Gene in a Bottle
Paul Thiessen

PHL 484:

Philosophy of Biological Science

Dr. Robert T. Pennock
Spring 2007


  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)-
Check here periodically for late-breaking news.

  1. Extra-credit talk opportunity:  Jan 24.  Luis H. Toledo-Pereyra, M.D.   Professor of Surgery and Director of Research, MSU Kalamazoo Center for Medical Studies  "Teaching Medicine through the History of Disease"  12-1:00 p.m. C-102 East Fee Hall
  2. Extra-credit talk opportunity:  Tuesday, February 13, 2007
    Dr. James ‘Jack’ Justus
    Noon: Job Talk in Fisheries & Wildlife Department (154 Nat Res)
    Title: “Defining Ecological Stability"
  3. Extra-credit talk opportunity: Tuesday, February 20, 2007
    Dr. Michael Nelson
    Noon: Job Talk in Fisheries & Wildlife Department (154 Nat Res)
    Title: “Evolutionarily Significant Units: Units of Conservation Worth Wanting?”
  4. Extra-credit talk opportunity:  Tuesday, February 27, 2007
    Dr. Evelyn Brister
    Noon: Job Talk in Fisheries & Wildlife Department (154 Nat Res)
    Title: “Tensions between Objectivity and Advocacy for Environmental Scientists”

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. We will look especially into evolutionary computation and the concepts that unite this emerging field of research. 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: 3 pm to 4:20 pm
Place: C-103 Holmes Hall.

Instructor Contact Info.

Name: Dr. Robert T. Pennock.
Office: Holmes Hall W-35.
Office hours: Mondays & Wednesdays 9 - 10 am, 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)
  • Kenneth A. DeJong. Evolutionary Computation. The MIT Press. (2002)

Tentative Reading Assignments

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

Week 1  
Jan 8 Introductory Business - No readings
Jan 10 Aristotle "Generation of Animals" - RPB Ch 1
Week 2  
Jan 15 MLK Holiday (No class)
Jan 17 Haldane "What is Life?" - RPB Ch 2
Week 3  
Jan 22 Dennett Darwin's Dangerous Idea Preface & Ch.1; Paley -"Natural Theology" - RPB Ch 3
Jan 24

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

Week 4  
Jan 29 Denton "Beyond the Reach of Chance" - RPB Ch 5 Dawkins "Accumulating Small Change" - RPB Ch 6
Jan 31 Bethall "Darwin's Mistake" - RPB Ch 8 & Gould "Darwin's Untimely Burial" - Ch 9
Week 5  
Feb 5

Dennett Darwin's Dangerous Idea Ch 3 & Ch.4

Feb 7

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

• Student Presentation - Eric Berling & Christian Orlic

Week 6  

Guest speaker Jack Justus
Readings - Sarkar "Wilderness Preservation and Biodiversity Preservation" & "Defining Biodiversity"

Feb 14

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

• Student presentation - Patrick Carden & Matt Faber

Week 7  
Feb 19

Guest speaker Dr. Michael Nelson
Readings - Leopold "The Land Ethic"

Feb 21

Dennett Darwin's Dangerous Idea Ch. 5 & 6

• Student presentation - Andrew Cuda & Lauren Liddell

Week 8  
Feb 26

Guest speaker Dr. Evelyn Brister - CANCELLED
Readings - Russow "Why Do Species Matter?"

Feb 28

GUEST SPEAKER resecheduled for today.  Today's reading and student presentation have been moved to Mar 12.

Take home mid-term exam assigned. Due March 2nd.

Mar 5 & 6

Week 9

Spring Break
Mar 12

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

• Student presentation - Zac Keeley & Melissa Gallardo

Mar 14

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

Student presentation - Matt Faber

Week 10  
Mar 19

Dennett Darwin's Dangerous Idea Ch.8 "Biology is Engineering"

Student presentation - Brian Martin

Mar 21

Ayala "Teleological Explanations" - RPB Ch 18

Student presentation - Zac Keeley

Week 11  
Mar 26

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

Student presentation - Lucas Watts & Brian Martin

Evolutionary computation research project assigned

Mar 28 Library Research Instruction w/ Angela Kille (Meet in Main Library Basement Instruction Room)
Week 12  
Apr 2

Gould "Darwinism & the Expansion of Evo Theory" - RPB Ch 10; Ayala "Beyond Darwinism?" - RPB Ch 11

EI lab (Hubbard Hall G36) open for evolutionary computation research project work.

Apr 4

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

Student presentation - Lauren Liddell

Student presentation - Andrew Cuda

Week 13  
Apr 9

DeJong Evolutionary Computation Ch.1 & 2

Student presentation - Patrick Carden

Evolutionary computation research project Due

Apr 11

DeJong Evolutionary Computation Ch. 3 & 4

Student presentation - Eric Berling


Week 14  
Apr 16

Dennett Darwin's Dangerous Idea Ch.12 "The Cranes of Culture", Ch.13 "Losing Our Minds to Darwin"

Student presentation - Melissa Gallardo

Research Proposal Due

Apr 18

Dennett Darwin's Dangerous Idea Ch.14 "The Evolution of Meanings", Ch 15 "The Emperor's New Mind and Other Fables".

Student presentation - Lucas Watts

Week 15  
Apr 23

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

Student presentation - Christian Orlic

Apr 25 Dennett Darwin's Dangerous Idea Ch.16 & 17 "On the Origin of Morality" & "Redesigning Morality"
Final Exam Week  
May ??? Final Exam Period - 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 & 2-3 page write-ups - 10% each
  • Evolutionary computation research project - 10%
  • Weekly quizzes or 1-page write-ups on readings - 15%
  • Mid-term exam - 15%
  • Research proposal - 5%
  • Final 15 page research paper. - 20%

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
  2. Oral presentation guide

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.

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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: 1/4/07.  Updated: 3/26/07
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