Chapman Waters

Biologists studying complex causal systems typically identify some factors as causes and treat other factors as background conditions. For example, when geneticists explain biological phenomena, they often foreground genes and relegate the cellular milieu to the background. But factors in the milieu are as causally necessary as genes for the production of phenotypic traits, even traits at the molecular level such as amino acid sequences. Gene-centered biology has been criticized on the grounds that because there is parity among causes, the “privileging” of genes reflects a reductionist bias, not an ontological difference. The idea that there is an ontological parity among causes is related to a philosophical puzzle identified by John Stuart Mill: what, other than our interests or biases, could possibly justify identifying some causes as the actual or operative ones, and other causes as mere background? The aim of this paper is to solve this conceptual puzzle and to explain why there is not an ontological parity among genes and the other factors. It turns out that solving this puzzle helps answer a seemingly unrelated philosophical question: what kind of causal generality matters in biology?

My aim in this article is to introduce readers to the topic of exploratory experimentation and briefly explain how the three articles that follow, by Richard Burian, Kevin Elliott, and Maureen O'Malley, advance our understanding of the nature and significance of exploratory research. I suggest that the distinction between exploratory and theory-driven experimentation is multidimensional and that some of the dimensions are continuums. I point out that exploratory experiments are typically theory-informed even if they are not theory-driven. I also distinguish between research programs and experiments. Research programs that are largely exploratory, such as the ones discussed in these case studies, can involve both exploratory and theory-driven experimentation

Leading philosophical accounts presume that Thomas H. Morgan’s transmission theory can be understood independently of experimental practices. Experimentation is taken to be relevant to confirming, rather than interpreting, the transmission theory. But the construction of Morgan’s theory went hand in hand with the reconstruction of the chief experimental object, the model organism Drosophila melanogaster . This raises an important question: when a theory is constructed to account for phenomena in carefully controlled laboratory settings, what knowledge, if any, indicates the theory’s relevance to phenomena outside highly controlled settings? The answer, I argue, is found within the procedural knowledge embedded within laboratory practice. †To contact the author, please write to: Minnesota Center for Philosophy of Science, University of Minnesota, Department of Philosophy, 831 Heller Hall, 271 19th Ave., University of Minnesota, Minneapolis, MN 55455‐0310; e‐mail: [email protected].

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.

I clarify the difference between pluralist and monist interpretations of levels of selection disputes. Lloyd has challenged my claim that a plurality of models correctly accounts for situations such as maintenance of the sickle-cell trait, and I revisit this example to show that competing theories don’t disagree about the existence of ‘high-level’ or ‘lowlevel’ causes; rather, they parse these causes differently. Applying Woodward’s theory of causation, I analyze Sober’s distinction between ‘selection of’ versus ‘selection for’. My analysis shows that this distinction separates true causes from pseudocauses, but it also reveals that the distinction is irrelevant to the levels debate; it makes no sense to say true causes are at higher levels and not lower levels. The levels debate is not about separating real causes from pseudocauses; it’s about finding useful ways to parse and disentangle causes.

Former discussions of biological generalizations have focused on the question of whether there are universal laws of biology. These discussions typically analyzed generalizations out of their investigative and explanatory contexts and concluded that whatever biological generalizations are, they are not universal laws. The aim of this paper is to explain what biological generalizations are by shifting attention towards the contexts in which they are drawn. I argue that within the context of any particular biological explanation or investigation, biologists employ two types of generations. One type identifies causal regularities exhibited by particular kinds of biological entities. The other type identifies how these entities are distributed in the biological world.

Scientific pluralism is an issue at the forefront of philosophy of science. This landmark work addresses the question, Can pluralism be advanced as a general, philosophical interpretation of science? Scientific Pluralism demonstrates the viability of the view that some phenomena require multiple accounts. Pluralists observe that scientists present various—sometimes even incompatible—models of the world and argue that this is due to the complexity of the world and representational limitations. Including investigations in biology, physics, economics, psychology, and mathematics, this work provides an empirical basis for a consistent stance on pluralism and makes the case that it should change the ways that philosophers, historians, and social scientists analyze scientific knowledge. Contributors: John Bell, U of Western Ontario; Michael Dickson, U of South Carolina; Carla Fehr, Iowa State U; Ronald N. Giere, U of Minnesota; Geoffrey Hellman, U of Minnesota; Alan Richardson, U of British Columbia; C. Wade Savage, U of Minnesota; Esther-Mirjam Sent, U of Nijmegen. Stephen H. Kellert is professor of philosophy at Hamline University and a fellow of the Minnesota Center for Philosophy of Science. Helen E. Longino is professor of philosophy at Stanford University. C. Kenneth Waters is associate professor of philosophy and director of the Minnesota Center for Philosophy of Science.

Philosophers of biology typically pose questions about individuation by asking “what is an individual?” For example, we ask, “what is an individual species”, “what is an individual organism”, and “what is an individual gene?” In the first part of this chapter, I present my account of the gene concept and how it is used in investigative practices in order to motivate a more pragmatic approach. Instead of asking “what is a gene?”, I ask: “how do biologists individuate genes?”, “for what purposes?”, and “do their practices of individuating genes serve these purposes?" In the second part of this chapter, I propose that we use this approach when analyzing concepts of organisms and biological individuals. Following philosophical pragmatism, I argue that we should abstain from attempts to situate individuation of Darwinian individuals or of holobionts in a philosophy of nature. Instead, we should analyze practices of individuating organisms in terms of three-place relations between the world, ideas, and human purposes and actions. I conclude with three lessons: an ontological, an epistemological, and a meta-philosophical lesson, which I suggest, apply to philosophy of science generally and to philosophy and metaphysics at large.

Philosophers’ traditional emphasis on theories, theoretical modeling, and explanation misguides research in philosophy of science. Articulating and applying core theories is part of scientific practice, but it is not the essence of scientific practice. Insofar as science has an essence, it is to systematically investigate and learn about what is not yet understood. This lecture analyzes genetics to articulate a broad-practice-centered approach to philosophy of science. It concludes by arguing that this approach can lead to richer, deeper, and more useful philosophies of science, philosophies that can better inform science policy and the public’s understanding of science.

Okasha claims at the outset of his book "Evolution and the Levels of Selection" that the Price equation lays bare the fundamentals underlying all selection phenomena. However, the thoroughness of his subsequent analysis of multi-level selection theories leads him to abandon his fundamentalist commitments. At critical points he invokes cost benefit analyses that sometimes favors the Price approach and sometimes the contextual approach, sometimes favors MLS1 and sometimes MLS2. And although he doesn’t acknowledge it, even the Price approach breaks down into a family of alternative equations that parse the causes in different ways, none of which is uniquely correct and none of which achieves the ultimate isolation of effects due to what Okasha believes are the fundamental causes. I argue that his book provides good reason to re-conceive our understanding of evolutionary theorizing in terms of a toolbox view and to stop subjecting the analyses of evolutionary concepts to a universalist standard.

Since the fundamental challenge that I laid at the doorstep of the pluralists was to defend, with nonderivative models, a strong notion of genic cause, it is fatal that Waters has failed to meet that challenge. Waters agrees with me that there is only a single cause operating in these models, but he argues for a notion of causal ‘parsing’ to sustain the viability of some form of pluralism. Waters and his colleagues have some very interesting and important ideas about the sciences, involving pluralism and parsing or partitioning causes, but they are ideas in search of an example. He thinks he has found an example in the case of hierarchical and genic selection. I think he has not.