<p>This dissertation explores philosophical problems in biology, particularly those relating to macroevolutionary theory. It is comprised of a series of three papers drawn from work that is currently at the publication, re-submission, and review stage of the journal refereeing process, respectively. The first two chapters concern the overarching contours of complex life, while the third zeroes in on the short and long-term prospects of human evolution.</p><p>The rhetorical journey begins with a thought experiment proposed by the late paleontologist Stephen Jay Gould. Gould hypothesized that replaying the "tape of life" would result in radically different evolutionary outcomes, both with respect to animal life in general and the human species in particular. Increasingly, however, biologists and philosophers are pointing to convergent evolution as evidence for replicability and predictability in macroevolution. Chapters 1 and 2 are dedicated to fleshing out the Gouldian view of life and its antithesis, clarifying core concepts of the debate (including contingency, convergence, constraint and causation), and interpreting the empirical data in light of these conceptual clarifications. Chapter 3 examines the evolutionary biological future of the human species, and the ways in which powerful new biotechnologies can shape it, for better and for worse. More detailed chapter summaries are provided below.</p><p>In Chapter 1, I critique a book-length excoriation of Gould's contingency theory written by the paleobiologist Simon Conway Morris, in which he amasses and marshals a good bulk of the homoplasy literature in the service of promoting a more robust, counter-factually stable account of macroevolution. I show that there are serious conceptual and empirical difficulties that arise in broadly appealing to the frequency of homoplasy as evidence for robustness in the history of life. Most important is Conway Morris's failure to distinguish between convergent (`externally' constrained) and parallel (`internally' constrained) evolution, and to consider the respective implications of these significantly different sources of homoplasy for a strong adaptationist view of life.</p><p>In so doing, I propose a new definition of parallel evolution, one intended to rebut the common charge that parallelism differs from convergence merely in degree and not in kind. I argue that although organisms sharing a homoplastic trait will also share varying degrees of homology (given common decent), it is the underlying developmental homology with respect to the generators directly causally responsible for the homoplastic event that defines parallel evolution and non-arbitrarily distinguishes it from convergence. I make use of the philosophical concept of `screening-off' in order to distinguish the proximate generators of a homoplastic trait from its more distal genetic causes (such as conserved master control genes).</p><p>In Chapter 2, I critically examine a recent assessment of the contingency debate by the philosopher John Beatty, in which he offers an interpretation of Gould's thesis and argues that it is undermined by iterative ecomorphological evolution. I develop and defend alternative concepts of contingency and convergence, and show how much of the evidence generally held to negate the contingency thesis not only fails to do so, but in fact militates in favor of the Gouldian view of life. My argument once again rests heavily on the distinction between parallelism and convergence, which I elaborate on and defend against a recent assault by developmental biologists, in part by recourse to philosophical work on the ontological prioritization of biological causes.</p><p>In Chapter 3, I explore the probable (and improbable) evolutionary biological consequences of intentional germ-line modification, particularly in relation to human beings. A common worry about genetic engineering is that it will reduce the pool of genetic diversity, creating a biological monoculture that could not only increase our susceptibility to disease, but even hasten the extinction of our species. Thus far, however, the evolutionary implications of human genetic modification have remained largely unexplored. In this Chapter, I consider whether the widespread use of genetic engineering technology is likely to narrow the present range of genetic variation, and if so, whether this would in fact lead to the evolutionary harms that some authors envision. By examining the nature of biological variation and its relation to population immunity and evolvability, I show that not only will genetic engineering have a negligible impact on human genetic diversity, but that it will be more likely to ensure rather than undermine the health and longevity of the human species. To this end, I analyze the relationship between genotypic and phenotypic variation, consider process asymmetries between micro and macroevolution, and investigate the relevance of evolvability to clade-level persistence and extinction.</p> / Dissertation

High-throughput technologies in biological sciences have led to an exponential growth in the amount of data generated over the past several years. This data explosion is forcing scientists to search for innovative computational designs to reduce the time-scale of biological system simulations, and enable rapid study of larger and more complex biological systems. In the field of immunobiology, one such simulation is known as DNA recombination. It is a critical process for investigating the correlation between disease and immune system responses, and discovering the immunological changes that occur during aging through T-cell repertoire analysis. In this project we design and develop a massively parallel method tailored for Graphics Processing Unit (GPU) processors by identifying novel ways of restructuring the flow of the repertoire analysis. The DNA recombination process is the central mechanism for generating diversity among antigen receptors such as T-cell receptors (TCRs). This diversity is crucial for the development of the adaptive immune system. However, modeling of all the α β TCR sequences is encumbered by the enormity of the potential repertoire, which has been predicted to exceed 10¹⁵ sequences. Prior modeling efforts have, therefore, been limited to extrapolations based on the analysis of minor subsets of the overall TCR β repertoire. In this study, we map the recombination process completely onto the GPU hardware architecture using the CUDA programming environment to circumvent prior limitations. For the first time, a model of the mouse TCRβ is presented to an extent which enabled the evaluation of the Convergent Recombination Hypothesis (CRH) comprehensively at a peta-scale level on a single GPU. Understanding the recombination process will allow scientists to better determine the likelihood of transplant rejections, immune system responses to foreign antigens and cancers, and plan treatments based on the genetic makeup of a given patient.

The sewing operation is an integral component of both Geometric Function Theory and Conformal Field Theory and in this thesis we explore the interplay between the two fields. We will first generalize Huang's Geometric Sewing Equation to the quasi-symmetric case. That is, given specific maps g(z) and f^{-1}(z), we show the existence of the sewing maps F_{1}(z) and F_{2}(z). Second, we display an algebraic procedure using convergent matrix operations showing that the coefficients of the Conformal Welding Theorem maps F(z) and G(z) are dependent on the coefficients of the map phi(z). We do this for both the analytic and quasi-symmetric cases, and it is done using a special block/vector decomposition of a matrix representation called the power matrix. Lastly, we provide a partial result: given specific maps g(z) and f^{-1}(z) with analytic extensions, as well as a particular analytic map phi(z), it is possible to provide a method of determining the coefficients of the complementary maps.

La bioactivité des chitooligosaccharides semble dépendre des degrés de Nacétylation et de polymérisation ainsi que de la distribution des unités répétitives D-glucosamine et N-acétyl-D-glucosamine. Afin de préparer des structures parfaitement définies, nous avons développé une nouvelle méthode basée sur la synthèse chimique totale d’oligosaccharides pouvant être décrite en trois étapes :1- préparation de quatre monosaccharides jouant le rôle de donneurs et accepteurs de GlcN et GlcNAc2- formation des oligosaccharides protégés suite à la réaction de couplage d’un donneur de GlcN/GlcNAc avec un accepteur de GlcN/GlcNAc3- suppression des groupes protecteurs permettant l’obtention des chitooligosaccharides cibles.Un avantage important de cette stratégie vient de sa convergence. Ainsi, chaque structure protégée de chitooligosaccharide peut être convertie en un nouveau donneur ou accepteur de glycosyle par modification chimique, conduisant ensuite aux chitooligosaccharides de plus haut DP. / Bioactivity of chitooligosaccharides seems to depend on their degrees of Nacetylationand polymerisation but also the sequence of the D-glucosamine and Nacetyl-D-glucosamine units. To prepare well defined structures, we have developeda new method based on the total chemical synthesis of oligosaccharides describedin three stages:1- preparation of four monosaccharides playing the role of donors and acceptors ofboth GlcN and GlcNAc2- formation of protected oligosaccharides by the coupling reaction of oneGlcN/GlcNAc donor with one GlcN/GlcNAc acceptor3- removal of protecting groups to generate targeted chitooligosaccharidesAn important advantage of this strategy is based on its convergence. Thus, eachprotected chitooligosaccharide structure can be converted into a new glycosyldonor or acceptor, thanks to chemical modifications, and then leads to higher DPchitooligosaccharides

The advent and massification of the ICTs and the widespread use of internet have transformed the way in which traditional media such as ratio and television communicate with the audience, not only because of the technological shift itself, but because of the convergence culture undergoing as a result of the new relationships taking place online.   Particularly, we wonder how the news’ organizations based in traditional media are adapting to these changes. Our assumption is that, although the news’ organizations have understood and are currently using the online technologies to present their information in varied ways with the intention to reach a broader audience and to generate higher levels of engagement, still much needs to be analyzed on how the contents are handled through each particular online platform.   Along this study, we propose to introduce the rationale of Nation Branding from a Cultural/Critical perspective as a tool to analyze how transnational news organizations present their contents, since, even when their purpose might not be to carry out directly a Nation Branding strategy, they might be falling into the use of certain features of the Nation Branding logics.   In order to perform this analysis, we explore, from a reductionist approach, the ways in which the English section of Radio Sweden International (a branch of Sveriges Radio, the public radio service in Sweden) has developed its online strategy, trying to identify: 1) whether Radio Sweden International is appropriating the logics of Nation Branding in the way they present their information; 2) if the online strategy of Radio Sweden International is oriented (either directly or indirectly) to build and/or enhance the “Brand Sweden”; and 3) the ways in which Radio Sweden International uses each specific digital platform in its online strategy.   We collected 1893 elements across the Twitter account (760), the news’ website (620), the podcasts (422), and the Facebook page (91) of Radio Sweden International, which were submitted to the classifications of the Nation Branding model known as “Anholt’s hexagon”. What we found was that, although 70.4% of the elements do fit within Anholt’s hexagon, 29.6% of the elements did not fit, these last elements corresponding to Domestic News and Self-Promotion of the organization, reason why a new classification of these elements was due, giving as a result 9 new categories of information different from Anholt’s model.   As a result of our empirical study, we concluded that there are indeed similarities between the way in which Radio Sweden International presents its information, and the form in which the Cultural/Critical developing perspective of Nation Branding proposes how the nation communicates within the convergent, global and networked society. Although Radio Sweden International does not have the direct task of promoting the image of Sweden outside the country, the ways in which this organization presents its information and uses the different online platforms can be related to the way in which Nation Branding intends to construct the image of the country both, inside and outside Sweden.

The sewing operation is an integral component of both Geometric Function Theory and Conformal Field Theory and in this thesis we explore the interplay between the two fields. We will first generalize Huang's Geometric Sewing Equation to the quasi-symmetric case. That is, given specific maps g(z) and f^{-1}(z), we show the existence of the sewing maps F_{1}(z) and F_{2}(z). Second, we display an algebraic procedure using convergent matrix operations showing that the coefficients of the Conformal Welding Theorem maps F(z) and G(z) are dependent on the coefficients of the map phi(z). We do this for both the analytic and quasi-symmetric cases, and it is done using a special block/vector decomposition of a matrix representation called the power matrix. Lastly, we provide a partial result: given specific maps g(z) and f^{-1}(z) with analytic extensions, as well as a particular analytic map phi(z), it is possible to provide a method of determining the coefficients of the complementary maps.

Previous research has demonstrated that individuals with a dual diagnosis often engage in challenging behavior as a means to fulfil their needs and wants. Functional behavioral assessments (FBA) are a way of evaluating these behaviors and creating effective interventions to reduce them and increase socially appropriate alternative behaviors. The present study assessed the convergent validity for three types of FBAs, including the Questions About Behavioral Function (QABF) questionnaire, trial-based functional analysis, and traditional functional analysis, for three adults with a dual diagnosis within a day program setting. Results found correspondence between two forms of assessments, the trial-based functional analysis and traditional functional analysis, for one out of the three subjects. Due to a lack of engagement in the targeted behavior for the other two subjects, results were inconclusive. Results of the QABF did not match those of the functional analyses for any of the subjects, suggesting that the assessment should be used with caution. The trial-based functional analysis may be a viable tool for assessing function for the challenging behavior of adults with a dual diagnosis, although it should not be used as a replacement for the traditional functional analysis.

[pt] Utiliza-se a variável de similaridade proposta por L. Crocco para transformar as equações da camada limite, hidrodinâmica e térmica no escoamento laminar bi-dimensional de um fluido com propriedades fisicas constantes em um canal convergente. As equações de conservação de massa, momentum e energia, que formam um sistema de três equações diferenciais parciais não lineares são modificadas num novo sistema composto de equações diferenciais ordinárias. Estes escoamentos, que admitem soluções similares são resolvidos e apresentam-se soluções para várias combinações dos parâmetros envolvidos. Na solução destes casos considera-se inclusive o efeito da função dissipação. Para alguns dos resultados obtidos no presente trabalho foi possível comparar com soluções existentes na literatura especializada, e uma excelente concordância foi observada. Entre os resultados apresentados, destacam-se expressões para o número de Nusselt local como função dos números de Prandtl e de Reynolds. / [en] The similarity variable proposed by L.Crocco is employed in this work to transform the boundary layer equations for the constant-property, two dimensional, laminar flow in a convergent channel. The governing equations (conservation of mass, momentum and energy) constitute a set of three non-linear partial differential equations. These equations are transformed into a simpler set of ordinary differential equations. Solutions of this transformed set are presented for several combinations of the relevant parameters. Among the effects studied in the heat generation due to viscous forces. When possible, comparisions with available results were made, and an excellent agreement was observed. Among the results presented, are of special practical interest the expressions for the local Nusselt number as a function of the Prandtl and Reynolds numbers.

As metaloproteases AAA/FtsH são componentes chave do controle da qualidade das proteínas inseridas nas membranas de mitocôndrias e cloroplastos. Em Arabidopsis thaliana, as proteases FtsH presentes nas membranas dos tilacóides formam um complexo heterohexamérico composto pelas subunidades FtsH1/FtsH5 (tipo A) e FtsH2/FtsH8 (tipo B). Este complexo está envolvido na reciclagem de proteínas foto-danificadas, especialmente da proteína D1, centro de reação do PSII. Algumas linhas de evidências indicam ainda que existe um limiar de concentração das proteases FtsH, necessário para a correta formação e desenvolvimento dos cloroplastos. Apesar da extensiva caracterização genética e molecular das proteases FtsH, o mecanismo regulatório do complexo FtsH dos cloroplastos não foi totalmente elucidado até o momento, contudo existem evidências de que a sua ativação pode estar relacionada a alta incidência luminosa e a outras condições de estresse. A presença de fatores proteicos auxiliares, foi testada como hipótese alternativa por nosso grupo, através do uso da protease FtsH5 como isca em um ensaio de duplo híbrido de leveduras. Este ensaio identificou uma proteína interagente putativa, nomeada FIP (FtsH5 Interacting Protein), a qual comprovadamente interage com FtsH5 e está localizada nas membranas dos tilacóides. De modo a investigar o papel regulatório putativo de FIP sobre a atividade do complexo FtsH, nós analisamos os padrões de expressão em uma ampla gama de condições de estresse a partir de dados públicos de microarranjos de DNA. Os perfis de expressão indicam que FIP pode ser um regulador negativo da atividade do complexo. Os resultados também sugerem que o complexo pode estar envolvido na resposta do cloroplasto a diferentes tipos de condições de estresse. O estudo da história evolutiva das proteínas interagentes FtsH5 e FIP evidenciou que as sequências homólogas a FIP são encontradas exclusivamente em musgos e plantas superiores, sugerindo assim que a origem de FIP pode estar relacionada a colonização terrestre. Todos os genes codificantes das proteases FtsH do complexo foram usados como \"query\" na busca por sequências homólogas, permitindo a classificação das proteases FtsH nos tipos A e B por inferência filogenética Bayesiana. Análises filogenéticas Bayesianas também foram feitas para FIP e as proteases FtsH tipos A e B, independentemente. A análise Mirrortree suportou a existência de coevolução entre FIP e as proteases FtsH tipo A. Por outro lado, nenhuma correlação foi encontrada entre FIP e as proteases FtsH tipo B, o que corrobora nossas observações experimentais anteriores. Além disso, o agrupamento portador de homólogos FIP pôde ser recuperado em uma filogenia mais completa das proteases FtsH do tipo A. Análises subsequentes mostraram que ambas as proteínas interagentes estão extensivamente sobre seleção negativa e que proteases FtsH tipo A são bastante conservadas, principalmente nos seus domínios internos. / Eukaryotic AAA/FtsH metalloproteases display a key role in the protein quality control of membrane-inserted proteins in mitochondria and chloroplasts. In Arabidopsis thaliana, chloroplast thylakoidal membranes FtsH proteases form a heterohexameric complex made by FtsH1/FtsH5 (type A) and FtsH2/FtsH8 (type B) subunits. This complex is involved in protein turnover of photo-damaged proteins, in particular the D1 protein at the PSII reaction center. Several lines of evidence also indicate that a FtsH threshold level is necessary for the proper formation and development of chloroplasts. Despite extensive genetic and molecular characterization of the FtsH proteases, the regulatory mechanism of the FtsH complex in chloroplasts has not yet been fully elucidated, however, there are evidences that its activation might be related to high light incidence and other stress conditions. The presence of auxiliary protein factors, as an alternative hypothesis, was tested by our group, through the use of the protease FtsH5 as bait in a yeast two-hybrid assay. This essay identified a putative interacting protein named FIP (FtsH5 Interacting Protein), which has been proved to interact with FtsH5 and be located at the thylakoid membranes. In order to investigate a putative regulatory role of FIP on FtsH complex activity, we analyzed gene expression patterns in a wide range of stress conditions from public DNA microarray data. The expression profiles indicate that FIP could be a negative regulator of the FtsH complex activity. The results also suggest that the complex may be involved in the chloroplast response to different types of stress conditions. In order to shed some light on the evolutionary history of FtsH5 and FIP interacting proteins, we have shown that FIP\'s homologous sequences were exclusively found in mosses and higher plants, suggesting that FIP origin might be related to the plant terrestrial colonization. All Arabidopsis FtsH complex-encoding genes were used as \"query\" sequences in search for homologous sequences, allowing us to classify the FtsH proteases in type A and B by Bayesian phylogenetic inference. Bayesian phylogenetic analyses were also run for FIP and FtsH types A and B proteases, independently. Mirrortree analysis supported coevolution between FIP and type A FtsH proteases. On the other hand, no correlation was found between FIP and type B FtsH homologues, which support our previous experimental observations. In addition, the FIP bearing cluster could be recovered in a more complete type A FtsH phylogeny. Subsequent analyzes have shown that both interacting proteins are extensively under negative selection and that type A FtsH are very conserved, mainly in its inner domains.

Executive functioning skills are paramount to our ability to purposefully and successfully mediate our actions within our day-to-day environment. Dysfunction of the executive system can result in a multitude of behavioral manifestations in all stages of life. Increasing evidence supports the use of rating scales to obtain a more comprehensive and ecologically valid understanding of an individual’s executive functioning. The current thesis involves two articles examining the use of behavioral rating scales in the assessment of executive functions. Study 1: In response to a recent proliferation of executive functions rating scales, this article reviews and discusses currently available scales for the assessment of executive functions across the lifespan. Study 2: This study derived an executive functions screener from the Behavioral Assessment System for Children (BASC-2-SRP-COL) for use in young adults and evaluated it against a well-known executive function rating scale (the Behavior Rating Inventory of Executive Function-Adult Version). / Graduate / 0622 / 0632 / eduggan@uvic.ca