Phil 247
Philosophy of Biology
Fall 2007, Wednesday, 5:00-7:50

1. Course Description

Since the 1970s philosophical interest in the biological sciences has exploded. This course will provide an introduction to the major issues in biology addressed by philosophers (and by biologists interested in the conceptual and foundational issues concerning their field).

The focus is necessarily selective. For example, this course will not historical development of biology prior to the mid-20th century. There will be more coverage of that material in Phil 147, the undergraduate philosophy of biology, and you are welcome to sample the readings on the webpage for that course or to attend lectures for that course when they are of interest.

2. Course Requirements

Students are expected to do the assigned reading and to attend all the class sessions. By 11 am prior to each class session each student should submit a one-paragraph comment or question to the course email list. These may either seek clarification about or raise objections to major points in the reading. The contributions should reflect an effort to understand the assigned material and should provide the context for the issue raised. There are also be three papers assigned during the quarter (due dates are October 20, November 10 (delayed unitl November 17) , and December 10--these dates do not correspond to class days). These papers should be in the range of 1,200 to 1,800 words and will be based largely on the material we are covering in class (i.e., they are not research papers). They should be submitted electronically in Word to papers@mechanism.ucsd.edu

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 biology. See the schedule of classes and readings below.

The literature in philosophy of biology is massive. Even the range of central, important papers exceeds what we can cover in this course. The list below includes many readings (marked with an asterisk) that we will not cover in class but which you may find useful, especially if you choose paper topics to which they are relevant.

4. Email List

There is an email list for this seminar: gradpbio@mechanism.ucsd.edu. 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: gradpbio-subscribe@mechanism.ucsd.edu. After you send the subscribe request, you will receive a reply from gradpbio-subscribe@mechanism.ucsd.edu 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 gradpbio-unsubscribe@mechanism.ucsd.edu.

4. Schedule of Classes

Readings marked with an asterisk are recommended only.

October 3: Setting the Stage--the Evolutionary Synthesis

Plutynski, A., & Ewens, W. J. (2006). Population genetics. In S. Sarkar & J. Pfeifer (Eds.), Philosophy of Science: An encyclopedia (pp. 578-585). New York: Routledge.

Semir Okasha, Population Genetics, Stanford encyclopedia of philosophy

*Sober, Elliott (2006). Natural selection. In S. Sarkar & J. Pfeifer (Eds.), Philosophy of Science: An encyclopedia (pp. 497-502). New York: Routledge.

October 10: Mechanisms of Evolution: Adaptationism and its Critics

Neutralism versus Selection

Beatty, J. (1984). Chance and natural selection. Philosophy of Science, 51, 183-211.

Millstein, R. L. (2002). Are Random Drift and Natural Selection Conceptually Distinct? Biology and Philosophy, 17, 33-53.

Adaptationism

Orzack, S. H., & Sober, E. (1994). Optimality models and the test of adaptationism. The American Naturalist, 143, 361-380.

Brandon, R., & Rausher, M. D. (1996). Testing Adaptationism: A Comment on Orzack and Sober. The American Naturalist, 148, 189-201.

Orzack, S. H., & Sober, E. (1996). How to formulate and test adaptationism. The American Naturalist, 148, 202-210.

*Gould, S. J., & Lewontin, R. C. (1979). The spandrels of San Marco and the Panglossian paradigm: A critique of the adaptationist programme. Proceedings of the Royal Society of London, Series B, 205, 581-598.

*Maynard Smith, J. (1978). Optimization theory in evolution. Annual Review of Ecology and Systematics, 9, 31-56.

*Beatty, J. (1997). Why do biologists argue like they do? Philosophy of Science, 64, S432-S443.

*Godfrey-Smith, P. (1999). Adaptationism and the power of selection. Biology and Philosophy, 14, 181-194.

*Okasha, S. (2006). Adaptation and adaptationism. S. Sarkar & J. Pfeifer (Eds.), Philosophy of Science: An encyclopedia (pp. 3-7). New York: Routledge.

October 17: Taxonomy and Ontology: Species and Higher Taxa

Hull, D. L. (1978). A matter of individuality. Philosophy of Science, 45, 335-360.

Kitcher, P. (1984). Species. Philosophy of Science, 51, 308-333.

Mayr, E. (1996). What is a Species and What Is Not? Philosophy of Science, 63, 262-277.

Sokal, R. R., & Crovello, T. J. (1970). The biological species concept: A critical evaluation. The American Naturalist, 104, 127-153.

Mishler, B. D., & Brandon, R. N. (1987). Individuality, pluralism, and the phylogenetic species concept. Biology and Philosophy, 2, 397-414.

*Ghiselin, M. T. (1974). A radical solution to the species problem. Systematic Zoology, 23, 536-544.

*Hull, D. L. (1976). Are species really individuals? Systematic Zoology, 25, 174-191.

*Mayr, E. (1987). The ontological status of species: Scientific progress and philosophical terminology. Biology and Philosophy, 2, 145-166.

*Ereshefsky, Marc (2007). Species. Stanford encyclopedia of philosophy.

October 24 (Delayed until October 31) : Reductionism and Evolution: Units and Levels of Selection

Wimsatt, W. C. (1980). Reductionistic research strategies and their biases in the units of selection controversies. In T. Nickles (Ed.), Scientific discovery: Case studies (pp. 213-259). Dordrecht: Reidel.

Wilson, D. S. (1989). Levels of selection: An alternative to individualism in the human sciences. Social Networks, 11, 257-272.

Wilson, D. S., & Wilson, E. O. (2008). Rethinking the theoretical foundations of sociobiology. Quarterly Review of Biology.

Wilson, R. A. (2006). Levels of selection. In M. Matthen & C. Stephens (Eds.), Handbook of the Philosophy of Science. Volume 2: Philosophy of Biology (pp. 155-176). New York: Elsevier.

*Hull, D. L. (1980). Individuality and selection. Annual Review of Ecology and Systematics, 11, 311-332.

*Elisabeth Lloyd (2005), Units and Levels of Selection, Stanford Encyclopedia of Philosophy

October 31 (Delayed unitl November 7) : Reductionism and Genetics: Molecular Genetics

Kitcher, Philip (1984), 1953 and all that: A Tale of Two Sciences, Philosophical Review 93:335-373.

Waters, C. K. (1994). Genes made molecular. Philosophy of Science, 61, 163-185.

Rosenberg, A. (1997). Reductionism redux: Computing the embryo. Biology and Philosophy, 12, 445-470.

*Maynard Smith, J. (2000). The concept of information in biology. Philosophy of Science, 67, 177-194.

*Griffiths, P. E., & Neumann-Held, E. M. (1999). The many faces of the gene. BioScience, 49, 656-662.

*James D. Watson and Francis H. C. Crick (1953), Molecular structure of Nucleic Acids Nature, 171, 737-738.

*Lindley Darden and James Tabery (2005), Molecular Biology, Stanford Encyclopedia of Philosophy

*Waters, C. K. (1990). Why the anti-reductionist consensus won't survive: The case of classical Mendelian genetics. In PSA 1990 (Vol. 1, pp. 129-139). East Lansing, MI: Philosophy of Science Association.

*Moss, L. (2003). One? two? (Too), many genes. The Quarterly Review of Biology, 78, 57-67.

*Knight, R. (2007). Reports of the death of the gene are greatly exaggerated. Biology and Philosophy, 22, 293-306.

*Downes, S. M. (2006). Biological information. S. Sarkar & J. Pfeifer (Eds.), Philosophy of Science: An encyclopedia (pp. 64-68). New York: Routledge.

November 7 (Delayed unitl November 14) : What about Development? Developmental Constraints

Amundson, R. (1994). Two concepts of constraint: Adaptationism and the challenge from developmental biology. Philosophy of Science, 61, 556-578.

Griffiths, P. E. (1996). Darwinism, process structuralism, and natural kinds. Philosophy of Science, 63, Supplement, S1-S9.

Wimsatt, W. C. (1999). Generativity, entrenchment, evolution, and innateness: Philosophy, evolutionary biology, and conceptual foundations of science. In V. G. Hardcastle (Ed.), Where biology meets psychology: Philosophical essays (pp. 139-179). Cambridge, MA: MIT Press.

*Gould, S. J., & Eldredge, N. (1977). Puncutated equilibria: the tempo and mode of evolution reconsidered. Paleobiology, 3, 115-151.

November 14 (Delayed unitl November 21 and will meet from 1:00 to 3:50): What about Development? Evolutionary-Developmental Biology

Griffiths, P. E., & Gray, R. (1994). Developmental systems and evolutionary explanation. Journal of Philosophy, 91, 277-304.

Griffiths, P. E., & Gray, R. (1997). Replicator II -- Judgement day. Biology and Philosophy, 12, 471-492.

Sterelny, K., Smith, K. C., & Dickison, M. (1996). The extended replicator. Biology and Philosophy, 11, 377-403.

Schaffner, K. F. (1988). Genes, behavior, and developmental emergentism: One Process, Indivisible? Philosophy of Science, 65, 209-252.

Griffiths, P. E., & Knight, R. (1998). What is the developmental challenge? Philosophy of Science, 65, 253-258.

*Jason Scott Robert, Brian K. Hall, and Wendy M. Olson, (2001), Bridging the gap between developmental systems theory and evolutionary developmental biology. Bioessays. 10, 954-62.

November 21 (This is the class likely to be cancelled): Genetics and Systems Biology: Post-Genomic Molecular Genetics

Griffiths, P. E., & Stotz, K. C. (in press). Gene. In D. Hull & M. Ruse (Eds.), Cambridge companion to the philosophy of biology. Cambridge, England: Cambridge University Press.

Stotz, K. C. (in press). 2001 and all that: a tale of a third science. Biology and Philosophy.

Sarkar, S. (2006). Molecular biology. In S. Sarkar & J. Pfeifer (Eds.), Philosophy of science: an encyclopedia (pp. 480-490). New York: Routledge

November 28: Complexity: Self-organization and Emergence

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.

Edelmann, J. B., & Denton, M. J. (2007). The uniqueness of biological self-organization: Challenging the Darwinian paradigm. Biology and Philosophy, 22, 579-601.

Kauffman, S. A., & Clayton, P. (2005). On emergence, agency, and organization. Biology and Philosophy, 21, 501-521.

*Kauffman, S. A., Logan, R. K., Este, R., Goebel, R., Hobill, D., & Shmulevich, I. (in press). Propogating organization: An enquiry. Biology and Philosophy.

December 5: What is Life? Minimal Living Systems

Collier, J. D. and Hooker, C. A. (1999). Complexly organized dynamical systems. Open Systems and Information Dynamics, 6, 241-302.

Ruiz-Mirazo, K. and Moreno, A. (2004). Basic autonomy as a step in the synthesis of life. Artificial Life, 10: 235-259.

*Bechtel, W. (2006). Biological mechanisms: Organized to maintain autonomy. In F. Boogerd, et al., Systems Biology: Philosophical Foundations. New York: Elsevier.

*Bruce Weber (2003), Life. Stanford encyclopedia of philosophy.

December 10: Final papers due