Syllabus for Functions and Mechanisms in the Life Sciences, Spring 2007 Valid HTML 4.01!
http://mypage.iu.edu/~colallen/Courses/X755/index.html — version 2007-04-12
HPSC X755 — Function and Mechanism in the Life Sciences
Meeting time: Tu 4:15:-6:45; Location: Sycamore 022

Instructor: Colin Allen, PhD <colallen@indiana.edu>
Office / Telephone: [Goodbody 113 / 855-8916] and [Eigenmann 804 / 856-3868]
Office hours: Thursdays 1-2 in Goodbody 113, and by appt.

Course Description

Among philosophers of biology, increasing attention is being paid to ways in which the notions of function and mechanism are linked. Meanwhile the life sciences are providing an increased appreciation of the complexity of the interactions that comprise biological systems at all levels, from molecular to ecological. What notions of function or mechanism are operative in the life sciences? And do the latest developments in biology undermine or support the idea that there are distinctively "functional" modes of explanation in the life sciences that have no counterparts in the physical sciences?

To address these questions, the first third of the course will be spent getting up to speed on the past and current literature on functions. The second third will be spent covering the more recent literature on mechanisms. The final third will be spent on applications to various issues in the life sciences, such as genomics, embryology, self-organization, and even the cognitive sciences (which I say should be considered a life science, even if some wish it weren't so). Along the way we will encounter many traditional questions in the philosophy of science, such as the nature of causation and the merits of reductionism.

Grading (Tentative)

Grades will be based on performance in the following four categories:

  1. Classroom presentations* (35%)
  2. First writing assignment due April 3 (20%)
  3. Second writing assignment due May 1 (35%)
  4. General participation in discussions (10%)

Assignments

Presentation (~10 mins): Report on a recent article (since 2000) that either cites or is cited by one of the assigned readings for Functions & Teleology portion of the class (it can be one of the optional readings if we did not discuss it in class, but please clear it with me first).

Writing assignment #1 (April 3): Pretend that you have been commissioned to write an entry for the SEP on "Mechanisms in the Life Sciences". Write an introduction to the topic of 3-5 paragraphs, and provide a table of contents as found in all SEP entries, with at least 3 additional sections. For each section briefly (in one paragraph) sketch the issues that should be addressed in that section. Starting with the readings listed on the syllabus, and extending it as you are able, provide a bibliography with brief annotations about relevance to the sections of your outline.

Writing assignment #2 (May 1): Either (a) develop your SEP-style entry to approx. 5000 words, or (b) write a critical, argumentative piece related to an issue mentioned in my (revised) "Teleleogy in Biology" article or in your "Mechanisms in the Life Sciences" article outline, or (c) survey some portion of the recent empirical literature (e.g., all the articles in a specific scientific journal for the past few years), tabulate the uses of the terms "function" and/or "mechanism" appearing in that literature, and use your data to assess whether philosophers of biology have adequately represented the those uses.

Schedule of Readings and Presentations

All readings will be placed on line where possible, and linked to this syllabus. Any other items that cannot be linked will be placed on photocopy reserve in the department. Some of the links may require access from within the IU campus network and others will require a password that will be given out in class.

This section is under construction — links to readings will be added as they become available. The exact ordering of readings later in the semester may change. Student presentations will also be added later.

Part 1: FUNCTIONS & TELEOLOGY [Full bibliographic information for Part 1 readings]
[1] 1/09 Functions 1: Teleological and Historical Preliminaries
[optional Allen & Bekoff 1994 ; also see historical references under 'Some Additional Resources' below]
 
[2] 1/16 Functions 2: A multiplicity of meanings
Wimsatt 1972
[optional: Ayala 1970 ; Nagel 1977a,1977b]
 
[3] 1/23 Functions 3: The duopoly
Cummins 1975 ; Millikan 1989; Griffiths 1993
[optional: Wright 1973 ; Neander 1991 ; Cummins 2002 ; Millikan 2002 ]
 
[4] 1/30 Functions 4: Biology, not philosophy of mind?
Amundson & Lauder 1994 ; Griffiths 2006
[optional: Bock & von Wahlert 1965 ; Rudwick 1964 ; Wouters 2005]
 
[5] 2/06 Functions 5: Here today, gone tomorrow?
Rosenberg 1997 ; Keller 2005 ; Walsh 2007
[optional: Keller 1999]
 
Part 2: MECHANISMS
[6] 2/13 Mechanisms 1: Why mechanisms?
Bechtel & Richardson 1993 (ch2) ; Machamer, Darden & Craver 2000
[optional: Westfall 1971; Glennan 1996 ; Glennan 2002 ; Winther 2006 ]
 
[7] 2/20 Mechanisms 2: What is a mechanism?
Presentations by Stephen Friesen [Skipper & Millstein] and Carlos Zednik [Bechtel 2007]
Woodward 2002
[optional: Craver 2007 (ch1)]
 
[8] 2/27 Mechanisms 3: Explanation
Presentations by Sean Valles [Walsh 2006] and Matt Carlson [Glennan 2002b]
Bechtel & Abrahamsen 2005 [preprint version]
[optional: Bechtel 2006 (ch2) ; Craver 2007 (chs2,3) ]
 
[9] 3/06 Mechanisms 4: Reduction
Presentations by Grant Goodrich [Craver Chapter 5 (not whole book!)] and Matt Schmelzer [Ruse 2005]
Gillett 2007
[optional: Weber 2005 (ch2) ; Bechtel 2007 ; Craver 2007 (ch5) ]
 
  [*] 3/13 SPRING BREAK
 
[10] 3/20 Mechanisms 5: Emergence
Presentations by Kari Theurer [Bechtel ms. on Reducing Psychology] and Kathryn Carter [Von Eckardt & Poland 2004]
Boogerd et al. 2005
[optional: Craver & Bechtel 2006]
 
[11] 3/27 Paul Griffiths visits class
Reread Griffith's 2006 and read Rosenberg 2006
 
Part 3: APPLICATIONS
[12] 4/03 Applications 1: Functions and mechanisms in the post genomic era
Presentations by Jason Lopez [Polger & Sufka 2004] and Kevin Houser [Dupre 1996, ch6]
Brazhnik 2002 ; Stotz 2007
 
[13] 4/10 Applications 2: Mechanisms of mind
Presentations by Jennifer Miller [Podos 2004] and Christopher Wach [Psillos 2004]
Aizawa & Gillett 2007
 
[14] 4/17 Applications 3: Formal methods
van Helden et al. 2002 ; Andrews et al. 2006
[optional: Gene Ontology Consortium 2000 ; Johansson et al. 2005]
 
  [*] 4/20 HPSC Colloquium : Title tba William Bechtel
 
[15] 4/24 Bill Bechtel visits class
a new Bechtel paper
 

Some Additional Resources

Please send other links/documents as you find them.

Teleology/Function Resources:

Mechanism resources:

Statement for Students with Disabilities
The Americans with Disabilities Act (ADA) is a federal anti-discrimination statute that provides comprehensive civil rights protection for persons with disabilities. Among other things, this legislation requires that all students with disabilities be guaranteed a learning environment that provides for reasonable accommodation of their disabilities. If you believe you have a disability requiring an accommodation, please contact IU Disability Services for Students.

Statement about Academic Misconduct
University rules concerning academic misconduct will be rigorously enforced in this class. See IU Code of Ethics, Part II for details.