HUMAN GENOME VARIATIONS AND EVOLUTION WITH A FOCUS ON THE ANALYSIS OF TRANSPOSABLE ELEMENTS

Genome sequence varies in numerous ways among individuals although the gross architecture is fixed for all humans. Retrotransposons create one of the most abundant structural variants in the human genome and are divided in many families, with certain members in some families, e.g., L1, Alu, SVA, and HERV-K, remaining active for transposition. Along with other types of genomic variants, retrotransponson-derived variants contribute to the whole spectrum of genome variants in humans. With the advancement of sequencing techniques, many human genomes are being sequenced at the individual level, fueling the comparative research on these variants among individuals. In this thesis, the evolution and functional impact of structural variations is examined primarily focusing on retrotransposons in the context of human evolution. The thesis comprises of three different studies on the topics that are presented in three data chapters. First, the recent evolution of all human specific AluYb members, representing the second most active subfamily of Alus, was tracked to identify their source/master copy using a novel approach. All human-specific AluYb elements from the reference genome were extracted, aligned with one another to construct clusters of similar copies and each cluster was analyzed to generate the evolutionary relationship between the members of the cluster. The approach resulted in identification of one major driver copy of all human specific Yb8 and the source copy of the Yb9 lineage. Three new subfamilies within the AluYb family – Yb8a1, Yb10 and Yb11 were also identified, with Yb11 being the youngest and most polymorphic. Second, an attempt to construct a relation between transposable elements (TEs) and tandem repeats (TRs) was made at a genome-wide scale for the first time. Upon sequence comparison, positional cross-checking and other relevant analyses, it was observed that over 20% of all TRs are derived from TEs. This result established the first connection between these two types of repetitive elements, and extends our appreciation for the impact of TEs on genomes. Furthermore, only 6% of these TE-derived TRs follow the already postulated initiation and expansion mechanisms, suggesting that the others are likely to follow a yet-unidentified mechanism. Third, by taking a combination of multiple computational approaches involving all types of genetic variations published so far including transposable elements, the first whole genome sequence of the most recent common ancestor of all modern human populations that diverged into different populations around 125,000-100,000 years ago was constructed. The study shows that the current reference genome sequence is 8.89 million base pairs larger than our common ancestor’s genome, contributed by a whole spectrum of genetic mechanisms. The use of this ancestral reference genome to facilitate the analysis of personal genomes was demonstrated using an example genome and more insightful recent evolutionary analyses involving the Neanderthal genome. The three data chapters presented in this thesis conclude that the tandem repeats and transposable elements are not two entirely distinctly isolated elements as over 20% TRs are actually derived from TEs. Certain subfamilies of TEs themselves are still evolving with the generation of newer subfamilies. The evolutionary analyses of all TEs along with other genomic variants helped to construct the genome sequence of the most recent common ancestor to all modern human populations which provides a better alternative to human reference genome and can be a useful resource for the study of personal genomics, population genetics, human and primate evolution.

Metaphilosophy and educating: Stephen C. Pepper's selectivism as a basis for educational excellence

Atheory of educating is always derived from philosophical tenets. In Western society these tenets are concerned primarily with the provision, maintenance and evolution of knowledge for use by future generations. The provision of knowledge for future generations is for the purpose of ensuring cultural and biological survival. Essentially this provision involves two major criteria: first, that only that knowledge which has been judged to be exce11 ent shou1d be passed on and, second, in add it ion to providing knowledge claims, the evidence for knowledge claims must also be extended in order to fully enrich meaning for an individual involved in a learning experience. Embedded in such a theory of educating are a concept of educational excellence and a concept of the provision of evidence for knowledge claims. This thesis applied the contributions of metaphilosophy to the concepts of educational excellence and the provision of evidence. The metaphilosophy of Stephen C. Pepper was examined for its contributions to a theory of educating and a concept of educational excellence. Metaphilosophy is concerned with making knowledge meaningful. It is a subject matter which may be studied in and of itself and it is a method for acquiring meaning by interpreting knowledge. Historically people have interpreted the knowledge of the world from basically four adequate world views which Pepper termed formism, mechanism, contextual ism and organicism. He later proposed a fifth world view which he termed selectivism. In this thesis these world views were shown to contribute in a variety of ways to educational excellence, most particularly as they allow for interpretations and analysis of evidence about knowledge claims. Selecti vismwas examined in depth and was shown to contribute to educational excellence in two major ways; first, as a world hypothesis which offers an interpretation of the evidence for knowledge claims and, second, as a metahypothesis which provides knowledge about the nature of knowledge. Finally the importance of metaphilosophy in contributing to cultural survival was demonstrated in a discussion of the potential impact of selectivism on a theory of educating and educational excellence.

Drumming toward communitas : a case study of facilitated recreational music making and the Arthurian method

The phenomenon of communitas has been described as a moment 'in and out of time' in which a collective of individuals may be experienced by one as equal and individuated in an environment stripped of structural attributes (Turner, 1 969). In these moments, emotional bonds form and an experience of perceived 'oneness' and synergy may be described. As a result of the perceived value of these experiences, it has been suggested by Sharpe (2005) that more clearly understanding how this phenomenon may be purposefully facilitated would be beneficial for leisure service providers. Consequently, the purpose of this research endeavor was to examine the ways in which a particular leisure service provider systematically employs specific methods and sets specific parameters with the intention of guiding participants toward experiences associated with communitas or "shared spirit" as described by the organization. A qualitative case study taking a phenomenological approach was employed in order to capture the depth and complexity of both the phenomenon and the purposefiil negotiation of experiences in guiding participants toward this phenomenon. The means through which these experiences were intentionally facilitated was recreational music making in a group drumming context. As such, an organization which employs specific methods of rhythm circle facilitation as well as trains other facilitators all over the world was chosen purposely for their recognition as the most respectable and credible in this field. The specific facilitator was chosen based on high recommendation by the organization due to her level of experience and expertise. Two rhythm circles were held, and participants were chosen randomly by the facilitator. Data was collected through observation in the first circle and participant- observation in the second, as well as through focus groups with circle participants. Interviews with the facilitator were held both initially to gain broad understanding of concepts and phenomenon as well as after each circle to reflect on each circle specifically. Data was read repeatedly to drawn out patterns which emerged and were coded and organized accordingly. It was found that this specific process or system of implementation lead to experiences associated with communitas by participants. In order to more clearly understand this process and the ways in which experiences associated with communitas manifest as a result of deliberate facilitator actions, these objective facilitator actions were plotted along a continuum relating to subjective participant experiences. These findings were then linked to the literature with regards to specific characteristics of communitas. In so doing, the intentional manifestation of these experiences may be more clearly understood for ftiture facilitators in many contexts. Beyond this, findings summarized important considerations with regards to specific technical and communication competencies which were found to be essential to fostering these experiences for participants within each group. Findings surrounding the maintenance of a fluid negotiation of certain transition points within a group rhythm event overall were also highlighted, and this fluidity was found to be essential to the experience of absorption and engagement in the activity and experience. Emergent themes of structure, control, and consciousness have been presented as they manifested and were found to affect experiences within this study. Discussions surrounding the ethics and authenticity of these particular methods and their implementation has also been generated throughout. In conclusion, there was a breadth as well as depth of knowledge found in unpacking this complex process of guiding individuals toward experiences associated with communitas. The implications of these findings contribute in broadening the current theoretical as well as practical understanding as to how certain intentional parameters may be set and methods employed which may lead to experiences of communitas, and as well contribute a greater knowledge to conceptualizing the manifestation of these experiences when broken down.

The shifting terrain of feminist theory and activism : university-based women's centres and third wave feminism

This thesis, based on the results of an organizational ethnography of a university-based feminist organization in Southern Ontario (the Centre), traces how third wave feminism is being constituted in the goals, initiatives, mandate, organizational structure, and overall culture of university-based feminist organizations. I argue that, from its inception, the meanings and goals of the Centre have been contested through internal critique, reflection, and discussion inspired by significant shifts in feminist theory that challenge the fundamental principles of second wave feminism. I identify a major shift in the development and direction of the Centre that occurs in two distinct phases. The first phase of the shift occurs with the emergence of an antioppression framework, which broadens the Centre's mandate beyond gender and sexism to consider multiple axes of identity and oppression that affect women's lives. The second phase of this shift is characterized by a focus on (trans) inclusion and accessibility and has involved changing the Centre's name so that it is no longer identified as a women's centre in order to reflect more accurately its focus on mUltiple axes of identity and oppression. Along with identifying two phases of a major shift in the direction of the Centre, I trace two discourses about its development. The dominant discourse of the Centre's development is one of progress and evolution. The dominant discourse characterizes the Centre as a dynamic feminist organization that consistently strives to be more inclusive and diverse. The reverse discourse undermines the dominant discourse by emphasizing that, despite the Centre's official attempts to be inclusive and to build diversity, little has actually changed, leaving women of colour marginalized in the Centre's dominant culture of whiteness. This research reveals that, while many of their strategies have unintended (negative) consequences, members of the Centre are working to build an inclusive politics of resistance that avoids the mistakes of earlier feminist movements and organizations. These members, along with other activists, actively constitute third wave feminism in a process that is challenging, contradictory, and often painful. A critical analysis of this process and the strategies it involves provides an opportunity for activists to reflect on their experiences and develop new strategies in an effort to further struggles for social justice and equity.

National energy policies of the Federal Republic of Germany and Canada in the 1970s and 1980s: are economic and/or environmental concerns responsible for change?

The thesis presents a comparison of the national energy policies of the Federal Republic of Germany and Canada from 1973 until the late 1980s. The purpose of this paper is to analyze whether economic and/or environmental concerns were responsible for changes in the· West-German and Canadian national energy policies. Furthermore, the feasibility of implementing a soft energy path in West-Germany and Canada is examined. For better comprehension of the policy-making process and implemented changes in the national energy policies of the two states, the West-German and Canadian parliamentary systems and the political cultures were compared. For the analysis, several events with international impact were taken as guidelines. Furthermore, based on statistical data, the West-German and Canadian energy production and consumption were analyzed. With reference to these results the degree of the de facto changes in the national energy policies were analyzed. In addition, the thesis discusses the possibilities which a soft energy path offers to both national governments to renounce themselves from the dependencies on a few energy resources. The thesis reveals that changes in the West-German and Canadian national energy policies, in their energy production and consumption are correlated to various world events. In particular, governmental reponses security of energy supply by the two international oil crises of 1973 and 1979/1980 demonstrate that changes in the West-German and Canadian national energy policies were implemented in reaction to economic concerns than environmental ones. With the policies "away from oil" and "off oil", the West-German and Canadian government implemented the i i substitution of oil through various diverse energy supply resources. However, energy savings concepts and policies were initiated through the first oil crisis in 1973. The world recessions in 1975 and 1982 had no 'profound impacts on the agenda of West-German and Canadian energy policies. As a consequence of the stagnation or the negative growth of the world economic market, changes in their energy production and consumption can be perceived. However, the West-German and Canadian energy production and consumption intensified with the augmentation of the world economy. During the period of study, environmental concerns were taken into account in the energy policy agendas of the Federal Republic of Germany and Canada but they were not of primary concern. wi thin the decade of. the 1980s notably more environmental considerations were taken into account in the energy policies of the two states. The two nuclear reactor accidents in 1979 and 1986 sharpened to various degrees West-German and Canadian public discourse of present energy supply mix and attitude towards energy production and consumption. The statistical data reflects yet no changes in the energy policies in regard to the position of nuclear power. However, in the next several years possible changes can be observed through statistical data, because the planning, the construction and possible phase out of nuclear power requires several years. Finally, the thesis reveals that the implementation of a soft energy path requires profound changes in the consumer behaviour. As several studies indicate, a soft energy path is technological and economically feasible for the Federal Republic of Germany and Canada, its implementation remains to be a political decision.

Enhancing teaching and learning speech acts: action research of Japanese as a foreign language /

This action research observes a second year Japanese class at a university where foreign language courses are elective for undergraduate students. In this study, using the six strategies to teach Japanese speech acts that Ishihara and Cohen (2006) suggested, I conducted three classes and analyzed my teaching practice with a critical friend. These strategies assist learners toward the development of their understanding of the following Japanese speech acts and also keep the learners to use them in a manner appropriate to the context: (I) invitation and refusal; (2) compliments; and (3) asking for a permission. The aim of this research is not only to improve my instruction in relation to second language (L2) pragmatic development, but also to raise further questions and to develop future research. The findings are analyzed and the data derived from my journals, artifacts, students' work, observation sheets, interviews with my critical friend, and pretests and posttests are coded and presented. The analysis shows that (I) after my critical friend encouraged my study and my students gave me some positive comments after each lesson, I gained confidence in teaching the suggested speech acts; (2) teaching involved explaining concepts and strategies, creating the visual material (a video) showing the strategies, and explaining the relationship between the strategy and grammatical forms and samples of misusing the forms; (3) students' background and learning styles influenced lessons; and (4) pretest and posttests showed that the students' Icvel of their L2 appropriate pragmatics dramatically improved after each instruction. However, after careful observation, it was noted that some factors prevented students from producing the correct output even though they understood the speech act differences.

A sequential analysis of therapist scaffolding and child concept formation in narrative therapy

Narrative therapy is a postmodern therapy that takes the position that people create self-narratives to make sense of their experiences. To date, narrative therapy has compiled virtually no quantitative and very little qualitative research, leaving gaps in almost all areas of process and outcome. White (2006a), one of the therapy's founders, has recently utilized Vygotsky's (1934/1987) theories of the zone of proximal development (ZPD) and concept formation to describe the process of change in narrative therapy with children. In collaboration with the child client, the narrative therapist formalizes therapeutic concepts and submits them to increasing levels of generalization to create a ZPD. This study sought to determine whether the child's development proceeds through the stages of concept formation over the course of a session, and whether therapists' utterances scaffold this movement. A sequential analysis was used due to its unique ability to measure dynamic processes in social interactions. Stages of concept formation and scaffolding were coded over time. A hierarchical log-linear analysis was performed on the sequential data to develop a model of therapist scaffolding and child concept development. This was intended to determine what patterns occur and whether the stated intent of narrative therapy matches its actual process. In accordance with narrative therapy theory, the log-linear analysis produced a final model with interactions between therapist and child utterances, and between both therapist and child utterances and time. Specifically, the child and youth participants in therapy tended to respond to therapist scaffolding at the corresponding level of concept formation. Both children and youth and therapists also tended to move away from earlier and toward later stages of White's scaffolding conversations map as the therapy session advanced. These findings provide support for White's contention that narrative therapists promote child development by scaffolding child concept formation in therapy.

Ontological constructivism : Negri and the philosophical foundations of a future communism

As we find in Empire and Multitude, Antonio Negri's political project IS a thoroughly Marxist analysis and critique of global or late capitalism. By modifying and updating Marx's conceptual tools, he is able to provide a clear account of capitalism's processes, its expanding reach, and the revolutionary potential that functions as its motor. By turning to Negri's philosophical works, however, we find that this political analysis is founded on a series of concepts and theoretical positions. This paper attempts to clarify this theoretical foundation, highlighting in particular what I term "ontological constructivism" - Negri's radical reworking of traditional ontology. Opposing the long history of transcendence in epistemology and metaphysics (one that stretches from Plato to Kant), this reworked ontological perspective positions individuals - not god or some other transcendent source - as the primary agents responsible for molding the ontological landscape. Combined with his understanding of kairos (subjective, immeasurable time), ontological constructivism lays the groundwork for opposing transcendence and rethinking contemporary politics.

Fitness to stand trial : how discourses of rationality, reasonableness and culpability inform the law and psychiatry to create standards of normal

The objective of this thesis is to demonstrate the importance of the concepts of rationality, reasonableness, culpability and autonomy that inform and support our conception of both the person and the punishable subject. A critical discourse analysis tracing these concepts through both the law and psychological tools used to evaluate the fitness of a person reveals that these concepts and their implied values are inconsistently applied to the mentally disordered who come into conflict with the law. I argue that the result of this inconsistency compromises a person's autonomy which is a contradiction to this concept as a foundational principle of the law. Ultimately, this thesis does not provide a solution to be employed in policy making, but its analysis leaves open possibilities for further exploration into the ways legal and social justice can be reconciled.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Metaphorical Interpretation: Measuring and Facilitating Growth.

Abstract A total of 378 grade 9 students participated in this study to address the problem that although metaphorical literacy and thought are expected and necessary for success in junior and senior high school and beyond, metaphorical concepts and thought are not required to be explicitly taught to these students. The students were from 20 different classes from 4 levels: English language learners (ELL), school to work (SSTW), applied, and academic. All were from 7 secondary schools within a board in southern Ontario. Nine classes made up the control group and 11 classes made up the treatment group. All classes were given 3 pretests and the posttest. The treatment group was given Socratic lessons and direct instruction on metaphorical thought and expressions during 1 semester and in conjunction with their other classroom material. The pretest scores (TOLD, Peabody, preproverbs concrete, and preproverbs abstract) did not reveal any effect of gender, but the academic students had higher scores than the applied students. The SSTW student results are more variable: (a) for the TOLD test, SSTW scores were between those of the academic and applied students; (b) for Peabody scores, SSTW students’ scores are the same as academic and are greater than applied; (c) for preproverbs concrete and preproverbs abstract, the SSTW scores are not different from the applied scores. The postproverbs concrete and postproverbs abstract scores for the treatment groups also showed no effect of gender but revealed that all students who received the treatment did better on their post scores. The positive changes of the treatment group illustrate a measured movement from literal understanding to abstract understanding using direct Socratic instruction and proverbs as a medium.

Variability in the Insect and Plant Adhesins, Mad1 and Mad2, within the Fungal Genus Metarhizium Suggest Plant Adaptation as an Evolutionary Force

Several species of the insect pathogenic fungus Metarhizium are associated with certain plant types and genome analyses suggested a bifunctional lifestyle; as an insect pathogen and as a plant symbiont. Here we wanted to explore whether there was more variation in genes devoted to plant association (Mad2) or to insect association (Mad1) overall in the genus Metarhizium. Greater divergence within the genus Metarhizium in one of these genes may provide evidence for whether host insect or plant is a driving force in adaptation and evolution in the genus Metarhizium. We compared differences in variation in the insect adhesin gene, Mad1, which enables attachment to insect cuticle, and the plant adhesin gene, Mad2, which enables attachment to plants. Overall variation for the Mad1 promoter region (7.1%), Mad1 open reading frame (6.7%), and Mad2 open reading frame (7.4%) were similar, while it was higher in the Mad2 promoter region (9.9%). Analysis of the transcriptional elements within the Mad2 promoter region revealed variable STRE, PDS, degenerative TATA box, and TATA box-like regions, while this level of variation was not found for Mad1. Sequences were also phylogenetically compared to EF-1a, which is used for species identification, in 14 isolates representing 7 different species in the genus Metarhizium. Phylogenetic analysis demonstrated that the Mad2 phylogeny is more congruent with 59 EF-1a than Mad1. This would suggest that Mad2 has diverged among Metarhizium lineages, contributing to clade- and species-specific variation, while it appears that Mad1 has been largely conserved. While other abiotic and biotic factors cannot be excluded in contributing to divergence, these results suggest that plant relationships, rather than insect host, have been a major driving factor in the divergence of the genus Metarhizium.

Affect, ontology, and pedagogy: An autoethnographic study on student-teacher relationships

In studying affect within the realm of student-teacher relationships my thesis project use the concept of “affect” as composed by Baruch Spinoza (1992, 2007). I focus specifically on how Deleuze (1988) interprets and implements the term within his own philosophy, as well as on Antonio Negri’s (2011, 1991) work on Spinoza including his and Michael Hardt’s (2000, 2004, 2009) more recent works. This thesis will explore Spinoza’s affect within the discourse of Affective Pedagogy and Critical Pedagogy while remaining committed to a Spinoizist ontology as outlined by Deleuze (1988). I used artefacts from my past experiences as a student and teacher to produce evocative writing pieces which act as affective continuances of my past experiences as a student, student-teacher, and teacher, and the relationships of affect that composed them. This project used these artefacts and the writings they produced as sites of intensity that are carried through from traces, to evocative thresholds, to concepts, and finally into analysis.