Gene in a Bottle
Paul Thiessen

PHL 484:

Philosophy of Biological Science

Dr. Robert T. Pennock
Spring 2004


  1. Course information
  2. Meeting time and location
  3. Instructor contact info
  4. Important Dates
  5. Required textbooks
  6. Tentative Reading Assignments
  7. Exams
  8. Grading system
  9. Attendance & Other Policies
  10. Scholastic dishonesty policy
  11. Study, Paper & Exam Tips
  12. Discussion Guidelines
  13. Additional information
  14. Useful Links

- Announcements (Last Updated 2/2/04)-
Check here periodically for late-breaking news.

  1. Check the reading schedulebelow for the dates you are assigned to give your presentation. Remember that you need to meet with me AT LEAST ONE WEEK PRIOR to your presentation to discuss what you plan to do. Be sure to read the evaluation guidelines for oral presentations. Presentation length: 15 minutes.

  2. On Wednesday, Feb 18th during class we will attend the talk "On Becoming a Nanoscientist: Shifting Identities in the Probe Microscopy Community" by Cyrus Mody of Cornell University, who is a Lyman Briggs School job candidate. To accommodate this, I have moved all the presentations one day back, as we discussed in class. The mid-term will be a take-home exam due to me on Friday.

Philosophy of Biological Science

Course number: PHL 484.
Description: The course will cover philosophical and methodological issues in biology. The first half of the course will provide students with a good overview of some of the standard discussions in the field, such as the nature of functional explanation, the theory of classification, the species concept, the structure and concepts of evolutionary theory, and some ethical issues related to biological research. In the second half of the course we will look in more detail at the extendibility of evolutionary theory beyond biology, to see how the Darwinian mechanism has a broad power and generality that puts is on a par with other laws in physics. We will look particularly at new theoretical and practical applications of evolution, especially at cutting-edge research in artificial life and evolutionary design. Finally, we will look into evolutionary ethics to see what like a Darwinian perspective may shed on our understanding of morality and what Darwin called "the moral sense." As an advanced senior seminar, this course will be conducted primarily in seminar format, emphasizing class discussion and student led presentations rather than lectures from the professor. We will work to develop skills of effective group discussion and oral presentation.
Prerequisite: Upper-division status


Meeting time and location

Days: Mondays and Wednesdays.
Time: 4:10 pm to 5:30 pm
Place: C-104 Holmes Hall.

Instructor Contact Info.

Name: Dr. Robert T. Pennock.
Office: Holmes Hall W-35.
Office hours: Tuesday 10:30 - 11:30 am, or first 10 minutes of class or by appointment or by open door.
Phone: 432-7701.

Please don't hesitate to contact me to talk about anything substantive related to class. Face-to-face discussions are always the most effective and enjoyable, so the best options are to drop by my office hours or talk to me after class. Send me an e-mail message to set up an appointment if you can't see me another time. (Whenever you send me e-mail or leave a phone message, be sure to give not just your name, but also indicate what course you are in.) I'm always happy to talk philosophy or to discuss your thoughts about your learning. However, if you were absent from class and need to get assignments, notes or other material you missed, you should get that from someone in your base group.

Also, please NEVER send me any attachment to an e-mail unless we have specifically arranged it in advance.


Important Dates

Required texts

  • Michael Ruse, Philosophy of Biology. Prometheus Press (2000)
  • Daniel C. Dennett. Darwin's Dangerous Idea: Evolution and the Meanings of Life. Simon & Schuster (1996)
  • John H. Holland. Emergence From Chaos to Order (Helix Books) Perseus Books Group ( 1999))

Tentative Reading Assignments

NOTE: This is a tentative reading list. Any changes will be announced. Read the selection before class.

Week 1  
Jan 12 Introductory Business - No readings
Jan 14 Aristotle "Generation of Animals" - RPB Ch 1
Week 2  
Jan 19 MLK Holiday (No class)
Jan 21 Haldane "What is Life?" � RPB Ch 2
Week 3  
Jan 26 Dennett Darwin's Dangerous Idea Preface & Ch.1; Paley � "Natural Theology" � RPB Ch 3
Jan 28

Dennett Darwin's Dangerous Idea Preface & Ch.2; Darwin � "Origin of Species" � RPB Ch 4

Week 4  
Feb 2 Denton "Beyond the Reach of Chance" � RPB Ch 5 Dawkins "Accumulating Small Change" � RPB Ch 6
Jan 4 Dennett Darwin's Dangerous Idea Ch.3
Week 5  
Feb 9

Bethall "Darwin's Mistake" � RPB Ch 8 & Gould "Darwin's Untimely Burial" � Ch 9

• Cyrena Knight & Evan Muzzall presentation

Feb 11

Dennett Darwin's Dangerous Idea Ch.4

• Erika Almaguer & Marcel Lenz presenation

Week 6  

Mayr "Species Concepts and their Applications" � RPB Ch 12 Hull "Ontological Status of Species as Evo Units" � RPB Ch 13

• Kyle Sparks & Katrina Walker presentation

Feb 18

Attend talk by Cyrus Mody (Cornell University) - "On Becoming a Nanoscientist: Shifting Identities in the Probe Microscopy Community".

Week 7  
Feb 23

Caplan "Have Species Become Declasse?" � RPB Ch 14 Ridley "Principles of Classification" � RPB Ch 15

• Roger Jump & Jude Pagel presentation

Feb 25

Dennett Darwin's Dangerous Idea Ch. 5 & 6

• Dan Bush& Vinayak Prasad presentation

Week 8  
Mar 1

Williams "Adaptation and Natural Selections" � RPB Ch 16 Kramer "Misuse of the Term Strategy" � RPB Ch 17

• Matt Horn & Sarah Stevens presenation

Mar 3

Dennett Darwin's Dangerous Idea Ch.7; Schaffner "Chemical Systems and Chemical Evolution" � RPB Ch 19

• Jeff Clune & Steve Kreis presentation

Take home mid-term exam assigned. Due March 5th.

Mar 8 & 10

Week 9

Spring Break
Mar 15 Dennett Darwin's Dangerous Idea Ch.8 "Biology is Engineering"
Mar 17 Ayala "Teleological Explanations" � RPB Ch 18
Week 10  
Mar 22

Dennett Darwin's Dangerous Idea Ch. 9 "Searching for Quality"

Steve Kreis presentation

Mar 24

Gould "Darwinism & the Expansion of Evo Theory" � RPB Ch 10

Vinayak Prasad presentation

Week 11  
Mar 29

Dennett Darwin's Dangerous Idea Ch.10 & 11 "Bully for Brontosaurus" & "Controversies Contained"

Marcel Lenz presentation

Mar 31 Library Instruction w/ Terry Link (Main Library Room 1 East)
Week 12  
Apr 5

Holland Emergence Ch.1, 2 & 3

Erika Almeguer presentation

Cyrena Knight presentation

Apr 7

Holland Emergence Ch. 4 & 6

Evan Muzzall presentation

Jude Pagel presentation

Week 13  
Apr 12

Holland Emergence Ch.7 & 8

Roger Jump presentation

Sarah Stevens presentation

Apr 14

Holland Emergence Ch. 9 & 10

Jeff Clune presentation

Research Proposal Due

Week 14  
Apr 19

Holland EmergenceCh. 11 & 12

Special Guest Speaker: John Holland (tentative date)

Apr 21

Dennett Darwin's Dangerous Idea Ch.12 "The Cranes of Culture"


Week 15  
Apr 26

Thomas Henry Huxley "Evolution and Ethics" RPB Ch 29; John L. Mackie "The Law of the Jungle" RPB Ch 30

Dan Bush presentation

Matt Horn presentation

Apr 28 Dennett Darwin's Dangerous Idea Ch.16 & 17 "On the Origin of Morality" & "Redesigning Morality"
Final Exam Week  
May 5th Final Exam Period 5:45 - 7:45 pm - Research paper due


  • Final exam: There will be no final exam, but we will meet during the final exam period to turn in research papers, hear research summaries and complete course evaluations.

Grading system

  • Regular attendance and class participation � 15%
  • Two formal oral presentations & 2-page write-ups � 10% each
  • Weekly quizzes or 1-page write-ups on readings � 15%
  • Mid-term exam � 20%
  • Research proposal � 5%
  • Final 15 page research paper. � 25%

Discussion: As a seminar-style tutorial course, at least half of each period will be devoted to discussion of the material. I expect that you will come to class having completed the assigned reading for the day, and prepared to discuss it in relation to lectures and presentations.

Presentations You will give two 12-15 minute oral presentations during the course, each time in a team of two (though not with the same person both times). You will have to work together to research the topic, after meeting with me at least a week in advance to get some guidance about what specifically to do, and what supplemental readings may be necessary. You and your partner will then prepare a lecture or demonstration to give to your classmates, practicing it in advance according to a sheet of guidelines for effective public speaking. In most cases you will also need to prepare a one-page handout on the material for the class. Finally, within a week of your presentation you must turn in a 2 to 3 page write-up of your presentation to me. Presentations will begin in the fourth week of the course. In the second week of the course I will ask for an ordered list of your presentation preferences, and will assign you to topics to give you as close to your preferences as is possible.

Attendance & Other Policies

  • Late essays will be accepted, but will be docked half a grade per day (e.g, from an equivalent of 4.0 to 3.5).
  • Class participation means not only attendance (5%) [Note: You get one unexcused absence w/o penalty, but then lose a percentage point for each additional missed day, or half a percentage point for arriving late or leaving early], but also regular and active participation in class discussions, workshops, etc. (10%). It is not possible to have a meaningful discussion or to get the most out of lecture unless you come to class having read and thought about the assigned material. Be prepared to answer questions I may ask about the reading and to engage in thoughtful, productive reflection upon it together with your classmates. Often we will break into small discussion groups, and it will waste your colleagues� valuable time if you have not read the material or completed an assigned exercise in advance.
  • Class will start promptly. Please be on time. Arriving late or leaving early counts as a half absence, or more if it causes disruption or inconvenience to your colleagues in class.
  • If for some reason you have to miss a class, you are responsible for getting notes and assignments from a fellow student. If you will have to miss a class because of a team commitment or a religious holiday you must let me know in advance so it will not count as an unexcused absence.

Scholastic dishonesty policy

  • Academic Dishonesty: We will discuss academic integrity in class, but you should know from the start that your work should always be your own. The penalty for cheating or plagiarism will be an F for the course. You are expected to have read MSU's policies on academic integrity.

Additional Information

  1. Paper formatting guidelines may be found within the section titled Study, Paper & Exam Tips

Discussion Guidelines

Here are the guidelines that you generated in class. Please also read my comments about discussion in the Study, Paper & Exam Tips section.

  • Don't monopolize discussion
  • Raise hands to be recognized
  • Don't interrupt someone who is speaking
  • Stay on topic
  • Listen to one another
  • Be open-minded
  • Be respectful of one another
  • Don't take comments personally
  • Use detailed examples sparingly, simple examples plintifully
  • Don't just restate
  • Don't be a jerk

Useful Links

Here I'll put links to other sites that you may find to have useful supplemental information. Let me know if you find ones that would be good to add.

Created: 1/6/04.  Updated: 4/7/04
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