Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-745bb68f8f-b6zl4 Total loading time: 0 Render date: 2025-01-13T19:47:20.139Z Has data issue: false hasContentIssue false

12 - Strategies for Discovering Mechanisms: Construction, Evaluation, Revision

Published online by Cambridge University Press:  31 August 2009

Lindley Darden
Lindley Darden
Affiliation:
University of Maryland, College Park
Get access

Summary

INTRODUCTION

The key ideas in the chapters in Part I on mechanisms and those in Part II on reasoning strategies now need to be integrated and extended. The chapters in Part I provide a characterization of mechanisms, based on an analysis of paradigm cases from molecular and neurobiology. Those chapters also begin a search for reasoning strategies for discovering mechanisms and for analyzing the role of mechanisms in understanding the relations among fields in biology. The chapters in Part II discuss reasoning strategies in scientific change, including the use of analogies, interfield theories, and abstract types of theories, as well as strategies for anomaly resolution.

Biologists often seek to discover mechanisms, as we have seen in previous chapters. The task now is to summarize and extend previous work on reasoning strategies for discovering mechanisms. When the discovery task is construed in an unconstrained way to find some sort of hypothesis, little guidance is available. It is not surprising that some philosophers relegated discovery to psychology, to the study of presumed “a-ha” discovery moments (Popper 1965). They had little to say about how to discover hypotheses or to revise them in light of anomalies. However, when the task is specified as the discovery of a mechanism, much can be said about how to proceed. The product guides the process of discovery, as stressed in Chapters 2 and 3.

Type
Chapter
Information
Reasoning in Biological Discoveries
Essays on Mechanisms, Interfield Relations, and Anomaly Resolution
 , pp. 271 - 312
Publisher: Cambridge University Press
Print publication year: 2006

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Allcghin, Douglas (1992), “How Do You Falsify a Question?: Crucial Tests versus Crucial Demonstrations,” in Hull, D., Forbes, M., and Okruhlik, K. (eds.), PSA 1992, v. 1. East Lansing, MI: Philosophy of Science Association, pp. 74–88.Google Scholar
Allchin, Douglas (1997), “A Twentieth-Century Phlogiston: Constructing Error and Differentiating Domains,” Perspectives on Science 5: 81–127.Google Scholar
Allchin, Douglas (1999), “Negative Results as Positive Knowledge, and Zeroing in on Significant Problems,”Marine Ecology Progress Series 191: 301–305.Google Scholar
Allchin, Douglas (2002), “Error Types,” Perspectives on Science 9: 38–58.CrossRefGoogle Scholar
Beatty, John (1995), “The Evolutionary Contingency Thesis,” in Lennox, James G. and Wolters, Gereon (eds.), Concepts, Theories, and Rationality in the Biological Sciences. Pittsburgh, PA: University of Pittsburgh Press, pp. 45–81.Google Scholar
Bechtel, William and Abrahamsen, Adele (2005), “Explanation: A Mechanist Alternative,” in Carl F. Craver and Lindley Darden (eds.), Special Issue: “Mechanisms in Biology,” Studies in History and Philosophy of Biological and Biomedical Sciences 36: 421–441.CrossRefGoogle ScholarPubMed
Bechtel, William and Richardson, Robert C. (1993), Discovering Complexity: Decomposition and Localization as Strategies in Scientific Research. Princeton, NJ: Princeton University Press.Google Scholar
Bogen, James (2004), “Analysing Causality: The Opposite of Counterfactual is Factual,” International Studies in the Philosophy of Science 18: 3–26.CrossRefGoogle Scholar
Bogen, James (2005), “Regularities and Causality; Generalizations and Causal Explanations,” in Carl F. Craver and Lindley Darden (eds.), Special Issue: “Mechanisms in Biology,” Studies in History and Philosophy of Biological and Biomedical Sciences 36: 397–420.CrossRefGoogle ScholarPubMed
Bogen, James and Woodward, James (1988), “Saving the Phenomena,” Philosophical Review 97: 303–352.CrossRefGoogle Scholar
Brenner, S., Jacob, F., and Meselson, M. (1961), “An Unstable Intermediate Carrying Information from Genes to Ribosomes for Protein Synthesis,” Nature 190: 576–581.CrossRefGoogle ScholarPubMed
Brewer, William F. and Clark A. Chinn (1994), “Scientists' Responses to Anomalous Data: Evidence from Psychology, History, and Philosophy of Science,” in Hull, D., Forbes, M., and Burian, R. M. (eds.), PSA 1994, v. 1. East Lansing, MI: Philosophy of Science Association, pp. 304–313.Google Scholar
Bridewell, Will (2004), Science as an Anomaly-Driven Enterprise: A Computational Approach to Generating Acceptable Theory Revisions in the Face of Anomalous Data. Ph.D. Dissertation, Department of Computer Science, University of Pittsburgh, Pittsburgh, PA.Google Scholar
Burian, Richard M. (1996b), “Some Epistemological Reflections on Polistes as a Model Organism,” in Turillazzi, S. and West-Eberhard, M. J. (eds.), Natural History and Evolution of an Animal Society: The Paper Wasp Case. Oxford: Oxford University Press, pp. 318–337.Google Scholar
Cain, Joseph A. and , Lindley Darden (1988), “Hull and Selection,” Biology and Philosophy 3: 165–171.CrossRefGoogle Scholar
Cairns, John, Overbaugh, Julie, and Miller, S. (1988), “The Origin of Mutants,” Nature 335: 142–145.CrossRefGoogle ScholarPubMed
Cartwright, Nancy (1989), Nature's Capacities and Their Measurement. Oxford: Oxford University Press.Google Scholar
Cartwright, Nancy (2004), “Causation: One Word, Many Things,” Philosophy of Science 71: 805–819.CrossRefGoogle Scholar
Craver, Carl F. (2001), “Role Functions, Mechanisms, and Hierarchy,” Philosophy of Science 68: 53–74.CrossRefGoogle Scholar
Craver, Carl F. (2002b), “Interlevel Experiments, Multilevel Mechanisms in the Neuroscience of Memory,” Philosophy of Science (Supplement) 69: S83–S97.Google Scholar
Craver, Carl F. and Lindley Darden (2001), “Discovering Mechanisms in Neurobiology: The Case of Spatial Memory,” in Machamer, Peter, Grush, R., and McLaughlin, P. (eds.), Theory and Method in the Neurosciences. Pittsburgh, PA: University of Pittsburgh Press, pp. 112–137.Google Scholar
Craver, Carl F. and Darden, Lindley (2005), “Introduction: Mechanisms Then and Now,” in Special Issue, “Mechanisms in Biology,” Studies in History and Philosophy of Biological and Biomedical Sciences 36: 233–244.CrossRefGoogle Scholar
Crick, Francis (1959), “The Present Position of the Coding Problem,” Structure and Function of Genetic Elements: Brookhaven Symposia in Biology 12: 35–39.Google ScholarPubMed
Crick, Francis (1988), What Mad Pursuit: A Personal View of Scientific Discovery. New York: Basic Books.Google Scholar
Culp, Sylvia (1997), “Establishing Genotype/Phenotype Relationships: GeneTargeting as an Experimental Approach,” Philosophy of Science (Proceedings) 64: S268– S278.Google Scholar
Darden, Lindley (1980), “Theory Construction in Genetics,” in Nickles, Thomas (ed.), Scientific Discovery: Case Studies. Dordrecht: Reidel, pp. 151–170.CrossRefGoogle Scholar
Darden, Lindley (1991), Theory Change in Science: Strategies from Mendelian Genetics. New York: Oxford University Press.Google Scholar
Darden, Lindley (1995), “Exemplars, Abstractions, and Anomalies: Representations and Theory Change in Mendelian and Molecular Genetics,” in Lennox, James G. and Wolters, Gereon (eds.), Concepts, Theories, and Rationality in the Biological Sciences. Pittsburgh, PA: University of Pittsburgh Press, pp. 137–158.Google Scholar
Darden, Lindley (2001), “Discovering Mechanisms: A Computational Philosophy of Science Perspective,” in Jantke, Klaus P. and Shinohara, Ayumi (eds.), Discovery Science (Proceedings of the 4th International Conference, DS2001). New York: Springer-Verlag, pp. 3–15.CrossRefGoogle Scholar
Darden, Lindley and Cain, Joseph A. (1989), “Selection Type Theories,” Philosophy of Science 56: 106–129.CrossRefGoogle Scholar
Darden, Lindley and Craver, Carl F. (2002), “Strategies in the Interfield Discovery of the Mechanism of Protein Synthesis,” Studies in History and Philosophy of Biological and Biomedical Sciences 33: 1–28.CrossRefGoogle Scholar
Didion, David (2003), “Relevant Bounds on Hierarchical Levels in the Description of Mechanisms,” History and Philosophy of the Life Sciences 25: 5–25.CrossRefGoogle Scholar
Dunbar, Kevin (1995), “How Scientists Really Reason: Scientific Reasoning in Real-World Laboratories,” in Sternberg, R. J. and Davidson, J. E. (eds.), The Nature of Insight. Cambridge, MA: MIT Press, pp. 365–395.Google Scholar
Elliott, Kevin (2004), “Error as Means to Discovery,” Philosophy of Science 71: 174–197.CrossRefGoogle Scholar
Franklin, Allan (1989), “The Epistemology of Experiment,” in Gooding, David, Pinch, Trevor, and Schaffer, Simon (eds.), The Uses of Experiment: Studies in the Natural Sciences. New York: Cambridge University Press, pp. 437–460.Google Scholar
Gentner, Dedre (1983), “Structure Mapping – A Theoretical Framework for Analogy,” Cognitive Science 7: 155–170.CrossRefGoogle Scholar
Gilbert, Scott F. and Bolker, Jessica A. (2001), “Homologies of Process and Modular Elements of Embryonic Construction,” Journal of Experimental Zoology 291: 1–12.CrossRefGoogle ScholarPubMed
Glennan, Stuart S. (1996), “Mechanisms and The Nature of Causation,” Erkenntnis 44: 49–71.CrossRefGoogle Scholar
Glennan, Stuart S. (2002), “Rethinking Mechanistic Explanation,” Philosophy of Science (Supplement) 69: S342–S353.Google Scholar
Glennan, Stuart S. (2005), “Modeling Mechanisms,” in Carl F. Craver and Lindley Darden (eds.), Special Issue: “Mechanisms in Biology,” Studies in History and Philosophy of Biological and Biomedical Sciences 36: 443–464.CrossRefGoogle ScholarPubMed
Gros, Francois, Hiatt, Howard, Gilbert, Walter, Kurland, Chuck G., Risebrough, R. W., and Watson, James D. (1961), “Unstable Ribonucleic Acid Revealed by Pulse Labeling of E. coli,” Nature 190: 581–585.CrossRefGoogle Scholar
Hanson, Norwood Russell (1963), The Concept of the Positron: A Philosophical Analysis. Cambridge, UK: Cambridge University Press.Google Scholar
Harman, Gilbert (1986), Change in View: Principles of Reasoning. Cambridge, MA: MIT Press.Google Scholar
Harré, Rom (1970), The Principles of Scientific Thinking. Chicago, IL: University of Chicago Press.CrossRefGoogle Scholar
Holyoak, Keith J. and Thagard, Paul (1995), Mental Leaps: Analogy in Creative Thought. Cambridge, MA: MIT Press.Google Scholar
Jacob, Francois and Monod, Jacques (1961), “Genetic Regulatory Mechanisms in the Synthesis of Proteins,” Journal of Molecular Biology 3: 318–356.CrossRefGoogle ScholarPubMed
Josephson, John R. and Josephson, Susan G. (eds.) (1994), Abductive Inference: Computation, Philosophy, Technology. New York: Cambridge University Press.CrossRefGoogle Scholar
Judson, Horace F. (1996), The Eighth Day of Creation: The Makers of the Revolution in Biology. Expanded Edition. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.Google Scholar
Karp, Peter (1990), “Hypothesis Formation as Design,” in Shrager, J. and Langley, P. (eds.), Computational Models of Scientific Discovery and Theory Formation. San Mateo, CA: Morgan Kaufmann, pp. 275–317.Google Scholar
Kauffman, Stuart A. (1971), “Articulation of Parts Explanation in Biology and the Rational Search for Them,” in Buck, Roger C. and Cohen, Robert S. (eds.), PSA 1970. Boston Studies in the Philosophy of Science, v. 8. Dordrecht: Reidel, pp. 257–272.CrossRefGoogle Scholar
Kitcher, Philip (1989), “Explanatory Unification and the Causal Structure of the World,” in Kitcher, Philip and Salmon, Wesley (eds.), Scientific Explanation. Minnesota Studies in the Philosophy of Science, v. 13. Minneapolis, MN: University of Minnesota Press, pp. 410–505.Google Scholar
Kuhn, Thomas (1970), The Structure of Scientific Revolutions. 2nd ed. Chicago, IL: The University of Chicago Press.Google Scholar
Lederberg, Joshua (1965), “Signs of Life: Criterion-System of Exobiology,” Nature 207: 9–13.CrossRefGoogle ScholarPubMed
Lenat, Douglas (1976), AM: An Artificial Intelligence Approach to Discovery in Mathematics as Heuristic Search. Ph.D. Dissertation. Stanford University, Stanford, CA.Google Scholar
Lloyd, Elizabeth (1987), “Confirmation of Ecological and Evolutionary Models,” Biology and Philosophy 2: 277–293.CrossRefGoogle Scholar
Machamer, Peter (2004), “Activities and Causation: The Metaphysics and Epistemology of Mechanisms,” International Studies in the Philosophy of Science 18: 27–39.CrossRefGoogle Scholar
Machamer, Peter, Darden, Lindley, and Craver, Carl (2000), “Thinking About Mechanisms,” Philosophy of Science 67: 1–25.CrossRefGoogle Scholar
Mayo, Deborah G. (1996), Error and the Growth of Experimental Knowledge. Chicago, IL: University of Chicago Press.CrossRefGoogle Scholar
Morowitz, Harold (1985), “Models for Biomedical Research: A New Perspective,” Report of the Committee on Models for Biomedical Research. Washington, DC: National Academy Press.
Morowitz, Harold and Smith, Temple (1987), “Report of the Matrix of Biological Knowledge Workshop, July 13–August 14, 1987,” Santa Fe, NM: Santa Fe Institute.
Nersessian, Nancy J. (1993), “In the Theoretician's Laboratory: Thought Experimenting as Mental Modeling,” in Hull, D., Forbes, M., and Okruhlik, K. (eds.), PSA 1992, v. 2. East Lansing, MI: Philosophy of Science Association, pp. 291–301.Google Scholar
Newton-Smith, W. H. (1981), The Rationality of Science. Boston, MA: Routledge & Kegan Paul.CrossRefGoogle Scholar
Nickles, Thomas (1987), “Methodology, Heuristics, and Rationality,” in Pitt, J. C. and Pera, M. (eds.), Rational Changes in Science. Dordrecht: Reidel, pp. 103–132.CrossRefGoogle Scholar
Popper, Karl R. (1965), The Logic of Scientific Discovery. New York: Harper Torchbooks.Google Scholar
Popper, Karl (1968), Conjectures and Refutations: The Growth of Scientific Knowledge. New York: Harper Torchbooks.Google Scholar
Psillos, Stathis (2004), “A Glimpse of the Secret Connexion: Harmonizing Mechanisms with Counterfactuals,” Perspectives on Science 12: 288–391.CrossRefGoogle Scholar
Rheinberger, Hans-Jörg (1997), Toward a History of Epistemic Things: Synthesizing Proteins in the Test Tube. Stanford, CA: Stanford University Press.Google Scholar
Rich, Alexander and Watson, James D. (1954a), “Physical Studies on Ribonucleic Acid,” Nature 173: 995–996.CrossRefGoogle Scholar
Rich, Alexander and Watson, James D. (1954b), “Some Relations Between DNA and RNA,” Proceedings of the National Academy of Sciences 40: 759–764.CrossRefGoogle Scholar
Rudge, David W. (1996), A Philosophical Analysis of the Role of Natural Selection Experiments in Evolutionary Biology. Ph.D. Dissertation, Department of History and Philosophy of Science, University of Pittsburgh, Pittsburgh, PA.Google Scholar
Schaffner, Kenneth (1993), Discovery and Explanation in Biology and Medicine. Chicago, IL: University of Chicago Press.Google Scholar
Shapere, Dudley (1980), “The Character of Scientific Change,” in Nickles, Thomas (ed.), Scientific Discovery, Logic and Rationality. Dordrecht: Reidel, pp. 61–101.CrossRefGoogle Scholar
Skipper, Robert A. Jr. (1999), “Selection and the Extent of Explanatory Unification,” Philosophy of Science 66 (Proceedings): S196-S209.CrossRefGoogle Scholar
Skipper, Robert A. Jr. (2000), The R.A. Fisher-Sewall Wright Controversy in Philosophical Focus: Theory Evaluation in Population Genetics. Ph.D. Dissertation, Department of Philosophy, University of Maryland, College Park, MD.Google Scholar
Skipper, Robert A. Jr. (2002), “The Persistence of the R. A. Fisher-Sewall Wright Controversy,” Biology and Philosophy 17: 341–367.CrossRefGoogle Scholar
Skipper, Robert A. Jr. and Millstein, Roberta L. (2005), “Thinking about Evolutionary Mechanisms: Natural Selection,” in Carl F. Craver and Lindley Darden (eds.), Special Issue: “Mechanisms in Biology,” Studies in History and Philosophy of Biological and Biomedical Sciences 36: 327–347.CrossRefGoogle ScholarPubMed
Steele, Edward J., Lindley, Robyn A., and Blanden, Robert B. (1998), Lamarck's Signature. Reading, MA: Perseus Books.Google Scholar
Tabery, James G. (2004), “Synthesizing Activities and Interactions in the Concept of a Mechanism,” Philosophy of Science 71: 1–15.CrossRefGoogle Scholar
Watson, James D. (1965), Molecular Biology of the Gene. New York: W. A. Benjamin.Google Scholar
Watson, James D. (1968), The Double Helix. New York: New American Library.Google Scholar
Watson, James D. and Crick, Francis (1953a), “A Structure for Deoxyribose Nucleic Acid,” Nature 171: 737–738.CrossRefGoogle Scholar
Weber, Marcel (2005), Philosophy of Experimental Biology. New York: Cambridge University Press.Google Scholar
Westfall, Richard S. (1977), The Construction of Modern Science: Mechanisms and Mechanics. New York: Cambridge University Press.Google Scholar
Wimsatt, William C. (1981) “Robustness, Reliability, and Overdetermination,” in Brewer, M. and Collins, B. (eds.), Scientific Inquiry and the Social Sciences. San Francisco, CA: Jossey-Bass, pp. 124–163.Google Scholar
Woodward, James (2002), “What Is a Mechanism? A Counterfactual Account,” Philosophy of Science (Supplement) 69: S366-S377.Google Scholar
Woodward, James (2003), Making Things Happen: A Theory of Causal Explanation. New York: Oxford University Press.Google Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×