•  421
    Genes made molecular
    Philosophy of Science 61 (2): 163-185. 1994.
    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 …Read more
  •  291
    Causes That Make a Difference
    Journal of Philosophy 104 (11): 551-579. 2007.
    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 t…Read more
  •  132
    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-…Read more
  •  127
    What was classical genetics?
    Studies in History and Philosophy of Science Part A 35 (4): 783-809. 2004.
    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 t…Read more
  •  126
    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…Read more
  •  108
    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 structur…Read more
  •  107
    Why Genic and Multilevel Selection Theories Are Here to Stay
    Philosophy of Science 72 (2): 311-333. 2005.
    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 ‘sel…Read more
  •  101
    What Concept Analysis in Philosophy of Science Should Be
    History and Philosophy of the Life Sciences 26 (1): 29-58. 2004.
    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 Reichenb…Read more
  •  101
    Causal regularities in the biological world of contingent distributions
    Biology and Philosophy 13 (1): 5-36. 1998.
    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 p…Read more
  •  96
    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 funda…Read more
  •  62
    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 …Read more
  •  60
    Scientific Pluralism (edited book)
    with Stephen H. Kellert and Helen E. Longino
    Univ of Minnesota Press. 2006.
    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?
  •  55
    Rosenberg's rebellion
    Biology and Philosophy 5 (2): 225-239. 1990.
  •  54
    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. …Read more
  •  52
    Tempered realism about the force of selection
    Philosophy of Science 58 (4): 553-573. 1991.
    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 causa…Read more
  •  49
    Natural selection without survival of the fittest
    Biology and Philosophy 1 (2): 207-225. 1986.
    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. Whi…Read more
  •  37
    Relevance logic brings hope to hypothetico-deductivism
    Philosophy of Science 54 (3): 453-464. 1987.
    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 re…Read more
  •  36
    Taking Analogical Inference Seriously: Darwin's Argument from Artificial Selection
    PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1986. 1986.
    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 nove…Read more
  •  35
    Okasha’s Unintended Argument for Toolbox Theorizing
    Philosophy and Phenomenological Research 82 (1): 232-240. 2011.
    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 doe…Read more
  •  31
    Molecules Made Biological
    Revue Internationale de Philosophie 54 (214(4)): 539--564. 2000.
  •  24
    5 The arguments in the Origin of Species
    In J. Hodges & Gregory Radick (eds.), The Cambridge Companion to Darwin, Cambridge University Press. pp. 116. 2003.
  •  23
    Ask Not "What is an Individual?"
    In O. Bueno, M. B. Fagan & R. Chen (eds.), Individuation Across Experimental and Theoretical Sciences, Oxford University Press. forthcoming.
    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?”…Read more
  •  21
    An Epistemology of Scientific Practice
    Philosophy of Science 86 (4): 585-611. 2019.
    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 th…Read more
  •  8
    The Pluralist Stance
    with Stephen H. Kellert and Helen E. Longino
    This essay introduces the volume Scientific Pluralism (Volume 19 of Minnesota Studies in Philosophy of Science). Varieties of recent pluralisms are surveyed, the difference between monism and pluralism vis a vis the sciences is clarified, and the authors’ notion of scientific pluralism is advanced.
  •  8
    Scientific Pluralism (edited book)
    with Stephen H. Kellert and Helen Longino
    University of Minnesota Press. 1956.
    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. In…Read more