Phil 285

Biological Mechanisms

Fall 2008, Thursday 5:00pm-7:50pm

Professor: William Bechtel Office Hours: Tuesday, 3:30-5:00 and by appointment
Office: HSS 8076 Email:
Telephone: 822-4461 Webpage:

1. Description of Course

To explain a phenomenon, biologists often appeal to the responsible mechanism. Over the past 15 years, philosophers of science have begun to analyze what mechanisms and mechanistic explanations are, how scientists represent and reason about mechanisms, the strategies and tools employed in discovering mechanisms, how accounts of mechanisms are generalized from model systems, ways in which mechanistic accounts are both reductionistic and holistic, and how mathematical modeling is used to understand mechanisms. The resulting research project has been labeled "the new mechanistic philosophy of science." We will be exploring these topics by considering papers by leading proponents of the new mechanism and examining research in biology and related disciplines that have provided the models for mechanistic accounts.

2. Course Requirements

All participants are expected to do the assigned reading and to attend all the seminar sessions. There are two options for students taking this seminar for grades:

A. Those students without significant background in philosophy of science may take take the seminar as a regular course. This will require writing weekly discussion comments and three papers between 1,200 and 1,800 words based on the material we cover in class. The discussion comments, involving a paragraph commenting or raising a question about a major point in the assigned reading, must be submitted to the email list (see below) by 11 AM prior to each seminar session. The three papers will be due on October 17, November 14, and December 8--these dates do not correspond to seminar dates. They should be submitted electronically in Word to

B. Those students with significant background in philosophy of science are encouraged to pursue the research option. This option will be directed toward preparing a paper to be submitted for publication. This will require picking a topic by the beginning of the course, leading a seminar session on relevant readings, and then presenting their own paper later in the seminar.

3. Texts

All of the reading assignments can be found on the web. Readings which are copy-projected are only available on a password controlled portion of the course website. The userid and password for this portion of the website are both mechanism. See the schedule of classes and readings below.

4. Email List

There is an email list for this seminar: It is required that you subscribe to this list. Do it IMMEDIATELY. You can always unsubscribe later if you drop the course. The purpose of the list is twofold--to enable me to communicate information about upcoming seminar sessions and to allow members of the seminar to raise questions or engage in discussion outside of the seminar. Initially the list will be unmoderated, which will enable all (but only) subscribers to send email to the list. (You will need to send email from the address you use to register for the list.) If this is abused, we will need to move to a moderated list.

To subscribe, you simply need to send an email message to the following address: After you send the subscribe request, you will receive a reply that will ask you to confirm your request. Follow the directions in this message to confirm your subscription. If you later want to remove yourself from this list, send email to

5. Schedule of Classes and Readings

The following schedule is subject to revision, especially in light of interests from the seminar. It does, though, provide a relatively accurate account of what we will cover and the reading that will be required.

September 25: The New Mechanistic Philosophy

Machamer, Peter, Lindley Darden, and Carl Carver (2000), Thinking About Mechanisms. Philosophy of Science 67: 1-25.

Craver, Carl F. and Darden, Lindley (2005). Introduction. Studies in the History and Philosophy of Biological and Biomedical Sciences 36: 233-244.

Bechtel, W. and Abrahamsen, A. (2005). Explanation: A Mechanistic Alternative. Studies in History and Philosophy of the Biological and Biomedical Sciences , 36, 421-441.

Thagard, Paul (1998). Explaining Disease: Causes, Correlations, and Mechanisms. Minds and Machines 8: 61-78.

October 2: Mechanism and Causality

Glennan, Stuart (1996). Mechanisms and the Nature of Causation. Erkenntnis 44: 49–71.

Woodward, James (2002). What is a Mechanism? A Counterfactual Account. Philosophy of Science (Supplement) 69: S366-S377.

Bogen, James (2005). Regularities and Causality; Generalizations and Causal Explanations. Studies in History and Philosophy of Biological and Biomedical Science, 36: 397-420.

October 9: Representing Mechanisms

Glennan, Stuart S. (2005). Modeling Mechanisms. Studies in History and Philosophy of Biological and Biomedical Sciences 36: 443-464.

Laura Perini. (2005). Explanation in Two Dimensions: Diagrams and Biological Explanation. Biology & Philosophy 20:2-3, 257-269.

Wright, Cory (forthcoming). Scientific Explanation: Mechanistic, Ontic, Epistemic.

October 16: Discovering and Testing Mechanisms: Reasoning Strategies

Darden, Lindley (2002). Strategies for Discovering Mechanisms: Schema Instantiation, Modular Subassembly, Forward/Backward Chaining. Philosophy of Science (Supplement ) 69: S354-S365

Thagard, Paul (2003). Pathways to Biomedical Discovery. Philosophy of Science 70, 235-254

October 23: Discovering and Testing Mechanisms: Experimental Strategies

Craver, Carl F. (2003). The Making of a Memory Mechanism. Journal of the History of Biology. 36(1): 153-195.

Darden, L., and Craver, Carl F.(2002) Strategies in the Interfield Discovery of the Mechanism of Protein Synthesis, Studies in the History and Philosophy of the Biological and Biomedical Sciences, 33, 1-28.

Bechtel, William (in press). The epistemology of evidence in cognitive neuroscience. In R. Skipper Jr., C. Allen, R. A. Ankeny, C. F. Craver, L. Darden, G. Mikkelson, and R. Richardson (eds.), Philosophy and the Life Sciences: A Reader. Cambridge, MA: MIT Press.

October 30: Generalizing Mechanisms From Model Cases (Marta Halina)

Ankeny, Rachel. (2007). Model organisms as case-based reasoning: Worms in contemporary biomedical science, In A. Creager, E. Lunbeck, and M.N. Wise. Chapel Hill, (eds.), Science without laws: Model systems, cases, exemplary narratives. Chapel Hill, NC: Duke University Press.

Bechtel, William (forthcoming). Generalization and Discovery Through Conserved Mechanisms: Cross Species Research on Circadian Oscillators.

Weber, Marcel. (2005). Model organisms: of flies and elephants in Philosophy of Experimental Biology. New York, NY: Cambridge University Press.

Steel, Daniel. (2007). Extrapolation, capacities, and mechanisms, In Across the boundaries: Extrapolation in biology and social science. New York, NY: Oxford University Press.

November 3: Organization and Emergence in Biological Mechanisms (rescheduled to 1:30-3:30 Monday due to PSA)

Boogerd, F. C., Bruggeman, F. J., Richardson, R. C., Stephan, A., & Westerhoff, H. V. (2005). Emergence and its place in nature: A case study of biochemical networks. Synthese, 145, 131-164.

Bechtel, W. (2007). Biological mechanisms: Organized to maintain autonomy. In F. Boogerd, et al., Systems Biology; Philosophical Foundations. New York: Elsevier

Bechtel, William (forthcoming). Complex Biological Mechanisms: Cyclic, Oscillatory, and Autonomous. In C. A. Hooker, Philosophy of Complex Systems. Handbook of the Philosophy of Science, Volume 10. Elsevier.

Moreno, Alvaro, Ruiz-Mirazo, Kepa, and Barandiaran, Xabier (forthcoming). The impact of the paradigm of complexity on the foundational frameworks of biology and cognitive science. In C. A. Hooker, Philosophy of Complex Systems. Handbook of the Philosophy of Science, Volume 10. Elsevier.

November 13: Evolutionary Mechanisms (Joyce Havstad)

Skipper, Robert A. and Millstein, Roberta L. (2005). Thinking about evolutionary mechanisms: Natural Selection. Studies in History and Philosophy of the Biological and Biomedical Sciences , 36, 327-347.

Barros, D. Benjamin (2008). Natural selection as a mechanism. Philosophy of Science, 75, 306-322.

November 20: Mechanism and Reduction: Interfield Theories

Background reading: Darden, L. and Maull, N. (1977). Interfield theories. Philosophy of Science, 44, 43-64.

Darden, Lindley (2005). Relations among fields: Mendelian, cytological and molecular mechanisms. Studies in the History and Philosophy of the Biological and Biomedical Sciences, 36, 349-371.

Bechtel, W. and Abrahamsen, A (2007). In search of mitochondrial mechanisms: Interfield excursions between cell biology and biochemistry. Journal of the History of Biology, 40, 1-33.

December 1: Mechanism and Reduction: Levels and Interlevel Research

Craver, Carl F. (2002).Interlevel Experiments and Multilevel Mechanisms in the Neuroscience of Memory, Philosophy of Science (Supplement) 69: S83-S97.

Craver, Carl F. (2005) Beyond Reduction: mechanisms, multifield integration and the unity of neuroscience Studies in the History and Philosophy of Biological and Biomedical Sciences 36: 373-395.

Craver, Carl F. and Bechtel, William (2007). Top-down causation without top-down causes. Biology and Philosophy, 22, 547-563

Bechtel, William (forthcoming). The Downs and Ups of Mechanistic Research: Circadian Rhythm Research as an Exemplar