Phil 147
Philosophy of Biology
Winter 2010, Tues., Thurs., 2:00-3:20 pm

1. Course Description

The various sciences each have a subject matter—biology, in particular, studies the processes involved in living organisms. Philosophy of biology likewise has a subject matter—biology itself. As a part of philosophy of science, a major part of the goal in philosophy of biology is to understand the ways in which biologists produce knowledge. This inquiry addresses such questions as: What kinds of explanations do biologists provide? What sort of epistemic status do the various claims of biology have? What kinds of investigatory tools does biology employ and how are they evaluated epistemicly? Beyond the methods and results of biology proper, philosophy of biology is interested in the relations between biology and other human inquiries. One focus is downwards to more fundamental sciences, giving rise to the question of how biology relates to physics and chemistry. Another focus is upwards to the social sciences and the humanities, generating questions about implications developments in biology have for such things as human social conduct and ethics. Lastly, developments in biology itself have given rise to core conceptual questions within biology such as what are species and how should one understand concepts such as fitness and function. These questions are theoretical questions in biology itself, and philosophers and biologists often engage each other directly in addressing these questions.

Our investigation of biology will look both at its history and its contemporary practice. The reason for turning to its history is that many of the fundamental ideas that guide contemporary biology were developed over the last 200 years and can be identified more crisply during the historical development of modern biology. Many of the same issues, continue to be the focus in contemporary biology. Students are invited and encouraged to draw upon their own knowledge of biology and its history in class discussions.

Given the nature of the class, substantial material will be presented in lectures that goes beyond what is included in the readings. Also, philosophy is an activity, and learning activities requires active engagement. Accordingly, class attendance and discussion is critical. Although we will have discussions on other occasions as well, several classes are designated as discussion classes and the topics for discussion in these classes will be determined by students.

2. Course Requirements

Class attendance is mandatory. Missing classes more than very occasionally will result in a reduction in your grade. To get the most out of the class, it is absolutely essential that you come to class having read the assigned material and being prepared to discuss it. This does not mean that you are expected to understand everything in the assigned reading prior to class. Part of the function of classes will be to clarify and interpret the assigned readings. To ensure that this happens and to foster subsequent discussions in class, you will be required to turn in a very short (one paragraph) comment or question on readings assigned during each week of the quarter. You can write about anything you found interesting, puzzling, strange, clearly wrong, provocative, etc. These will be graded as acceptable or unacceptable. To ensure that your submission is acceptable, your comment or question must demonstrate that you have read and thought about the assigned material. (Your paragraph may focus on one specific part of the reading--do not try to discuss everything.) These must be submitted as email (as plain text, not as attachments) to phil147@mechanism.ucsd.edu by 6AM on days marked with an asterisk in the schedule of classes below. You must turn in eight acceptable weekly assignments to receive a passing grade for the course. (If I do not respond with a note that your submission is unacceptable, you can assume that it acceptable.)

Your base grade in the course will be based on two examinations and one 3-5 page paper. The mid-term and final examination will each count for 30% of your grade and the paper will count for 40% of the grade. The paper, due by NOON on Friday, February 26, must be on one of the topics that will be assigned in class. If possible, the paper should be submitted in Word by email attachment (please be sure to check for viruses before submitting your file!) to papers@mechanism.ucsd.edu. Above average or below averge participation in class discussions can result in a raising or lowering of your final grade from what is determined by the above percentages on these other assignments.

3. Texts

All of the reading assignments can be found by following links on the web site. See the schedule of classes and readings below.

4. Email List

There is an email distribution lists for this course. 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 to allow me to distribute information regarding due dates for assignments, changes of schedule, etc. Some of this information is crucial, and some of it may be distributed early on. To subscribe, you simply need to send an email message to the following address: philbio-subscribe@mechanism.ucsd.edu. After you send the subscribe request, you will receive a reply from philbio-subscribe@mechamism.ucsd.edu that will ask you to confirm your request. Follow the directions in this message to confirm you subscription. If you later want to remove yourself from this list, send email to philbio-unsubscribe@mechanism.ucsd.edu.

Only I have authorization to send mail to this list. There should be no spam. If you receive mail from this list that is not from me, be assured that I will as well and will take measures to block further abuse. (The welcome message you receive suggests that you can send email to the list. Sorry, but you cannot. If there is interest in setting up a voluntary discussion list for the class to which anyone can submit, I am happy to do so, but participation will not make it required.)

5. Schedule of Classes and Readings

Note: This schedule of reading assignments is tentative and subject to revision. When powerpoints from lectures are available, there will be a link from the lecture title to the pdf file. Dates with asterisks are dates on which comments/question paragraphs on the reading are due. These comments/questions must be sent to phil147@mechanism.ucsd.edu by 6 AM on the dates indicated.

Recommended: William Havey: On The Motion Of The Heart And Blood In Animals.

January 7: The Cell Theory

History of Biology: Cell Theory and Cell Structure: http://www.biologyreference.com/Gr-Hi/History-of-Biology-Cell-Theory-and-Cell-Structure.html

Theodor Schwann (1838), Microscopical Researches into the Accordance in the Structure and Growth of Animals and Plants, Author's Preface and pp. 1-9, 161-215.

Useful links: Richard Robinson, Cell theory: http://fig.cox.miami.edu/~cmallery/150/unity/cell.text.htm

*January 12: The Chemistry of Life

Justig Liebig (1838), Animal Chemistry, or organic chemistry in its application to phyiology and pathology, Preface and pp. 1-23.

Louis Pasteur (1860), “Infusorian Animalcules Living Without Free Oxygen and Determining Fermentation,” pp. 303-307.

Buchner, Eduard (1897). "Alcoholic Fermentation Without Yeast Cells," translation by Herbert C. Friedmann of "Alkoholische Gährung ohne Hefezellen," originally published in Ber. Dt. Chem. Ges. 30, 117-124.

Useful links: John Pebble, History of Biology: Biochemistry http://www.biologyreference.com/Gr-Hi/History-of-Biology-Biochemistry.html

January 14 : Vitalism and Organized Mechanisms

Xavier Bichat, Physiological Researches on Life and Death. (Translated by F. Gold. Boston: Richardson and Lord, 1827, pp. 9-24.)

William Bechtel and Robert C. Richardson, Vitalism, Routledge Encyclopedia of Philosophy.

Claude Bernard, Introduction à l'étude de la médecine expérimentale. (Paris: J.B. Baillière et Fils, 1865, pp. 85-92, 101-4, 107-112, 265-301.).

*January 19: Discussion

January 21: Background to Darwin

Phillip Sloan (2008), Evolution, Stanford Encylopedia of Philosophy, Part 1.

Charles Darwin (1859), On the origin of species (introduction and chapters 1-3).

Useful links: Vassiliki Betty Smocovitis, History of Evolutionary Thought, http://www.biologyreference.com/Gr-Hi/History-of-Evolutionary-Thought.html; 17th-19th Century Discoveries that Led to the Acceptance of Biological Evolution, http://anthro.palomar.edu/evolve/default.htm

*January 26: Darwin's Account of Evolution by Natural Selection

Charles Darwin (1859), On the origin of species (chapters 4, 6, 9, 14).

Phillip Sloan (2008), Evolution, Stanford Encyclopedia of Philosophy, Part 2.

James Lennox (2004), Darwinism, Stanford Encyclopedia of Philosophy, Parts 1 and 2.

Useful link: About Darwin http://www.aboutdarwin.com/index.html

January 28: 19th Century Reactions to Darwin

Samuel Wilberforce (1860). On Darwin's Origin of Species. Essays Contributed to the Quarterly Review, 2 Vols., (London, 1874), I.92-95.

Huxley, Thomas H. Time and Life: Mr. Darwin's "Origin of Species" Macmillan's Magazine (1859).

Phillip Sloan, Evolution, Stanford Enclycopledia of Philosophy, Part 3.1.

*February 2: Discussion

February 4: Midterm Exam

February 9: Mendel: Darwin’s Savior or Opponent?

Gregor Mendel (1865), Experiments in Plant Hybridization, Verhandlungen des Naturforschenden Vereines in Brüun, 4, 3-47.

Hans-Jörg Rheinberger and Staffan Müller-Wille (2009), Gene, Stanford Encyclopedia of Philosophy, Parts 1 and 2.

Useful Links: An Introduction to Mendelian Genetics http://anthro.palomar.edu/mendel/default.htm; Lynn Nyhart, History of Biology: Inheritance, http://www.biologyreference.com/Gr-Hi/History-of-Biology-Inheritance.html

*February 11: The Evolutionary Synthesis

Semir Okasha (2006), Population Genetics, Stanford Encyclopedia of Philosophy.

Phillip Sloan (2008), Evolution, Stanford Encyclopedia of Philosophy, Part 3.2.

Useful links: Synthetic Theory of Evolution: An Introduction to Modern Evolutionary Concepts and Theories http://anthro.palomar.edu/synthetic/default.htm; Paul Cabe, Population Genetics, http://www.biologyreference.com/Ph-Po/Population-Genetics.html

February 16: Ontology of Evolution: Species

Marc Ereshefsky (2007), Species, Stanford Encyclopedia of Philosophy.

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

Useful link: Ann E. Kessen and Robert M. Zink, Species, http://www.biologyreference.com/Se-T/Species.html; Defining a Species, http://evolution.berkeley.edu/evosite/evo101/VADefiningSpecies.shtml; Species Problem (Wikipedia), http://en.wikipedia.org/wiki/Species_problem

*February 18: Ontology of Evolution: Units and Levels

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

Useful link: Unit of Selection (Wikipedia), http://en.wikipedia.org/wiki/Unit_of_selection; Barry Sinervo, Levels of Selection, http://bio.research.ucsc.edu/~barrylab/classes/animal_behavior/LEVELS.HTM

February 23: Teleology and Function

Larry Wright (1973), Functions, The Philosophical Review, 82, pp. 139-168; especially the section entitled "An alternative view."

Cummins, Robert (1975), Functional analysis, The Journal of Philosophy, 72, 761-745; especially part III.

Colin Allen (2003), Teleological Notions in Biology, Stanford Encyclopedia of Philosophy.

*February 25: Discussion

February 26: 3-5 Page paper due by NOON. Email to papers@mechanism.ucsd.edu

March 2: Bringing Back Organisms and Development

S. J. Gould and R. Lewontin. (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.

Scott F. Gibert (2003). The morphogenesis of evolutionary developmental biology. International Journal of Developmental Biology, 47, 467-477.

Paul E. Griffiths, & Russell D. Gray (2001), Darwinism and Developmental Systems, in S. Oyama, P.E. Griffiths, R.D. Gray (Eds) Cycles of Contingency: Developmental Systems and Evolution, pp. 195-218. Cambridge: MIT Press.

Useful link: Evo-devo, http://evolution.berkeley.edu/evolibrary/article/evodevo_01; Evolutionary Developmental Biology (Wikipedia), http://en.wikipedia.org/wiki/Evolutionary_developmental_biology

*March 4: Biology and the New Mechanistic Philosophy of Science

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

Lindley Darden and James Tabery (2009), Molecular Biology. Stanford Encylopedia of Philosophy.

Bechtel, W. and Abrahamsen, A. (2009). Decomposing, Recomposing, and Situating Circadian Mechanisms: Three Tasks in Developing Mechanistic Explanations. In Leitgeb, H. and Hieke, A. (Eds.), Reduction and Elimination in Philosophy of Mind and Philosophy of Neuroscience (pp. 173-186). Frankfurt: Ontos Verlag.

March 9: Living Mechanisms as Complex Systems

Bruce Weber, (2008). Life. Stanford Encyclopedia of Philosophy

Bechtel, W. and Abrahsmen, A. (2010). Complex biological mechanisms: Cyclic, oscillatory, and autonomous. In C. A. Hooker (Ed.), Philosophy of complex systems. Handbook of the philosophy of science, Volume 10. New York: Elsevier.

Userful Link: Mitchel Resnick and Brian Silverman Exploring Emergence, http://llk.media.mit.edu/projects/emergence/

*March 11: Discussion

March 18 : Final Exam: 3:00-6:00