Matching Items (4)
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- All Subjects: digital humanities
- All Subjects: Evolutionary developmental biology
- Creators: Creath, Richard
Description
A central task for historians and philosophers of science is to characterize and analyze the epistemic practices in a given science. The epistemic practice of a science includes its explanatory goals as well as the methods used to achieve these goals. This dissertation addresses the epistemic practices in gene expression research spanning the mid-twentieth century to the twenty-first century. The critical evaluation of the standard historical narratives of the molecular life sciences clarifies certain philosophical problems with respect to reduction, emergence, and representation, and offers new ways with which to think about the development of scientific research and the nature of scientific change.
The first chapter revisits some of the key experiments that contributed to the development of the repression model of genetic regulation in the lac operon and concludes that the early research on gene expression and genetic regulation depict an iterative and integrative process, which was neither reductionist nor holist. In doing so, it challenges a common application of a conceptual framework in the history of biology and offers an alternative framework. The second chapter argues that the concept of emergence in the history and philosophy of biology is too ambiguous to account for the current research in post-genomic molecular biology and it is often erroneously used to argue against some reductionist theses. The third chapter investigates the use of network representations of gene expression in developmental evolution research and takes up some of the conceptual and methodological problems it has generated. The concluding comments present potential avenues for future research arising from each substantial chapter.
In sum, this dissertation argues that the epistemic practices of gene expression research are an iterative and integrative process, which produces theoretical representations of the complex interactions in gene expression as networks. Moreover, conceptualizing these interactions as networks constrains empirical research strategies by the limited number of ways in which gene expression can be controlled through general rules of network interactions. Making these strategies explicit helps to clarify how they can explain the dynamic and adaptive features of genomes.
The first chapter revisits some of the key experiments that contributed to the development of the repression model of genetic regulation in the lac operon and concludes that the early research on gene expression and genetic regulation depict an iterative and integrative process, which was neither reductionist nor holist. In doing so, it challenges a common application of a conceptual framework in the history of biology and offers an alternative framework. The second chapter argues that the concept of emergence in the history and philosophy of biology is too ambiguous to account for the current research in post-genomic molecular biology and it is often erroneously used to argue against some reductionist theses. The third chapter investigates the use of network representations of gene expression in developmental evolution research and takes up some of the conceptual and methodological problems it has generated. The concluding comments present potential avenues for future research arising from each substantial chapter.
In sum, this dissertation argues that the epistemic practices of gene expression research are an iterative and integrative process, which produces theoretical representations of the complex interactions in gene expression as networks. Moreover, conceptualizing these interactions as networks constrains empirical research strategies by the limited number of ways in which gene expression can be controlled through general rules of network interactions. Making these strategies explicit helps to clarify how they can explain the dynamic and adaptive features of genomes.
ContributorsRacine, Valerie (Author) / Maienschein, Jane (Thesis advisor) / Laubichler, Manfred D (Thesis advisor) / Creath, Richard (Committee member) / Newfeld, Stuart (Committee member) / Morange, Michel (Committee member) / Arizona State University (Publisher)
Created2016
Description
This dissertation begins to lay out a small slice of the history of morphological research, and how it has changed, from the late 19th through the close of the 20th century. Investigators using different methods, addressing different questions, holding different assumptions, and coming from different research fields have pursued morphological research programs, i.e. research programs that explore the process of changing form. Subsequently, the way in which investigators have pursued and understood morphology has witnessed significant changes from the 19th century to modern day research. In order to trace this shifting history of morphology, I have selected a particular organ, teeth, and traced a tendril of research on the dentition beginning in the late 19th century and ending at the year 2000. But even focusing on teeth would be impossible; the scope of research on this organ is far too vast. Instead, I narrow this dissertation to investigation of research on a particular problem: explaining mammalian tooth morphology. How researchers have investigated mammalian tooth morphology and what counts as an explanation changed dramatically during this period.
ContributorsMacCord, Katherine (Author) / Maienschein, Jane (Thesis advisor) / Laubichler, Manfred (Thesis advisor) / Laplane, Lucie (Committee member) / Kimbel, William (Committee member) / Creath, Richard (Committee member) / Hurlbut, Benjamin (Committee member) / Arizona State University (Publisher)
Created2017
Description
Elizabeth Grumbach, the project manager of the Institute for Humanities Research's Digital Humanities Initiative, shares methodologies and best practices for designing a digital humanities project. The workshop will offer participants an introduction to digital humanities fundamentals, specifically tools and methodologies. Participants explore technologies and platforms that allow scholars of all skills levels to engage with digital humanities methods. Participants will be introduced to a variety of tools (including mapping, visualization, data analytics, and multimedia digital publication platforms), and how and why to choose specific applications, platforms, and tools based on project needs.
ContributorsGrumbach, Elizabeth (Author)
Created2018-09-26
Description
Computational tools in the digital humanities often either work on the macro-scale, enabling researchers to analyze huge amounts of data, or on the micro-scale, supporting scholars in the interpretation and analysis of individual documents. The proposed research system that was developed in the context of this dissertation ("Quadriga System") works to bridge these two extremes by offering tools to support close reading and interpretation of texts, while at the same time providing a means for collaboration and data collection that could lead to analyses based on big datasets. In the field of history of science, researchers usually use unstructured data such as texts or images. To computationally analyze such data, it first has to be transformed into a machine-understandable format. The Quadriga System is based on the idea to represent texts as graphs of contextualized triples (or quadruples). Those graphs (or networks) can then be mathematically analyzed and visualized. This dissertation describes two projects that use the Quadriga System for the analysis and exploration of texts and the creation of social networks. Furthermore, a model for digital humanities education is proposed that brings together students from the humanities and computer science in order to develop user-oriented, innovative tools, methods, and infrastructures.
ContributorsDamerow, Julia (Author) / Laubichler, Manfred (Thesis advisor) / Maienschein, Jane (Thesis advisor) / Creath, Richard (Committee member) / Ellison, Karin (Committee member) / Hooper, Wallace (Committee member) / Renn, Jürgen (Committee member) / Arizona State University (Publisher)
Created2014