| Professor: William Bechtel | Office Hours: Wednesday, 2:00-4:00 |
| Office: HSS 8076 | Email: phil147@mechanism.ucsd.edu |
| Telephone: 822-4461 | Webpage: mechanism.ucsd.edu/~bill/teaching/philbio/ |
| Teaching Assistant: Lisa Damm | Office Hour: Tuesday 10:30-11:30 |
| Office: HSS 8089 | Email: ldamm@ucsd.edu |
As a result of the fires in San Diego and the closing of UCSD for the week of October 24th, the schedule for the latter part of the quarter, including the due date for the paper, have been amended. Changes are shown in red.
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 have read the assigned material and 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 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 the beginning of class on November 27 changed to November 29, 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!). 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. Readings which are copy-projected are only available on a password controlled portion of the course website. 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 7 AM on the dates indicated.
Recommended:
William Havey: On The Motion Of The Heart And Blood In Animals: http://www.fordham.edu/halsall/mod/1628harvey-blood.html
October 2: The Cell Theory
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: Cell theory: http://fig.cox.miami.edu/~cmallery/150/unity/cell.text.htm
*October 4: The Chemistry of Life
Louis Pasteur (1860), “Infusorian Animalcules Living Without Free Oxygen and Determining Fermentation,” pp. 303-307.
Justig Liebig, Animal Chemistry, pp. 17ff.
From Friedrich Wöhler’s urine to Eduard Buchner’s alcohol ( Herbert C. Friedmann, 1997). In A. Cornish-Bowden (Ed). New Beer in an Old Bottle: Eduard Buchner and theGrowth of Biochemical Knowledge, pp. 67–122, Universitat de València, Valencia, Spain, 1997
http://bip.cnrs-mrs.fr/bip10/newbeer/friedmn.pdf
October 9: 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
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.).
Recommended:
E. Benton (1974). Vitalism in 19th century thought: A typology and reassessment. Studies in History and Philosophy of Science, 5, 17-48
*October 11: Discussion
October 16 : Background to Darwin
Phillip Sloan, Evolution, Part 1
http://plato.stanford.edu/entries/evolution/Charles Darwin, On the origin of species (introduction and chapters 1-3): http://www.literature.org/authors/darwin-charles/the-origin-of-species/
17th-19th Century Discoveries that Led to the Acceptance of Biological Evolution
http://anthro.palomar.edu/evolve/default.htm
*October 18: Darwin's Account of Evolution by Natural Selection
Charles Darwin, On the origin of species (chapters 4, 6, 9, 14)
http://www.literature.org/authors/darwin-charles/the-origin-of-species/Phillip Sloan, Evolution, Part 2
http://plato.stanford.edu/entries/evolution/James Lennox, Darwinism, Parts 1 and 2
http://plato.stanford.edu/entries/darwinism/
October 23 New Date: October 30: 19th Century Reactions to Darwin
Samuel Wilberforce: On Darwin's Origin of Species, 1860: http://www.fordham.edu/halsall/mod/1860wilberforce-darwin.html
Huxley, Thomas H. Time and Life: Mr. Darwin's "Origin of Species" Macmillan's Magazine (1859)
Phillip Sloan, Evolution, Part 3.1
http://plato.stanford.edu/entries/evolution/
*October 25 New Date: November 1 : Discussion
October 30 New Date: November 6: Midterm Exam
*November 1 New Date: November 8: Mendel: Darwin’s Savior or Opponent?
Gregor Mendel (1865), Experiments in Plant Hybridization, Verhandlungen des Naturforschenden Vereines in Brüun, 4, 3-47.
http://www.mendelweb.org/Mendel.htmlHans-Jörg Rheinberger and Staffan Müller-Wille, Gene, Parts 1 and 2
http://plato.stanford.edu/entries/gene/Recommended:
An Introduction to Mendelian Genetics
http://anthro.palomar.edu/mendel/default.htm
November 6 New Date November 13: The Evolutionary Synthesis
Semir Okasha, Population Genetics
http://plato.stanford.edu/entries/population-genetics/Phillip Sloan, Evolution, Part 3.2
http://plato.stanford.edu/entries/evolution/Recommended:
Synthetic Theory of Evolution: An Introduction to Modern Evolutionary Concepts and Theories
http://anthro.palomar.edu/synthetic/default.htm
*November 8 New Date November 15: What are species?
Marc Ereshefsky, Species
http://plato.stanford.edu/entries/species/Ernest Mayr (1996). What is a Species and What Is Not? (Philosophy of Science, 63, 262-277.
http://www.aaas.org/spp/dser/evolution/history/mayr.shtml
November 13 Class cancelled: What gets selected?
Elisabeth Lloyd, Units and Levels of Selection
http://plato.stanford.edu/entries/selection-units/
*November 20: Discussion
(no *) November 15 New Date November 27: 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.
Recommended:
Colin Allen, Teleological Notions in Biology
http://plato.stanford.edu/entries/teleology-biology/
*November 20 See Above : Discussion
*November 27 New Date November 29: Bringing Back Organisms and Development
Note: Paper due by beginning of class
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.
http://www.aaas.org/spp/dser/evolution/history/spandrel.shtmlPaul 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.
http://paul.representinggenes.org/webpdfs/darwin.PDFRecommended:
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.
(no *) November 29 New Date December 4: Molecular and Cellular Mechanisms
Lindley Darden and James Tabery, Molecular Biology
http://plato.stanford.edu/entries/molecular-biology/This reading is now recommend, not required: James D. Watson and Francis H. C. Crick (1953), Molecular structure of Nucleic Acids Nature, 171, 737-738.
http://www.nature.com/nature/dna50/watsoncrick.pdfHans-Jörg Rheinberger and Staffan Müller-Wille, Gene, Parts 3 and 4
http://plato.stanford.edu/entries/gene/This reading is added to this class: Bruce Weber, Life
http://plato.stanford.edu/entries/life/See also:
Seeking the Secret of Life: The DNA story in New York City
http://library.cshl.edu/DNAinNY/Oral history collection at Cold Spring Harbor Laboratory
http://library.cshl.edu/OH/mainMovie.html
December 4 This class is cancelled: Living Mechanisms
Bruce Weber, Life
http://plato.stanford.edu/entries/life/Bechtel, W. (2007). Biological mechanisms: Organized to maintain autonomy. In F. Boogerd, et al., Systems Biology: Philosophical Foundations. New York: Elsevier.
*December 6: Discussion
December 13: Final Exam: 3:00-6:00