ‘population thinking’. Students fail to recognise that natural selection refers to changes in the distribution of certain traits at the population level, the collective, resulting from interactions between individual organisms and their environment at the next lower level in the system. Processes like selection are emergent processes in hierarchical systems, where patterns in a collective are generated by interactions at the lower level. By helping students develop an emergent process schema that enables them to recognise that even random interactions at one level in a system can generate predictable patterns at a higher level, their understanding of natural selection should improve. Some studies have shown this to be an effective approach for teaching other emergent processes. Instructional recommendations based on these studies are presented here, but more research is needed to determine the full extent to which this approach can improve students’ understanding.     

Phenotypic plasticity in hydrozoans: morph reversibility.

The life cycle of Hydrozoans typically comprises two phases: the polyp, either solitary or colonial, with generally a benthic habitat, and the medusa which lives in the plankton. In its typical metagenetic cycle, the medusa is budded from the polyp, which is the product of sexual reproduction of medusae. However, several alternative reproduction patterns have also been described. In particular some species are able to perform a regressive transformation of the medusae that transform themselves into polyps bypassing sexual reproduction. In a species with alternative morphs switched by the environment, the more labile is the correlation between environmental factors acting on the genetic switch and the factors to which the resulting form is adapted, the more hazardous will be the development of either body form. However, we can explain the evolutionary advantage offered by reversion between morphs of these plastic species living in shallow water unpredictable environments: should produced medusae be released in the "wrong" environment, they would still have a chance of survival under another form.