C. Kenneth Waters

This paper investigates what molecular biology has done for our understanding of the gene. I base a new account of the gene concept of classical genetics on the classical dogma that gene differences cause phenotypic differences. Although contemporary biologists often think of genes in terms of this concept, molecular biology provides a second way to understand genes. I clarify this second way by articulating a molecular gene concept. This concept unifies our understanding of the molecular basis of a wide variety of phenomena, including the phenomena that classical genetics explains in terms of gene differences causing phenotypic differences.

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.

Watson and Crick’s discovery of the structure of DNA led to developments that transformed many biological sciences. But what were the relevant developments and how did they transform biology? Much of the philosophical discussion concerning this question can be organized around two opposing views: theoretical reductionism and layer-cake antireductionism. Theoretical reductionist and their anti-reductionist foes hold two assumptions in common. First, both hold that biological knowledge is structured like a layer cake, with some biological sciences, such as molecular biology cast at lower levels of organization, and others, such as classical genetics, cast at higher levels. Second, both assume that scientific knowledge is structured by theory and that the productivity of scientific research depends on whether the underlying theory identifies the fundamentals upon which the phenomena to be explained and investigated depend. In the first part of this paper, I challenge these assumptions. In the second part, I show how recasting the basic theory of classical genetics made it possible to retool the methodologies of genetics. It was the investigative power of these retooled methodologies, and not the explanatory power of a gene-based theory, that transformed biology.

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.

What should philosophers of science accomplish when they analyze scientific concepts and interpret scientific knowledge? What is concept analysis if it is not a description of the way scientists actually think? I investigate these questions by using Hans Reichenbach's account of the descriptive, critical, and advisory tasks of philosophy of science to examine Karola Stotz and Paul Griffiths' idea that poll-based methodologies can test philosophical analyses of scientific concepts. Using Reichenbach's account as a point of departure, I argue that philosophy of science should identify and clarify epistemic virtues and describe scientific knowledge in relation to these virtues. The role of concept analysis is to articulate scientific concepts in ways that help reveal epistemic virtues and limitations of particular sciences. This means an analysis of the gene concept should help clarify the explanatory power and limitations of gene-based explanations, and should help account for the investigative utility and biases of gene-centered sciences. I argue that a philosophical analysis of gene concept that helps achieve these critical aims should not be rejected on the basis of poll-based studies even if such studies could show that professional biologists don't actually use gene terminology in precise ways corresponding to the philosophical analysis

Traditional approaches in philosophy of biology focus attention on biological concepts, explanations, and theories, on evidential support and inter-theoretical relations. Newer approaches shift attention from concepts to conceptual practices, from theories to practices of theorizing, and from theoretical reduction to reductive retooling. In this article, I describe the shift from theory-focused to practice-centered philosophy of science and explain how it is leading philosophers to abandon fundamentalist assumptions associated with traditional approaches in philosophy of science and to embrace scientific pluralism. This article comes in three parts, each illustrating the shift from theory-focused to practice-centered epistemology. The first illustration shows how shifting philosophical attention to conceptual practice reveals how molecular biologists succeed in identifying coherent causal strands within systems of bewildering complexity. The second illustration suggests that analyzing how a multiplicity of alternative models function in practice provides an illuminating approach for understanding the nature of theoretical knowledge in evolutionary biology. The third illustration demonstrates how framing reductionism in terms of the reductive retooling of practice offers an informative perspective for understanding why putting DNA at the center of biological research has been incredibly productive throughout much of biology. Each illustration begins by describing how traditional theory-focused philosophical approaches are laden with fundamentalist assumptions and then proceeds to show that shifting attention to practice undermines these assumptions and motivates a philosophy of scientific pluralism.

Darwinians are realists about the force of selection, but there has been surprisingly little discussion about what form this realism should take. Arguments about the units of selection in general and genic selectionism in particular reveal two realist assumptions: (1) for any selection process, there is a uniquely correct identification of the operative selective forces and the level at which each impinges; and (2) selective forces must satisfy the Pareto-style requirement of probabilistic causation. I argue that both assumptions are false; we must temper realism about the force of selection and revise the way we think about probabilistic causation.

This chapter introduces a distinctive approach for scientific metaphysics. Instead of drawing metaphysical conclusions by interpreting the most basic theories of science, this approach draws metaphysical conclusions by analyzing how multifaceted practices of science work. Broadening attention opens the door to drawing metaphysical conclusions from a wide range of sciences. This chapter analyzes conceptual practice in genetics to argue that the reality investigated by biologists lacks an overall structure. It expands this conclusion to motivate the no general structure thesis, which states that the world lacks a general, overall structure that spans scales. It concludes that the no general structure thesis counts as metaphysics because it says something very important and general about the world. This thesis informs science as well as philosophy of science, and it provides a useful perspective for societies that look upon science to help solve complex problems in our changing world.

Philosophers now treat the relationship between classical genetics and molecular biology as a paradigm of nonreduction and this example is playing an increasingly prominent role in debates about the reducibility of theories in other sciences. This paper shows that the anti-reductionist consensus about genetics will not withstand serious scrutiny. In addition to defusing the main anti-reductionist objections, this critical analysis uncovers tell-tale signs of a significant reduction in progress. It also identifies philosophical issues relevant to gaining a better understanding of what is now happening in genetics and of what we might expect to happen in other sciences.

Susan Mills and John Beatty proposed a propensity interpretation of fitness (1979) to show that Darwinian explanations are not circular, but they did not address the critics' chief complaint that the principle of the survival of the fittest is either tautological or untestable. I show that the propensity interpretation cannot rescue the principle from the critics' charges. The critics, however, incorrectly assume that there is nothing more to Darwin's theory than the survival of the fittest. While Darwinians all scoff at this assumption, they do not agree about what role, if any, this principle plays in Darwin's theory of natural selection. I argue that the principle has no place in Darwin's theory. His theory does include the idea that some organisms are fitter than others. But greater reproductive success is simply inferred from higher fitness. There is no reason to embody this inference in the form of a special principle of the survival of the fittest.

Clark Glymour has argued that hypothetico-deductivism, which many take to be an important method of scientific confirmation, is hopeless because it cannot be reconstructed in classical logic. Such reconstructions, as Glymour points out, fail to uphold the condition of relevance between theory and evidence. I argue that the source of the irrelevant confirmations licensed by these reconstructions lies not with hypothetico-deductivism itself, but with the classical logic in which it is typically reconstructed. I present a new reconstruction of hypothetico-deductivism in relevance logic that does maintain the condition of relevance between theory and evidence. Hence, if hypothetico-deductivism is an important rationale in science, we have good reason to believe that the logic underlying scientific discourse is captured better by relevance logic than by its classical counterpart

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.

Although historians have carefully examined exactly what role the analogy between artificial and natural selection might have played in Charles Darwin's discovery of natural selection, philosophers have not devoted much attention to the way Darwin employed the analogy to justify his theory. I suggest that philosophers tend to belittle the role that analogies play in the justification of scientific theories because they don't understand the special nature of analogical inference. I present a novel account of analogical argument developed by Julian Weitzenfeld and then use it to carry out an in-depth analysis of Darwin's argument from artificial selection.

Philosophers now treat the relationship between Classical Mendelian Genetics and molecular biology as a paradigm of nonreduction and this example is playing an increasingly prominent role in debates about the reducibility of theories ranging from macrosocial science to folk psychology. Patricia Churchland (1986), for example, draws an analogy between the alleged elimination of the “causal mainstay” of classical genetics and her view that today’s psychological theory will be eliminated by neuroscience. Patricia Kitcher takes an autonomous rather than eliminativist view of the reported nonreduction in genetics and reasons that psychology will retain a similar autonomy from lower level sciences (1980 and 1982). Although Churchland and Kitcher offer different interpretations of the apparent failure of molecular biology to reduce classical genetics, they agree that this failure will help illuminate theoretical relations between psychology and lower level sciences. The appearance of the Mendelian example along side the usual ones from physics and chemistry marks a turning point in philosophy of science.