When Enlightenment science was first introduced in earnest into Russia as part of Peter I's programme of westernisation, the Orthodox Church's view of scientific truth remained the received wisdom and enlightenment science was looked upon as heretical, alien and un-Russian. After Peter's death the Church and other conservative forces in Russia attempted to reassert the traditional system of scientific belief, but Peter's vision had an energetic and enthusiastic supporter in the scientist and polymath MV Lomonosov, whose defence of Enlightenment science against such opposition is illustrated by particular reference to the Copernican Revolution. However, unlike scientists such as Benjamin Franklin in America, Lomonosov did not pursue Enlightenment values into the realm of social and political enquiry, but saw instead Enlightenment science as an instrument for the furtherance of Peter's model of the Russian autocratic state. The political and sociological writers discussed in connection with the Darwinian Revolution, Chemyshevsky, Pisarev, Mikhailovsky, Lavrov and Kropotkin, were all committed to scientific method, but their various responses to Darwinism were significantly coloured by the fact that the struggle for existence in nature described by Darwin seemed more of a piece with the conclusions of western Social Darwinists in favour of a competitive capitalist society, than with the sort of communal society that these Russian writers sought to justify in rational scientific terms. The specific Russian historical moment is of central importance: the Origin of Species appeared in Russia just at the time of the Emancipation, when a major concern of Russian radical thought was that Russian society should bypass capitalism and proceed directly to a socialist form of society. Both the scientific revolutions are examined in this study with reference to specifically Russian political and sociological issues arising from the particular Russian cultural and historical context into which they were received.

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Social behaviour is common in nature. Yet, for over a century and half, scholars have struggled in vain to offer a satisfactory account of its evolution under Darwinian natural selection. In this thesis I propose that three fundamental assumptions in the Darwinian explanation of social behaviour are at the root of the problem. They are: 1. The basic Darwinian philosophy that evolutionary change occurs by one inherent trait replacing another in an organism. 2. The collapse of social behaviour, in its entirety, into a single, narrow concept called “altruism.” 3. The assumption that such “altruism” arises from a mutation at a single gene locus, where it supplants “selfishness” as an alternative allele. The thesis identifies some insights from Hume’s analysis of human morality and sociality that suggest the proper circumstances of social interactions in humans. We see from Hume’s analysis that nothing inherent in human nature needs to change in order to move beyond parenting to sociality. Hume identifies two principles in human nature — selfishness and empathy — that are the ultimate basis of human sociality. Empathy expands self-interest to include relatives and associates, but not strangers. And that suffices to form small, primitive human societies. For large, cosmopolitan societies, Hume suggests they are maintained only through human inventions such as governments and justice. Hume’s explanation precludes the need for a weaker “altruistic gene” to supplant a fitter “selfish gene” as a condition for social evolution, which has been the basis of the Darwinian explanatory difficulty. / Thesis / Doctor of Philosophy (PhD)

Mathematical models with fixed parameters have a long history of use in describing the dynamics of populations in ecological interactions. However, in many instances, evolutionary changes in species characteristics can have a significant influence on these dynamics. Using evolutionary game theory, we incorporate evolution into population dynamic models and apply the resulting “Darwinian dynamic” models to study the effects that evolutionary changes can have on populations in several ecological scenarios. We start with a single species (Chapter 2), then add a competitor (Chapter 3), and a predator (Chapter 4). In Chapter 2, a rigorous mathematical analysis of the Darwinian logistic model for a single species shows that stable equilibria occur at strategies that maximize population size rather than growth rate. We apply this model to the data obtained from an experimental study on genetically perturbed populations of the flour beetle Tribolium castaneum. In Chapter 3, we apply a Darwinian dynamic modification of the Lotka-Volterra model to investigate circumstances under which evolution will change expected competitive outcomes. We compare the results of our Darwinian Lotka-Volterra model to studies in which unusual observations were made in studies of the flour beetles T. castaneum and T. confusum, including a reversal in the “winner” of competitive exclusion, and evolution from exclusion to coexistence. Chapters 2 and 3 provide one of the few examples in which evolutionary game theory has been successfully applied to empirical data. From a foundation provided by the Darwinian logistic equation, we build Darwinian dynamic models with two and three trophic levels to study effects of evolution on some basic ecological interactions in Chapter 4. We show how a consumer can cause a resource (producer) species to evolve to a mean strategy that increases its growth rate rather than its population size. We also briefly study how predation on the consumer species can affect equilibrium strategies of species lower in the food chain. Our results show how evolutionary game theoretic methods can be useful for studying both theoretical and applied problems that arise due to evolutionary processes, even when they occur on a ecological time scale. They provide a foundation for the future study of evolutionary effects in larger complex networks of interacting species.

The Hox gene complement of zebrafish, medaka, and fugu differs from that of other gnathostome vertebrates. These fishes have seven to eight Hox clusters compared to the four Hox clusters described in sarcopterygians and shark. The clusters in different teleost lineages are orthologous, implying that a “fish-specific” Hox cluster duplication has occurred in the stem lineage leading to the most recent common ancestor of zebrafish and fugu. The timing of this event, however, is unknown. To address this question, we sequenced four Hox genes from taxa representing basal actinopterygian and teleost lineages and compared them to known sequences from shark, coelacanth, zebrafish, and other teleosts. The resulting gene genealogies suggest that the fish-specific Hox cluster duplication occurred coincident with the origin of crown group teleosts. In addition, we obtained evidence for an independent Hox cluster duplication in the sturgeon lineage (Acipenseriformes). Finally, results from HoxA11 suggest that duplicated Hox genes have experienced diversifying selection immediately after the duplication event. Taken together, these results support the notion that the duplicated Hox genes of teleosts were causally relevant to adaptive evolution during the initial teleost radiation.

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In Annie Proulx's interview with Charlie Rose, she states that her stories come "from place." Ecocriticism has been the predominant lens with which to understand Proulx's work; however, ecocriticism's nebulous tenets and theoretical deficiencies perpetuate sentimental pastoralism of geographical determinism. The shaping impact of Wyoming's environment in Proulx's work lends itself to an evolutionary perspective. Proulx's fiction, like evolutionary theory, examines humanity's unique, reciprocal relationship with nature. The evolutionary approach provides readers with a framework to understand the human relationship to our environment, a theme Proulx's work examines. This approach also augments current criticism that notes the importance of place but does not utilize the relevant framework of evolution. Current evolutionary theory provides the theoretical framework necessary to shed light on the relationship between Proulx's colorful characters and the environment that shapes them. Utilizing this evolutionary framework and textual analysis, I examine two short stories, "The Half-Skinned Steer" and "Wamsutter Wolf."

abstract: A major goal of synthetic biology is to recapitulate emergent properties of life. Despite a significant body of work, a longstanding question that remains to be answered is how such a complex system arose? In this dissertation, synthetic nucleic acid molecules with alternative sugar-phosphate backbones were investigated as potential ancestors of DNA and RNA. Threose nucleic acid (TNA) is capable of forming stable helical structures with complementary strands of itself and RNA. This provides a plausible mechanism for genetic information transfer between TNA and RNA. Therefore TNA has been proposed as a potential RNA progenitor. Using molecular evolution, functional sequences were isolated from a pool of random TNA molecules. This implicates a possible chemical framework capable of crosstalk between TNA and RNA. Further, this shows that heredity and evolution are not limited to the natural genetic system based on ribofuranosyl nucleic acids. Another alternative genetic system, glycerol nucleic acid (GNA) undergoes intrasystem pairing with superior thermalstability compared to that of DNA. Inspired by this property, I demonstrated a minimal nanostructure composed of both left- and right-handed mirro image GNA. This work suggested that GNA could be useful as promising orthogonal material in structural DNA nanotechnology. / Dissertation/Thesis / Ph.D. Chemistry 2011

Les gènes impliquées dans la reproduction évoluent rapidement et sont très souvent soumis à sélection positive. L’objectif de ma thèse a été d’étudier l’évolution de certains de ces gènes, potentiellement impliqués dans le phénomène de spéciation via leur implication dans les barrières prézygotiques.Nos résultats montrent que pour le gène SAL1, impliqué dans la reconnaissance phéromonale chez le porc, trois acides aminés sous sélection positive participent à la liaison de la phéromone spécifique porcine. Nous avons également réalisé l’analyse évolutive des gènes prouvés expérimentalement comme ayant un rôle dans l’interaction spermatozoïde-ovocyte lors de la fécondation. Chacune des dix neuf espèces de vertébrés étudiées présente un profil évolutif particulier pour ces gènes, caractérisé par le gain et la perte de gènes, ainsi que la position des acides aminés sous sélection positive. L’évolution divergente de l’ensemble de ces gènes pourrait être impliquée dans la spéciation ou au moins dans le renforcement des barrières d’espèces.Enfin, le serveur web PhyleasProg a été conçu au cours de la thèse. Cet outil permet désormais aux scientifiques, peu aguerris aux méthodes d’analyses phylogénétiques, d’acquérir simplement et rapidement un grand nombre de résultats sur l’histoire évolutive de leurs gènes d’intérêts. / Genes involved in reproduction evolve rapidly and are often under positive selection. The objective of this work was to study the evolution of some of these genes, potentially involved in speciation, through their involvement in prezygotic barriers.Our results show that for the SAL1 gene, involved in pheromonal recognition in pig, three amino acids under positive selection participate in the specific binding of the pig pheromone. We also perform an evolutionary analysis of genes experimentally shown to be involved in the sperm-oocyte interaction during fertilization. Each of the nineteen species studied exhibit a particular pattern of evolution, characterized by gene gains and losses, as well as the position of amino acids under positive selection. The divergent evolution of all these genes could be involved in speciation or at least in the reinforcement of species barriers.Finally, the PhyleasProg web server was designed during the thesis. This tool permits to scientists with no experience in phylogenetic analyses to acquire a large number of results quickly and easily on the evolutionary history of their genes of interest.

Wuthering Heights was significantly shaped by the pre-Darwinian scientific debate in ways that look ahead to Darwin's evolutionary theory more than a decade later. Wuthering Heights represents a cultural response to new and disturbing ideas. Darwin's enterprise was scientific; Emily Brontë's poetic. Both, however, were seeking to find ways to express their vision of the nature of human beings. The language and metaphors of Wuthering Heights suggest that Emily Brontë's vision was, in many ways, similar to Darwin's.