Transitions in individuality.

The evolution of multicellular organisms is the premier example of the integration of lower levels into a single, higher-level individual. Explaining the evolutionary transition from single cells to multicellular organisms is a major challenge for evolutionary theory. We provide an explicit two locus genetic framework for understanding this transition in terms of the increase of cooperation among cells and the regulation of conflict within the emerging organism. Heritability of fitness and individuality at the new level emerge as a result of the evolution of organismal functions that restrict the opportunity for conflict within and ensure cooperation among cells. Conflict leads, through the evolution of adaptations that reduce it, to greater individuality and harmony for the organism.     

The phylogeny of polar fishes and the structure,function and molecular evolution of hemoglobin

Fishes thriving in polar habitats offer many opportunities for comparative approaches to understanding protein thermal adaptations. Investigations on the remarkable evolutionary adaptations to these environments of basic proteins such as hemoglobin, the oxygen carrier, can provide new insights into the mechanisms studied in temperate organisms and can shed light on convergent processes evolved in response to thermal adaptations. At the molecular level, hemoglobins are one of the most intriguing systems for studying the relationships between environmental conditions and adaptations. This review summarizes the current knowledge on molecular structure, biological function and phylogeny of hemoglobins of fish species living in both polar habitats but having different evolutionary histories. In benthic, non-migratory, cold-adapted fishes, the stability of thermal conditions may have generated no or few variations in selective pressures on globin sequences through evolutionary time, so that sequences retain the species phylogenetic “signal”. In pelagic, migratory, cold-adapted or temperate fishes, variations in selective pressures on globin sequences caused by variations in temperature accompanying the dynamic life style may have disrupted the phylogenetic “signal” in phenetic trees.     

THE SOCIAL ORGANISM: CONGRESSES,PARTIES, AND COMMITTEES

We propose that what makes an organism is nearly complete cooperation, with strong control of intraorganism conflicts, and no affiliations above the level of the organism as unified as those at the organism level. Organisms can be made up of like units, which we call fraternal organisms, or different units, making them egalitarian organisms. Previous definitions have concentrated on the factors that favor high cooperation and low conflict, or on the adapted outcomes of organismality. Our approach brings these definitions together, conceptually unifying our understanding of organismality. Although the organism is a concerted cluster of adaptations, nearly all directed toward the same end, some conflict may remain. To understand such conflict, we extend Leigh's metaphor of the parliament of genes to include parties with different interests and committees that work on particular tasks.     

Intrinsic noise and the design of the genetic machinery

Darwinian theory envisages 'selection pressure' as a stress imposed on the genotype by the environment. However, noise in the replicative and translational mechanisms in itself imposes a significant 'pressure' on the adaptive fitness of the organism. We propose that the biosphere has been shaped by both extrinsic (environmental) and intrinsic (noise-generated) factors. Because noise has been a remorseless and ever-present background to the evolutionary process, adaptations to this intrinsic pressure include not only a variety of familiar genetic mechanisms but also many anatomical and life-style characteristics that focus on the transmission of information between generations.     

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.     

Cooperation and conflict in the evolution of individuality. IV. Conflict mediation and evolvability in Volvox carteri

The continued well being of evolutionary individuals (units of selection and evolution) depends upon their evolvability, that is their capacity to generate and evolve adaptations at their level of organization, as well as their longer term capacity for diversifying into more complex evolutionary forms. During a transition from a lower- to higher-level individual, such as the transition between unicellular and multicellular organisms, the evolvability of the lower-level (cells) must be restricted, while the evolvability of the new higher-level unit (multicellular organism) must be enhanced. For these reasons, understanding the factors leading to an evolutionary transition should help us to understand the factors underlying the emergence of evolvability of a new evolutionary unit. Cooperation among lower-level units is fundamental to the origin of new functions in the higher-level unit. Cooperation can produce a new more complex evolutionary unit, with the requisite properties of heritable fitness variations, because cooperation trades fitness from a lower-level (the costs of cooperation) to the higher-level (the benefits for the group). For this reason, the evolution of cooperative interactions helps us to understand the origin of new and higher-levels of fitness and organization. As cooperation creates a new level of fitness, it also creates the opportunity for conflict between levels of selection, as deleterious mutants with differing effects at the two levels arise and spread. This conflict can interfere with the evolvability of the higher-level unit, since the lower and higher-levels of selection will often "disagree" on what adaptations are most beneficial to their respective interests. Mediation of this conflict is essential to the emergence of the new evolutionary unit and to its continued evolvability. As an example, we consider the transition from unicellular to multicellular organisms and study the evolution of an early-sequestered germ-line in terms of its role in mediating conflict between the two levels of selection, the cell and the cell group. We apply our theoretical framework to the evolution of germ/soma differentiation in the green algal group Volvocales. In the most complex member of the group, Volvox carteri, the potential conflicts among lower-level cells as to the "right" to reproduce the higher-level individual (i.e. the colony) have been mediated by restricting immortality and totipotency to the germ-line. However, this mediation, and the evolution of an early segregated germ-line, was achieved by suppressing mitotic and differentiation capabilities in all post-embryonic cells. By handicapping the soma in this way, individuality is ensured, but the solution has affected the long-term evolvability of this lineage. We think that although conflict mediation is pivotal to the emergence of individuality at the higher-level, the way in which the mediation is achieved can greatly affect the longer-term evolvability of the lineage.     

De Novo Evolution of Complex, Global and Hierarchical Gene Regulatory Mechanisms

Gene regulatory networks exhibit complex, hierarchical features such as global regulation and network motifs. There is much debate about whether the evolutionary origins of such features are the results of adaptation, or the by-products of non-adaptive processes of DNA replication. The lack of availability of gene regulatory networks of ancestor species on evolutionary timescales makes this a particularly difficult problem to resolve. Digital organisms, however, can be used to provide a complete evolutionary record of lineages. We use a biologically realistic evolutionary model that includes gene expression, regulation, metabolism and biosynthesis, to investigate the evolution of complex function in gene regulatory networks. We discover that: (i) network architecture and complexity evolve in response to environmental complexity, (ii) global gene regulation is selected for in complex environments, (iii) complex, inter-connected, hierarchical structures evolve in stages, with energy regulation preceding stress responses, and stress responses preceding growth rate adaptations and (iv) robustness of evolved models to mutations depends on hierarchical level: energy regulation and stress responses tend not to be robust to mutations, whereas growth rate adaptations are more robust and non-lethal when mutated. These results highlight the adaptive and incremental evolution of complex biological networks, and the value and potential of studying realistic in silico evolutionary systems as a way of understanding living systems.     

Can adaptation lead to extinction?

Ever since J.B.S. Haldane proposed the idea, evolutionary biologists are aware that individual level adaptations do not necessarily lead to optimal population performance. A few deeply mathematical models, drawing from a diverse range of systems, even predict that individual selection can lead to the extinction of the whole population, a phenomenon which has become known as evolutionary suicide. Due to the complexity of both following adaptation and determining the exact cause of an extinction, evolutionary suicide has remained untested empirically. However, three recent empirical studies suggest that it may occur, and that suicide should be taken seriously as a potentially important evolutionary phenomenon. Here we ask whether or not evolutionary suicide can occur, briefly reviewing the theoretical and empirical evidence. We further highlight systems which may be used to test whether or not individual level selection can cause extinction.     

Why there are no objective values: A critique of ethical intuitionism from an evolutionary point of view

Using concepts of evolutionary game theory, this paper presents a critique of ethical intuitionism, or non-naturalism, in its cognitivist and objectivist interpretation. While epistemological considerations suggest that human rational learning through experience provides no basis for objective moral knowledge, it is argued below that modern evolutionary theory explains why this is so, i.e., why biological organisms do not evolve so as to experience objective preferences and obligations. The difference between the modes of the cognition of objective and of valuative environmental attributes is explained with reference to different modes of natural selection acting on the cognitive apparatus of the organism. The negative implications are pointed out which the observable diversity of intraspecific behavioural adaptations and of cultural values has for the cognitivist, objectivist foundation of ethics. Eventually a non-cognitivist alternative to ethical intuitionism is outlined in terms of empirical authority relations, with the ritualisation of dominance-submission patterns as the evolutionary origin of human charismatic authority.     

Adaptation to environmental temperature is a major determinant of molecular evolutionary rates in archaea

Methods to infer the ancestral conditions of life are commonly based on geological and paleontological analyses. Recently, several studies used genome sequences to gain information about past ecological conditions taking advantage of the property that the G+C and amino acid contents of bacterial and archaeal ribosomal DNA genes and proteins, respectively, are strongly influenced by the environmental temperature. The adaptation to optimal growth temperature (OGT) since the Last Universal Common Ancestor (LUCA) over the universal tree of life was examined, and it was concluded that LUCA was likely to have been a mesophilic organism and that a parallel adaptation to high temperature occurred independently along the two lineages leading to the ancestors of Bacteria on one side and of Archaea and Eukarya on the other side. Here, we focus on Archaea to gain a precise view of the adaptation to OGT over time in this domain. It has been often proposed on the basis of indirect evidence that the last archaeal common ancestor was a hyperthermophilic organism. Moreover, many results showed the influence of environmental temperature on the evolutionary dynamics of archaeal genomes: Thermophilic organisms generally display lower evolutionary rates than mesophiles. However, to our knowledge, no study tried to explain the differences of evolutionary rates for the entire archaeal domain and to investigate the evolution of substitution rates over time. A comprehensive archaeal phylogeny and a non homogeneous model of the molecular evolutionary process allowed us to estimate ancestral base and amino acid compositions and OGTs at each internal node of the archaeal phylogenetic tree. The last archaeal common ancestor is predicted to have been hyperthermophilic and adaptations to cooler environments can be observed for extant mesophilic species. Furthermore, mesophilic species present both long branches and high variation of nucleotide and amino acid compositions since the last archaeal common ancestor. The increase of substitution rates observed in mesophilic lineages along all their branches can be interpreted as an ongoing adaptation to colder temperatures and to new metabolisms. We conclude that environmental temperature is a major factor that governs evolutionary rates in Archaea.     

Selfish DNA: A Sexually-Transmitted Nuclear Parasite

A quantitative population genetics model for the evolution of transposable genetic elements is developed. This model shows that "selfish" DNA sequences do not have to be selectively neutral at the organismic level; indeed, such DNA can produce major deleterious effects in the host organism and still spread through the population. The model can be used to explain the evolution of introns within eukaryotic genes; this explanation does not invoke a long-term evolutionary advantage for introns, nor does it depend on the hypothesis that eukaryotic gene structure may be an evolutionary relic. Transposable genes that carried information specifying sexual reproduction in the host organism would favor their own spread. Consequently, it is tempting to speculate that some of the genes controlling sex were originally selected as transposable elements.     

Reviving the superorganism

Individuals become functionally organized to survive and reproduce in their environments by the process of natural selection. The question of whether larger units such as groups and communities can possess similar properties of functional organization, and therefore be regarded as "superorganisms", has a long history in biological thought. Modern evolutionary biology has rejected the concept of superorganisms, explaining virtually all adaptations at the individual or gene level. We criticize the modern literature on three counts. First, individual selection in its strong form is founded on a logical contradiction, in which genes-in-individuals are treated differently than individuals-in-groups or species-in-communities. Imposing consistency clearly shows that groups and communities can be organisms in the same sense that individuals are. Furthermore, superorganisms are more than just a theoretical possibility and actually exist in nature. Second, the view that genes are the "ultimate" unit of selection is irrelevant to the question of functional organization. Third, modern evolutionary biology includes numerous conceptual frameworks for analyzing evolution in structured populations. These frameworks should be regarded as different ways of analyzing a common process which, to be correct, must converge on the same conclusions. Unfortunately, evolutionists frequently regard them as competing theories that invoke different mechanisms, such that if one is "right" the others must be "wrong". The problem of multiple frameworks is aggravated by the fact that major terms, such as "units of selection", are defined differently within each framework, yet many evolutionists who use one framework to argue against another assume shared meanings. We suggest that focusing on the concept of organism will help dispell this fog of semantic confusion, allowing all frameworks to converge on the same conclusions regarding units of functional organization.     

Comprendre la dépression : apport de la psychologie évolutionniste

Darwinian medicine considers that many symptoms are the organism’s defence mechanisms and adaptations that have been inherited and shaped by natural selection. But in many cases, signs and symptoms of disease are of no benefit to human survival and are in fact deregulations of normal mechanisms. Evolutionary explanations help us understand how some human affective and emotional processes could have an adaptive value and enable us to cope with a wide spectrum of situations. But the wide range of intensity levels and different forms, ranging from low moods to major depression with psychotic features, suggest that these symptoms cannot always be explained by adaptation: where is the cut-off point? In this paper, we describe the evolutionary concepts related to adaptation as applied to the emotions, particularly focusing on low mood and depression, and discuss their possible functional and adaptive role.     

Genetic-evolutionary basis of symbiosis doctrine

The author presents the current notion of symbiosis as one of the main adaptation of an organism to changeable environment. Symbiosis is considered as a super organism genetic system within which there are different interactions (including mutualism and antagonism). Genetic integration of symbiotic partners can be realized as cross regulation of their genes, exchange of gene products (proteins, RNA), gene amplification and sometimes gene transfer between organisms. On the phenotypic level these processes result in signal interactions, integration of partner metabolic systems and development of symbiotic organs. Co-evolution is considered as an assemblage of micro- and macroevolution processes basing on pre-adaptations and proceeding under influence of different forms of natural selection (individual, frequency-depended and kin selection). Symbiosis can be compared with sexual process since both are the forms of organism integration characterized by different genetic mechanisms and evolutionary consequences. The genome evolution in symbiotic microorganisms can proceed by: 1) simplification of genome in obligate symbiosis (loss of genes that are necessary for independent existence, transfer of some genes to the host organism); 2) complication of genome in facultative symbiosis (increase in genome plasticity, structural and functional differentiation of genome into systems controlling free-living and symbiotic parts of life cycle). Most of symbiotic interactions are correlated to an increase in genetic plasticity of an organism that can lead to evolutionary saltations and origin of new forms of life.     

Physiological Adaptations (By the Example of the Exotrophy Process in Fish)

By the example of a complex process of exotrophy in fish, which includes not only search for and consumption, but also digestion of the victim, as well as transfer of products of its depolymerization into the internal organism medium, different types of physiological adaptations are described: adaptations of elementary functions, the local or subsystem adaptations, the organismal or supersystem ones, as well as the superorganism adaptations including victim-symbiotic, populational, and biocenotic ones.     

Prolegomenon for a hypothesis on music as expression of an evolutionary early homeostatic feedback-mechanism. A biomusicological proposal.

Musical experience and creativity are regarded to be largely depending on cultural conditions and hence on higher cognitive functions. True as this may be, there are, however, numerous responses to music-the urge to make music taken into account-which derive from deeper levels of the human organism, namely from arousing alternatively moderating vegetative and limbic functions. Although the behavioral intensity and quality emanating from such evolutionary early nervous structures may be affected by cultural influence, they still seem to be essentially independent. Similar specific responses to acoustical and/or motor patterned stimuli are found among some other higher vertebrates which like humans are equipped with sophisticated mechanisms for hearing, sound production and locomotion, well tuned to each other. However, it is even today an open question whether these manifestations of auditive-phonatory-locomotor abilities just are analogues or if they share a common evolutionary background. The current discussion on this matter has accumulated data which apparently support the latter view pointing to that sexual selection would be the common force, first suggested by Charles Darwin (153). Other, and still more recent data in genetics and neuroscience, may be interpreted as hints at that the common origin would be a more elemental organismic feature, a metabolic-homeostatic variable which due to its evolutionary strength eventually created the platform for a radiation of adaptations concerning species-specific patterned sounds and locomotions with a broad spectrum of tasks, among them sexual selection. This line of reasoning is here, under reference to recent biological data, made the basis for a hypothetical model of music as an expression of an early homeostatic feedback mechanism. Accordingly, in music there is a central variable, a “heart” or a “core”, which is not to be found exclusively in music but appears globally as a releasing mechanism for basic endocrine, autonomous and elementally cognitive functions. It is of acoustical or motoric nature, or of a combination of these characters, and is performed in repetitive trains of impulses. It is further assumed that the target of its operations is mainly proteins with a regulatory effect on the cellular and synaptic states. The principal representatives for these proteins are growth factors, especially the NGF which originally was regarded as a growth stimulator within the peripheral and sympathetical systems but which eventually appeared to be also a synergetic modulator of neuro-endocrine-immuno-reactions, i.e. of the three central homeostatic systems (5, 80). One can speculate that this variable is functionally active at an elemental level such that it has escaped to be knocked out by forceful “higher” and evolutionary younger factors (49:13). This hypothesis — that music has its roots within and is a part of a globally occurring natural acoustical-motoric stimulus, manifested in a great variety of auditory and motoric behavior in humans and among some other higher vertebrates — implies that humankind has developed this stimulus into a category of acoustical structures which oscillate round an instable point of equilibrium. Exactly such structures, not stochastic but neither too predictable, affect the organism mainly on a sensory-vegetative level (59, 102, 137, 151). They are in addition perceptionally optimal in creating cortical space-temporal neural patterns with strong interhemispheric coherence (110, 130). According to this scenario, music did not originate from a human need of communication or as an aspect of sexual selection. It emerged from elemental processes within the individual organism with the aspiration to maintain his bodily and mental fitness, thus on a pre-social level. What was beneficial to the single individual in his fight for survival, was good also for the group and its survival. Starting from that platform music has evolved in symbiosis with dance and play within a large spectrum of social functions, where sexual selection and ritual and autonomously aesthetical tasks got a focal role that increased over time and always was accompanied by emotional events. Behind, the ticking in the deep structure of music of this in cultural-ethical terms totally value-neutral archaic mechanism goes on without pause, contributing to the maintenance of an optimal functional balance in body and mind of the individual, and the group as well.     

The effect of temperature on catalytic and regulatory functions of pyruvate kinases of the rainbow trout and the Antarctic fish Trematomus bernacchii

1. The effects of temperature on the catalytic and regulatory properties of pyruvate kinases from the temperate-zone rainbow trout and the Antarctic fish Trematomus bernacchii were examined. 2. The K(m) value of pyruvate kinase for one of its two substrates, phosphoenolpyruvate, is temperature-dependent, and is lowest at temperatures that closely coincide with the habitat temperatures of the two fishes. 3. Two regulatory functions of pyruvate kinase, feedforward activation by fructose diphosphate and feedback inhibition by ATP, are temperature-independent. Enzyme-ADP interaction is also temperature-independent. 4. It is concluded that enzyme-substrate and enzyme-modulator interactions are important factors in short-term and in evolutionary adaptations by poikilotherms to changes in temperature. Though the K(m) for substrate may vary in apparently adaptive manners, the regulatory functions of an enzyme appear to be unchanged over the range of temperatures experienced by the organism in Nature.     

Tasks and perspectives of development of evolutionary physiology

The paper considers the main tasks facing evolutionary physiology as well as the methods that allow these tasks to be solved. It is shown that alongside with traditional, classical methods (phylogenetic, ontogenetic, experimental, clinical), there developed and got recognition in the present-day evolutionary physiology principally new methodological approaches important for solution of actual problems of this discipline. It is the method of mathematical modeling of functions, which makes it possible not only to study on the model, in temporary scales convenient for analysis, evolution of the given functions under the given actions, but also to model the evolutionary process itself in its different manifestations. It is the method of gene engineering that allows studying processes of formation of specific functional systems, their interaction and “mutual adjustment” at the organism level. It is lastly the method of tissue cultures allowing reconstruction under artificial conditions various systems of organism and study of regularities and mechanisms of morphogenesis and formation of functions. The paper discusses trends of development of evolutionary physiology for the last few years, considers perspective directions of studies, using specific examples, and shows possible ways for practical applications of fundamental investigations in the field of evolutionary physiology. Journal variant of the report published in the Collection of Papers “Tendency of Development of Physiological Sciences,” St. Petersburg, 2000.     

STABILIZING SELECTION AND THE COMPARATIVE ANALYSIS OF ADAPTATION

Comparative studies tend to differ from optimality and functionality studies in how they treat adaptation. While the comparative approach focuses on the origin and change of traits, optimality studies assume that adaptations are maintained at an optimum by stabilizing selection. This paper presents a model of adaptive evolution on a macroevolutionary time scale that includes the maintenance of traits at adaptive optima by stabilizing selection as the dominant evolutionary force. Interspecific variation is treated as variation in the position of adaptive optima. The model illustrates how phylogenetic constraints not only lead to correlations between phylogenetically related species, but also to imperfect adaptations. From this model, a statistical comparative method is derived that can be used to estimate the effect of a selective factor on adaptive optima in a way that would be consistent with an optimality study of adaptation to this factor. The method is illustrated with an analysis of dental evolution in fossil horses. The use of comparative methods to study evolutionary trends is also discussed.     

Historic and functional biology: the inadequacy of a system theory of evolution

In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and the important historical questions of evolutionary biology in its scientific context is recommended.