Phil 204A
From Reduction to Complexity and Autonomy
Core Course in Philosophy of Science

Fall 2017, Monday, 4:00-6:50

Professor: William Bechtel Office Hours: Thursday, 3:00-4:30 and by appointment
Office: HSS 8076 Email:
Telephone: 822-4461


Wiki Site:

1. Seminar Description

This seminar explores central themes in philosophy of science. Since pioneering work in the mid-20th century, reductiion has been a major theme in philosophy of science. The term reduction, however, means different things to different people: for some it constrasts with emergence or holism, for others it is perfectly consistent.

For the most part, discussions of reduction have addressed only linear, near-equilibrium systems. Many of the challenges to some forms of reduction (especially those common in philosophy) stem from the recognition that many physical systems and all biological organisms exhibit complex dynamical behavior as a result of non-sequential organization of non-linear processes. This recognition has led to significant new developments in the sciences themselves and is pushing philosophers of science to think in new ways. Instead of a layer-cake reduction model, some philosophers of science insist on a multi-scale approach. One strategy for addressing the organization that gives rise to complex behavior is network analysis. Another is the adaptation of concepts from classical mechanics such as constraint to understand self-organizing systems and conctrol hierarchies. Drawing upon these notions, numerous theorists have advanced conceptions of living systems as autonomous systems.

2. Seminar Requirements

Active intellectual engagement with the readings for the course is essential to develop an understanding of the issues addressed in this seminar. Accordingly, the course has a wiki site ( Each registered participant in the seminar is expected to post an approximately 300 word discussion note on the readings assigned each week by the Saturday before the seminar meeting. These discussion notes should engage one of the readings in a critical fashion. The goal is not to summarize the reading since everyone will have read the paper. Rather do one or more of the following or something similar: (1) identify ideas that you find novel and exciting, (2) show a way in which the claims or arguments of the paper might be questioned, or (3) shows some important implications or applications of the ideas in the paper. Note, you need to be very selective; each reading raises a number of issues and you should focus in on one issue that can be constructively addressed in a short discussion. Each participant (including anyone just sitting in on the seminar) should read all of the posted discussion notes and comment on at least two of them by either questioning or extending what is said in the note.

Those registered for the seminar are also expected to write two papers (due dates are October 27 and December 11). These papers should be in the range of 1,500 to 2,000 words and will be based largely on the material we are covering in class (i.e., they are not research papers). Suggested topics will be provided about ten days before papers are due. Papers should be submitted electronically in Word to

For the final grade the two papers and contributions to the wiki site will count equally.

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 complexity. See the schedule of classes and readings below.

4. Academic honesty

Integrity of scholarship is essential for an academic community. The University expects that both faculty and students will honor this principle and in so doing protect the validity of University intellectual work. For students, this means that all academic work must be done by the individual who submits it, without unauthorized aid of any kind. All papers, including discussion pieces., that you submit must be written by you in your own words. If you need to quote someone, be sure to use quotation marks and identify the source. In preparing to writepapers you are encouraged to work with your peers. But the actual writing must be yours. You may ask others to read and provide feedback on your writing, but they should not re-write the text for you. Rather, they can provide comments and you undertake the rewriting.

5. Schedule of Seminars

October 2: Reduction in the Logicist Tradition

Nagel, E. (1961). The structure of science. New York: Harcourt Brace. Chapter 11

Schaffner, K. F. (1967). Approaches to reduction. Philosophy of Science, 34, 137-147.

Recommended for those with little background, not required: Bechtel, W. (1988). Philosophy of Science. Hillsdale, NJ: Erlbaum. Chapters 2: Logical positivism: The received view in philosophy of science and 3: Challenges to logical positivism.

October 9: Reduction in the Mechanist Tradition

Wimsatt, W. C. (1976). Reductive explanation: A functional account. In R. S. Cohen, C. A. Hooker, A. C. Michalos & J. van Evra (Eds.), PSA-1974 (pp. 671-710). Dordrecht: Reidel. As reprinted in Wimsatt, W. C. (2007). Re-engineering philosophy for limited beings: Piecewise approximations to reality. Cambridge, MA: Harvard University Press, Chapter 11.

Machamer, P., Darden, L., Craver, C. F. (2000). Thinking about mechanisms. Philosophy of Science, 67, 1-25.

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

October 16: Complex Dynamics in Physical Systems

Hooker, C. A. (2011). Introduction to philosophy of complex systems: A. Towards a framework for complex systems. In C. A. Hooker (Ed.), Handbook of complex systems. Vol 10. Handbook of the philosophy of science (pp. 3-90). Amsterdam: Elsevier. Required: pp. 3-40 and 53-63.

Bishop, R. C. (2011). Metaphysical and epistemological issues in complex systems. In C. A. Hooker (Ed.), Handbook of complex systems. Vol 10. Handbook of the philosophy of science (pp. 105-135). Amsterdam: Elsevier.

Recommended, not required: Hooker, C. A. (2011). Conceptualizing reduction, emergence and self-organization in complex dynamical systems. In C. A. Hooker (Ed.), Philosophy of Complex Systems. Volume 10 of the Handbook of the Philosophy of Science (pp. 195-222): Elsevier.

October 23: Complex Dynamics in Biological Systems

Rosen, R. (1985). Organisms as causal systems which are not mechanisms: An essay into the nature of complexity. In R. Rosen (Ed.), Theoretical biology and complexity: Three Essays on the Natural Philosophy of Complex Systems (pp. 165-203). New York: Academic Press.

Bechtel, W. (2010). The downs and ups of mechanistic research: Circadian rhythm research as an exemplar. Erkenntnis, 73, 313-328

Wolkenhauer, O., & Muir, A. (2011). The complexity of cell-biological systems. In C. A. Hooker (Ed.), Philosophy of complex systems (pp. 355-384). Amsterdam: Elsevier.

Recommended, not required: Bechtel, W., & Abrahamsen, A. (2011). Complex biological mechanisms: Cyclic, oscillatory, and autonomous. In C. A. Hooker (Ed.), Philosophy of complex systems. Handbook of the philosophy of science (Vol. 10, pp. 257-285). New York: Elsevier.

October 30: Modeling and Explaining at Multiple Scales

Batterman, R. W. (2017). Autonomy of theories: An explanatory problem. Noûs

Bursten, J. R. (2016). Multiscale modeling: Beyond non-mereological relations. Phil Sci Archive.

Gross, F., & Green, S. (2017). The Sum of the Parts: Large-Scale Modeling in Systems Biology. Philosophy, Theory, and Practice in Biology, 9, 10; especially parts IV and V.

Recommended but nto required: Green, S., & Batterman, R. (2017). Biology meets physics: Reductionism and multi-scale modeling of morphogenesis. Stud Hist Philos Biol Biomed Sci, 61, 20-34.

Recommended but not required: Batterman, R. W. (2013). The Tyranny of Scales. In R. W. Batterman (Ed.), The Oxford Handbook of Philosophy of Physics. Oxford: Oxford University Press.

November 6: Network Science and the Systematic Study of Organization

Watts, D., & Strogratz, S. (1998). Collective dynamics of small worlds. Nature, 393, 440-442.

Barabási, A.-L., & Bonabeau, E. (2003). Scale-free networks. Scientific American, 50-59.

Alon, U. (2007). Network motifs: Theory and experimental approaches. Nature Reviews Genetics, 8, 450-461.

Green, S., Şerban, M., Scholl, R., Jones, N., Brigandt, I., & Bechtel, W. (2017). Network analyses in systems biology: new strategies for dealing with biological complexity. Synthese

Recommended but not required: Levy, A., & Bechtel, W. (2013). Abstraction and the organization of mechanisms. Philosophy of Science, 80, 241-261.

November 13: A New Conceptual Framework for Mechanism: Constraints, Control, and Heterarchy

Pattee, H. H. (1972). The nature of hierarchical controls in living matter. In R. Rosen (Ed.), Foundations of Mathematical Biology (Vol. 1: Subcellular systems, pp. 1-22). New York: Academic Press.

Hooker, C. A. (2013). On the Import of Constraints in Complex Dynamical Systems. Foundations of Science, 18, 757-780. Part 1 required; parts 2 and 3 recommended.

Winning, J. and Bechtel, W. (manuscript). Rethinking causality in biological and neural mechanisms: Constraints and control

Recommended but not required: Pattee, H. H. (1970). The problem of biological hierarchy. In C. H. Waddington (Ed.), Towards a theoretical biology 3: Drafts (pp. 117-136). Edinburgh: Edinburgh University Press.

November 20: Autonomy in Single-Celled Organisms

Varela, F. J. (1979). Principles of biological autonomy. New York: North Holland. Part 1. Especially chapters 1-4 and 7.

Moreno, A., & Mossio, M. (2015). Biological autonomy: A philosophical and theoretical inquiry. Dordrecht: Springer. Chapters 1 and 3.

November 27: Interlevel Causation: Bottom-up and Top-down

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

Moreno, A., & Mossio, M. (2015). Biological autonomy: A philosophical and theoretical inquiry. Dordrecht: Springer, Chapter 2.

Bechtel, W. (2017). Top-down causation in biology and neuroscience. In M. Paolini Paoletti & F. Orilia (Eds.), Philosophical and scientific perspectives on downward causation (pp. 203-231). New York: Routledge.

December 4: Autonomy in Multi-Cellular Organisms

Moreno, A., & Mossio, M. (2015). Biological autonomy: A philosophical and theoretical inquiry. Dordrecht: Springer, Chapter 6

Dupre, J., & O'Malley, M. A. (2009). Varieties Of Living Things: Life At The Intersection Of Lineage And Metabolism. Philosophy and Theory in Biology, 1.