I present an account of classical genetics to challenge theory-biased approaches in the philosophy of science. Philosophers typically assume that scientific knowledge is ultimately structured by explanatory reasoning and that research programs in well-established sciences are organized around efforts to fill out a central theory and extend its explanatory range. In the case of classical genetics, philosophers assume that the knowledge was structured by T. H. Morgan’s theory of transmission and that research throughout the later 1920s, 30s, and 40s was (...) organized around efforts to further validate, develop, and extend this theory. I show that classical genetics was structured by an integration of explanatory reasoning and investigative strategies . The investigative strategies, which have been overlooked in historical and philosophical accounts, were as important as the so-called laws of Mendelian genetics. By the later 1920s, geneticists of the Morgan school were no longer organizing research around the goal of explaining inheritance patterns; rather, they were using genetics to investigate a range of biological phenomena that extended well beyond the explanatory domain of transmission theories. Theory-biased approaches in history and philosophy of science fail to reveal the overall structure of scientific knowledge and obscure the way it functions.Author Keywords: Investigation; Genetic approach; Structure of knowledge; Classical genetics. (shrink)

In 1957, Francis Crick outlined a startling vision of life in which the great diversity of forms and shapes of macromolecules was encoded in the one-dimensional sequence of nucleic acids. This paper situates Crick's new vision in the debates of the 1950s about protein synthesis and gene action. After exploring the reception of Crick's ideas, it shows how they differed radically from a different model of protein synthesis which enjoyed wide currency in that decade. In this alternative model, advocated by (...) Linus Pauling and other luminaries, three-dimensional templates directed the folding of proteins. Even though it was always considered somewhat speculative, this theory was supported by a number of empirical results originating in different experimental systems. It was eventually replaced by a model in which the forms and shapes of macromolecules resulted solely from their amino acid sequence, dramatically simplifying the problem of protein synthesis which Crick was attempting to solve in 1957. (shrink)

Exploratory experimentation and high-throughput molecular biology appear to have considerable affinity for each other. Included in the latter category is metagenomics, which is the DNA-based study of diverse microbial communities from a vast range of non-laboratory environments. Metagenomics has already made numerous discoveries and these have led to reinterpretations of fundamental concepts of microbial organization, evolution, and ecology. The most outstanding success story of metagenomics to date involves the discovery of a rhodopsin gene, named proteorhodopsin, in marine bacteria that were (...) never suspected to have any photobiological capacities. A discussion of this finding and its detailed investigation illuminates the relationship between exploratory experimentation and metagenomics. Specifically, the proteorhodopsin story indicates that a dichotomous interpretation of theory-driven and exploratory experimentation is insufficient and that an interactive understanding of these two types of experimentation can be usefully supplemented by another category, "natural history experimentation". Further reflection on the context of metagenomics suggests the necessity of thinking more historically about exploratory and other forms of experimentation. (shrink)

There has been relatively little effort to provide a systematic overview of different forms of exploratory experimentation (EE). The present paper examines the growing subdiscipline of nanotoxicology and suggests that it illustrates at least four ways that researchers can engage in EE: searching for regularities; developing new techniques, simulation models, and instrumentation; collecting and analyzing large swaths of data using new experimental strategies (e.g., computer-based simulation and "high-throughput" instrumentation); and structuring an entire disciplinary field around exploratory research agendas. In order (...) to distinguish these and other activities more effectively, the paper proposes a taxonomy that includes three dimensions along which types of EE vary: (1) the aim of the experimental activity, (2) the role of theory in the activity, and (3) the methods or strategies employed for varying experimental parameters. (shrink)

Starting with some illustrative examples, I develop a systematic account of a specific type of experimentation--an experimentation which is not, as in the "standard view", driven by specific theories. It is typically practiced in periods in which no theory or--even more fundamentally--no conceptual framework is readily available. I call it exploratory experimentation and I explicate its systematic guidelines. From the historical examples I argue furthermore that exploratory experimentation may have an immense, but hitherto widely neglected, epistemic significance.

: The increasing attention on experiment in the last two decades has led to important insights into its material, cultural and social dimensions. However, the role of experiment as a tool for generating knowledge has been comparatively poorly studied. What questions are asked in experimental research? How are they treated and eventually resolved? And how do questions, epistemic situations, and experimental activity cohere and shape each other? In my paper, I treat these problems on the basis of detailed studies of (...) research practice. After presenting several cases from the history of electricity—Dufay, Ampère, and Faraday—I discuss a specific type of experiment—the "exploratory experiment"—and analyze how it works in concept formation. I argue that a fuller understanding of experiment can only be achieved by intertwining historical and philosophical perspectives in such a way that the very separation of the two become questioable. (shrink)

It is considered in some quarters that hypothesis‐driven methods are the only valuable, reliable or significant means of scientific advance. Data‐driven or ‘inductive’ advances in scientific knowledge are then seen as marginal, irrelevant, insecure or wrong‐headed, while the development of technology—which is not of itself ‘hypothesis‐led’ (beyond the recognition that such tools might be of value)—must be seen as equally irrelevant to the hypothetico‐deductive scientific agenda. We argue here that data‐ and technology‐driven programmes are not alternatives to hypothesis‐led studies in (...) scientific knowledge discovery but are complementary and iterative partners with them. Many fields are data‐rich but hypothesis‐poor. Here, computational methods of data analysis, which may be automated, provide the means of generating novel hypotheses, especially in the post‐genomic era. BioEssays 26:99–105, 2004. © 2003 Wiley Periodicals, Inc. (shrink)

Recent molecular biology has seen the development of genomics as a successor to traditional genetics. This paper offers an overview of the structure, epistemology, and history of contemporary genomics. A particular focus is on the question to what extent the genome contains, or is composed of, anything that corresponds to traditional conceptions of genes. It is concluded that the only interpretation of genes that has much contemporary scientific relevance is what is described as the "developmental defect" gene concept. However, developmental (...) defect genes typically only correspond to general areas of the genome and not to precise chemical structures . The parts of the genome to be identified for an account of the processes of normal development are highly diverse, little correlated with traditional genes, and act in ways that are highly dependent on the cellular and higher level environment. Despite its historical development out of genetics, genomics represents a radically different kind of scientific project. (shrink)