Hypothesis Formation and Qualitative Reasoning in Molecular Biology
STANFORD UNIV CA DEPT OF COMPUTER SCIENCE
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This dissertation investigates scientific reasoning from a computational perspective. The investigation focuses on a program of research in molecular biology that culminated in the discovery of a new mechanism of gene regulation in bacteria, called attenuation. The dissertation concentrates on a particular type of reasoning called hypothesis formation. Hypothesis-formation problems occur when the outcome of an experiment predicted by a scientific theory does not match that observed by a scientist. I present methods for solving hypothesis formation problems that have been implemented in a computer program called HYPGENE. This work is also concerned with how to represent theories of molecular biology in a computer, and with how to use such theories to predict experimental outcomes I present a framework for performing these tasks that is implemented in a program called GENSIM. I tested both HYPGENE and GENSIM on sample problems that biologists solved during their research on attenuation. The dissertation includes a historical study of the attenuation research. THis study is novel because it examines a large, complex, and modern program of scientific research. The document treats hypothesis formation as a design problem, and uses design methods to solve hypothesis-formation problems.
- Genetic Engineering and Molecular Biology
- Computer Programming and Software