Matching Items (4)
Filtering by
- All Subjects: developmental evolution
- All Subjects: digital humanities
- Creators: Creath, Richard
- Creators: Laubichler, Manfred D
Description
Understanding changes and trends in biomedical knowledge is crucial for individuals, groups, and institutions as biomedicine improves people’s lives, supports national economies, and facilitates innovation. However, as knowledge changes what evidence illustrates knowledge changes? In the case of microbiome, a multi-dimensional concept from biomedicine, there are significant increases in publications, citations, funding, collaborations, and other explanatory variables or contextual factors. What is observed in the microbiome, or any historical evolution of a scientific field or scientific knowledge, is that these changes are related to changes in knowledge, but what is not understood is how to measure and track changes in knowledge. This investigation highlights how contextual factors from the language and social context of the microbiome are related to changes in the usage, meaning, and scientific knowledge on the microbiome. Two interconnected studies integrating qualitative and quantitative evidence examine the variation and change of the microbiome evidence are presented. First, the concepts microbiome, metagenome, and metabolome are compared to determine the boundaries of the microbiome concept in relation to other concepts where the conceptual boundaries have been cited as overlapping. A collection of publications for each concept or corpus is presented, with a focus on how to create, collect, curate, and analyze large data collections. This study concludes with suggestions on how to analyze biomedical concepts using a hybrid approach that combines results from the larger language context and individual words. Second, the results of a systematic review that describes the variation and change of microbiome research, funding, and knowledge are examined. A corpus of approximately 28,000 articles on the microbiome are characterized, and a spectrum of microbiome interpretations are suggested based on differences related to context. The collective results suggest the microbiome is a separate concept from the metagenome and metabolome, and the variation and change to the microbiome concept was influenced by contextual factors. These results provide insight into how concepts with extensive resources behave within biomedicine and suggest the microbiome is possibly representative of conceptual change or a preview of new dynamics within science that are expected in the future.
ContributorsAiello, Kenneth (Author) / Laubichler, Manfred D (Thesis advisor) / Simeone, Michael (Committee member) / Buetow, Kenneth (Committee member) / Walker, Sara I (Committee member) / Arizona State University (Publisher)
Created2018
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
At the interface of developmental biology and evolutionary biology, the very
criteria of scientific knowledge are up for grabs. A central issue is the status of evolutionary genetics models, which some argue cannot coherently be used with complex gene regulatory network (GRN) models to explain the same evolutionary phenomena. Despite those claims, many researchers use evolutionary genetics models jointly with GRN models to study evolutionary phenomena.
How do those researchers deploy those two kinds of models so that they are consistent and compatible with each other? To address that question, this dissertation closely examines, dissects, and compares two recent research projects in which researchers jointly use the two kinds of models. To identify, select, reconstruct, describe, and compare those cases, I use methods from the empirical social sciences, such as digital corpus analysis, content analysis, and structured case analysis.
From those analyses, I infer three primary conclusions about projects of the kind studied. First, they employ an implicit concept of gene that enables the joint use of both kinds of models. Second, they pursue more epistemic aims besides mechanistic explanation of phenomena. Third, they don’t work to create and export broad synthesized theories. Rather, they focus on phenomena too complex to be understood by a common general theory, they distinguish parts of the phenomena, and they apply models from different theories to the different parts. For such projects, seemingly incompatible models are synthesized largely through mediated representations of complex phenomena.
The dissertation closes by proposing how developmental evolution, a field traditionally focused on macroevolution, might fruitfully expand its research agenda to include projects that study microevolution.
criteria of scientific knowledge are up for grabs. A central issue is the status of evolutionary genetics models, which some argue cannot coherently be used with complex gene regulatory network (GRN) models to explain the same evolutionary phenomena. Despite those claims, many researchers use evolutionary genetics models jointly with GRN models to study evolutionary phenomena.
How do those researchers deploy those two kinds of models so that they are consistent and compatible with each other? To address that question, this dissertation closely examines, dissects, and compares two recent research projects in which researchers jointly use the two kinds of models. To identify, select, reconstruct, describe, and compare those cases, I use methods from the empirical social sciences, such as digital corpus analysis, content analysis, and structured case analysis.
From those analyses, I infer three primary conclusions about projects of the kind studied. First, they employ an implicit concept of gene that enables the joint use of both kinds of models. Second, they pursue more epistemic aims besides mechanistic explanation of phenomena. Third, they don’t work to create and export broad synthesized theories. Rather, they focus on phenomena too complex to be understood by a common general theory, they distinguish parts of the phenomena, and they apply models from different theories to the different parts. For such projects, seemingly incompatible models are synthesized largely through mediated representations of complex phenomena.
The dissertation closes by proposing how developmental evolution, a field traditionally focused on macroevolution, might fruitfully expand its research agenda to include projects that study microevolution.
ContributorsElliott, Steve (Author) / Creath, Richard (Thesis advisor) / Laubichler, Manfred D. (Thesis advisor) / Armendt, Brad (Committee member) / Forber, Patrick (Committee member) / Pratt, Stephen (Committee member) / Arizona State University (Publisher)
Created2017
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