Master of Science / Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively incorporate multi-disciplinary analyses and synthesize results from various sources when answering real-life questions. In this thesis, a novel web-based phylogeny reconstruction system with a real-time interactive environment, called Qphyl (short for quartet-based phylogenetic analysis) is introduced. The Qphyl system uses a new interactive approach to enable biologists to greatly improve the final results through effectively dynamic interaction with the computation, e.g., to move the computation back and forth to different stages so users can check the intermediate results, compare results from different methods and carry out certain manual refinements using their biological domain-specific knowledge in the decision making on how a tree should be reconstructed. Currently the alpha version of this web-based interactive system has been released and accessible through the URL: http://ww-test.it.usyd.edu.au/sogrid/qphyl/.

Master of Science / Phylogenetic tree reconstruction is a prominent problem in computational biology. Currently, all computational methods have their limitations and work well only for simple problems of small size. No existing method can guarantee that trees constructed for real-world problems are true phylogenetic trees for large and complex problems mainly because the existing computational models are not very biologically realistic. It has become a serious issue for many important real-life applications which often desire accurate results from phylogenetic analysis. Thus, it is very crucial to effectively incorporate multi-disciplinary analyses and synthesize results from various sources when answering real-life questions. In this thesis, a novel web-based phylogeny reconstruction system with a real-time interactive environment, called Qphyl (short for quartet-based phylogenetic analysis) is introduced. The Qphyl system uses a new interactive approach to enable biologists to greatly improve the final results through effectively dynamic interaction with the computation, e.g., to move the computation back and forth to different stages so users can check the intermediate results, compare results from different methods and carry out certain manual refinements using their biological domain-specific knowledge in the decision making on how a tree should be reconstructed. Currently the alpha version of this web-based interactive system has been released and accessible through the URL: http://ww-test.it.usyd.edu.au/sogrid/qphyl/.

Yes / Alzheimer’s disease irrevocably challenges a person’s capacity to communicate with others. Earlier research on these challenges focused on the language disorders associated with the condition and situated language deficit solely in the limitations of a person’s cognitive and semantic impairments. This research falls short of gaining insight into the actual interactional experiences of a person with Alzheimer’s and their family. Drawing on a UK data set of 70 telephone calls recorded over a two-and-a-half year period (2006–2008) between one elderly woman affected by Alzheimer’s disease, and her daughter and son-in-law, this paper explores the role which communication (and its degeneration) plays in family relationships. Investigating these interactions, using a conversation analytic approach, reveals that there are clearly communicative difficulties, but closer inspection suggests that they arise due to the contingencies that are generated by the other’s contributions in the interaction. That being so, this paper marks a departure from the traditional focus on language level analysis and the assumption that deficits are intrinsic to the individual with Alzheimer’s, and instead focuses on the collaborative communicative challenges that arise in the interaction itself and which have a profound impact on people’s lives and relationships.

This thesis addresses the question of whether or not online interactional practices are systematically different from interaction in other contexts, particularly spoken interaction. I will establish how the organization of online interaction demonstrates participants orientations to the technological affordances of the online medium. The dataset for the study comprises one-to-one interaction between friends, conducted using the chat application of the social networking site, Facebook. Chat logs and screen capture data were used to analyze how participants engaged in, and managed, their unfolding interaction. The data were analyzed using conversation analysis (CA). CA was developed originally for the analysis of spoken talk, but in this dissertation it provides an empirical basis for comparing Facebook chat and spoken interaction. The thesis demonstrates how CA can be used for analyzing online interaction. The first analytic chapter provides an overview of how participants organize the generic orders of interaction. The findings suggest that participants draw on their knowledge of both spoken and written interaction when managing the particular interactional constraints and affordances of Facebook chat. The second analytic chapter focuses on chat openings, comparing them to openings in spoken interaction. The findings reveal some similarities, but also systematic differences which orient to the design of the chat software. The third analytic chapter examines topic management, including topic-initiation, topic change and the management of simultaneous topics. The findings suggest that the CA categorization of topic-initiating turns could potentially be extended by also analyzing action-orientation and also the epistemic stance displayed. The analysis also reveals remarkable similarities between topic change in spoken interaction and in Facebook chat. Finally in this chapter I show how organizational components of spoken interaction, such as adjacency pairs and tying techniques, are used to manage simultaneous topics. The final analytic chapter focuses on self-repair in Facebook chat. The analysis reveals that self-repairs completed during message construction orient to the same interactional contingencies as self-repairs in spoken interaction. However, the affordances of Facebook chat enable these repairs to be hidden from the recipient. Visible repairs tend to be corrections, with the affordances impacting the sequential placement of such repairs. Finally, I show how participants self-repair in response to the actions of their co-participant. Overall, the findings reveal a number of similarities between the organization of Facebook chat and spoken interaction. The analysis also reveals that participants attend to the technological affordances of Facebook in a variety of ways. Finally, this thesis demonstrates that, while there are differences between the interactional practices of spoken and online written interaction, CA can be used to analyze, and subsequently explain, such differences.

This thesis aims to provide a close analysis of poetry slam in the United Kingdom and United States, using the tools of ethnography and discourse analysis to produce an in-depth account, which is sensitive to the discursively constructed, situated meanings of slam participants. The aim is to explore how slam is understood by its participants, producing a partial ethnography, rather than a definitive history, defence or critique of slam. The thesis is based predominantly on research conducted in four key sites (Bristol and London in the U.K. and Chicago and New York in the U.S.), and considers how slam has been reconstructed in different geographical and social contexts. In addition, this study seeks to highlight issues around: the ways in which artists understand art worlds and their positions within them; the multiple and complex power relations with which art world participants engage; the transient, enduring and virtual communities which art world participants form; the local, translocal and transnational networks which connect these communities and individuals; and the interactions between new/avant-garde and established/dominant art worlds. It is hoped that this analysis will enrich substantially the existing meagre body of research into poetry slam, providing valuable theoretical contributions to the study of art worlds and the social construction of self and relationships. Beyond this, the thesis aims to elucidate a social scientific paradigm which links micro level analyses with macro level social structures and processes, by allying work from multiple theoretical perspectives including those of interactionism, Antonio Gramsci, Pierre Bourdieu and discourse analysis. This paradigm is mobilised to illuminate how slam participants actively construct their identities and negotiate the complex power relations which structure their everyday interactions. In line with the poetic focus of this research, each analytic chapter of this thesis concludes with a haiku. I begin with this thought: Power relations/Are complex navigations/Through interaction.

How do non-vocal practices function within sequences? This thesis addresses silence and gesture in the context of social interaction involving human participants through the framework of conversation analysis (CA) to answer this question. Although it is certainly possible, and indeed common, for gestures and other non-vocal practices to occur during talk, this thesis focuses on those that occur without accompanying talk. In order to understand the role of non-vocal practices in this environment, we must first understand the role of silence (or the absence of talk) in participants’ interactions. How does silence function within the sequential environment? How does context affect how silence and nonvocal practices are treated by participants? If one organisation (or aspect of an organisation) is affected, are all organisations (or aspects of that organisation) affected? I draw on psychological, sociological, and linguistic literature to show why silence and gesture are related in interactional research and how this affects conversation analytic methodology. The work that forms this thesis brings together cross-cultural perspectives and technical advances with respect to silence and non-vocal practices both individually and when they occur together (i.e. non-vocal practices without accompanying talk). I begin with a broad overview of research and theories of gesture and silence before discussing CA as a method and its relationship to silence and non-vocal practices. The empirical studies begin with silence in relation to culture and context and issues in analysing and transcribing silence. I then examine how one sequential environment, in which psychotherapy clients are obligated to respond by orienting to the therapeutic agenda, has a preference structure that is very different from ordinary conversation. In this sequential environment, silence and elaboration are marks of preferred responses rather than dispreferred. The preference structure is made particularly visible through accountability that becomes relevant when a client’s response is produced promptly following the therapist’s overtly therapeutic action. Silence in this environment contributes Inaction and Silent Action in Interaction 3 to clients’ performance of sincerity and participation in the psychotherapeutic process, and non-vocal practices during longer silences can show that the client remains engaged with the sequence. Many authors have accounted for silences that are not treated by participants as problematic by applying constructs such as ‘continuing states of incipient talk’. This construct, however, is variably used and has not been developed through empirical examination. It does not adequately explain interactions that involve silence or gesture, as I show through a content analysis and systematic review. After recommending that researchers engage with participant orientations in environments that differ from canonical conversations, I describe an environment that is commonly thought of as constituting a ‘continuing state of incipient talk’ – television-watching. I show that contrary to some claims about ‘incipient talk’ environments, although response relevance is relaxed, both sequence organisation and turn-taking are strongly oriented to by participants. Compared to ordinary conversation, television-watching also involves more gestures and other nonvocal practices without accompanying talk. I examine how non-vocal practices without accompanying talk are used in interaction. As responsive actions, gestures can be used without accompanying talk as a resource for doing sensitive interactional work, particularly in places where giving offence might be a concern. Non-vocal practices can also be used in other situations to accomplish sequential actions that could otherwise be spoken. These uses of non-vocal practices create methodological questions for conversation analysis, which has traditionally focused on the talk of participants. By clearly distinguishing between actions and turns (two classic CA concepts) and examining the timing of non-vocal practices, I show that non-vocal practices can have a clearly defined role in sequence organisation. CA can thus be a useful method for examining the entire situation of social interaction, including non-vocal practices.

This thesis is about the resources that speakers can draw on when producing actions, both verbal and non-vocal. It considers how identity categories, gaze and touch can contribute to action in everyday interactions. The study stemmed from an interest in how lesbian identity is made relevant by lesbian speakers in everyday co-present interaction. A corpus of approximately 23.5 hours of video-recordings was gathered: households self-designated as lesbian (including couples, families, and housemates) video recorded some of their everyday interactions (including mealtimes, watching television, and playing board games). Using the tools of Conversation Analysis and working with the video recordings and transcripts of the interactions, several ways of making a lesbian identity relevant through talk were identified. As the analysis progressed, it was found that many references to sexual identity were produced fleetingly; they were not part of or integral to the ongoing talk, and were not taken up as a topic by participants. Rather, this invoking of a participant s sexual identity appears to contribute to a particular action that is being produced. It was found that invokings of other identities, for example relating to occupation, nationality, and race, worked in a similar way, and this is explored in relation to explanations and accounts. Where the first half of the thesis focuses on verbal invokings of identity in relation to action, the second half of the thesis considers some of the non-vocal resources that participants incorporate into their actions. It was found that when launching a topic related to something in the immediate environment, speakers can use gaze to ensure recipiency. Also, when producing potentially face-threatening actions such as teases, reprimands or insults, speakers can use interpersonal touch to mitigate the threat. In addition to showing how identities can be made relevant in everyday interaction, the findings of this thesis highlight the complexity of action design, and that in co-present interaction the physical resources available to participants also need to be taken into account.

Using the theoretical approach of discursive psychology, this thesis examines the interactive uses of mental state talk, in particular the term want , in everyday family interaction. In mainstream cognitive psychology mental state terms are examined as words which signify internal referents. How individuals come to competently participate in social interaction is formulated as a problem of how individual, isolated minds come to understand the contents of other minds. This thesis challenges these individualistic notions and examines notions of wanting as interactionally managed participants concerns. The data are taken from two sources; a set of video recordings taken from a series of fly-on-the-wall documentary programmes which each focus on a particular family and videotapes of mealtimes recorded by three families. Recordings were initially transcribed verbatim and sections related to the emerging themes within the thesis were subsequently transcribed using the Jefferson notation system. These transcripts were then analysed, alongside repeated viewings of the video recordings. The thesis considers a range of analytic themes, which are interlinked via one of the primary research questions, which has been to examine how, and to what end, speakers routinely deploy notions of wanting in everyday talk-in-interaction. A major theme has been to highlight inherent problems with work in social cognition which uses experimental tasks to examine children s Theory of Mind and understanding of desires . I argue that the assumptions of this work are a gross simplification of the meaning wanting for both children and adults. A further theme has been to examine the sequential organisation of directives and requests in both adults and children s talk. Finally, I examine speakers practices for rejecting a proposal regarding their actions and for denying a formulation of their motivations by a co-interactant. The conclusions of the thesis show that expressions of wanting are practical expressions which work within a flow of interactional and deontic considerations and that making claims regarding one s own or others wants is entirely a social matter. I argue that rather than being examined for what they may reveal about the mind , mental state terms may be fruitfully examined as interactional matters.

Within the stream of research on entrepreneurial opportunity there is a school of thought that affords entrepreneurs an agentic role in the creation of opportunities – with opportunities understood as a combination of both product and market innovation. Recently scholars working from this Creative Model have associated the opportunity shaping work of entrepreneurs with sensemaking – a social process in which teams gather information, ascribe meaning, and take action in the face of the uncertainties, which some have said define the context of entrepreneurship. Few, if any, scholars have studied the naturally occurring conversations between entrepreneurial team members as they discuss the information, meaning, and action relevant to their innovation efforts. This dissertation makes a contribution to current understanding of entrepreneurship by capturing the naturally occurring conversations of innovative entrepreneurial teams in action, analyzing these recorded conversations for use of sensemaking language, and comparing the language patterns between teams that achieve different levels of performance.

This thesis focuses on multilocus methods designed to detect single nucleotide polymorphisms (SNPs) that are associated with disease using case-control data. I study multilocus methods that allow for interaction in the regression model because epistasis is thought to be pervasive in the etiology of common human diseases. In contrast, the single-SNP models widely used in genome wide association studies (GWAS) are thought to oversimplify the underlying biology. I consider both pairwise interactions between individual SNPs and modular interactions between sets of biologically similar SNPs. Modular epistasis may be more representative of disease processes and its incorporation into regression analyses yields more parsimonious models. My methodological work focuses on strategies to increase power to detect susceptibility SNPs in the presence of genetic interaction. I emphasize the effect of gene-gene independence constraints and explore methods to relax them. I review several existing methods for interaction analyses and present their first empirical evaluation in a GWAS setting. I introduce the innovative retrospective Tukey score test (RTS) that investigates modular epistasis. Simulation studies suggest it offers a more powerful alternative to existing methods. I present diverse applications of these methods, using data from a multi-stage GWAS on prostate cancer (PRCA). My applied work is designed to generate hypotheses about the functionality of established susceptibility regions for PRCA by identifying SNPs that affect disease risk through interactions with them. Comparison of results across methods illustrates the impact of incorporating different forms of epistasis on inference about disease association. The top findings from these analyses are well supported by molecular studies. The results unite several susceptibility regions through overlapping biological pathways known to be disrupted in PRCA, motivating replication study.