Etienne Geoffroy Saint-Hilaire, commonly known as Geoffroy, studied animals, their anatomy and their embryos, and teratogens at the National Museum of Natural History in Paris, France in the eighteenth and nineteenth centuries. Geoffroy also helped develop several specialized fields in the life sciences, including experimental embryology. In his efforts to experimentally demonstrate the theory of recapitulation, Geoffroy developed techniques to intervene in the growth of embryos to see whether they would develop into different kinds of organisms. Moreover, Geoffroy emphasized the concept of l'unite de composition (the unity of plan). Geoffroy disputed in 1830 with Georges Cuvier over whether form or function matters most for the study of anatomy and whether the transformation of organic forms can occur over time. Geoffroy's conceptual contributions, as well as his experimental research, influenced embryological research on animal morphology and teratogens, and later the field of evolutionary paleontology.

Georges Cuvier, baptized Georges Jean-Leopold Nicolas-Frederic Cuvier, was a professor of anatomy at the National Museum of Natural History in Paris, France, through the late eighteenth and early nineteenth centuries. Scholars recognize Cuvier as a founder of modern comparative anatomy, and as an important contributor to vertebrate paleontology and geology. Cuvier studied the form and function of animal anatomy, writing four volumes on quadruped fossils and co-writing eleven volumes on the natural history of fish with Achille Valenciennes. Moreover, Cuvier constructed a system of classification based on specific and well-articulated principles to help anatomists classify animal taxa. Cuvier had public debate in 1830 with Etienne Geoffroy Saint-Hilaire, a dispute centered on whether form or function matters most for the study of anatomy and whether the transmutation of organic forms can occur over time. Cuvier's opinions influenced the development of biology in France, and his arguments against transmutation of types influenced the reception of Charles Darwin's theory of evolution by natural selection among many French naturalists.

In 1928 Ezra Seymour Gosney founded the non-profit Human Betterment Foundation (HBF) in Pasadena, California to support the research and publication of the personal and social effects of eugenic sterilizations carried out in California. Led by director Gosney and secretary Paul Popenoe, the HBF collected data on thousands of individuals in California who had been involuntarily sterilized under a California state law enacted in 1909. The Foundation's assets were liquidated following Gosney's death in 1942. In 1943, Gosney's daughter donated the remaining assets to the California Institute of Technology (Caltech) in Pasadena, California to establish the Gosney research fund for biological research. Between 1928 and 1942, the HBF published extensively on what they believed to be the benefits of sterilization to both patient and society. The HBF and its members existed within the larger context of the American eugenics movement and scientific institutions, including the Eugenics Record Office at Cold Spring Harbor Laboratory in Cold Spring Harbor, New York, which bolstered the movement's goals of the control of human reproduction and human heredity. Moreover, the model sterilization legislation written by the HBF was disseminated throughout the world to eugenics enthusiasts eager to pass laws limiting the reproduction of people they considered to be unfit.

David Starr Jordan studied fish and promoted eugenics in the US during the late nineteenth and early twentieth centuries. In his work, he embraced Charles Darwin s theory of evolution and described the importance of embryology in tracing phylogenic relationships. In 1891, he became the president of Stanford University in Stanford, California. Jordan condemned war and promoted conservationist causes for the California wilderness, and he advocated for the eugenic sterilization of thousands of Americans. Like many American eugenicists of the early twentieth century, Jordan combined ideas of Mendelian genetics and of Darwinian natural selection to form a basis for limiting or encouraging reproduction in certain individuals and groups based on their perceived hereditary fitness. Like other eugenicists, Jordan s attempt to control the reproductive fate of entire populations marked an episode in the history of reproduction and biology in which its concepts increasingly influenced the social and cultural contexts.

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.