Gene in a Bottle
Paul Thiessen

PHL 484:

Philosophy of Biological Science

Dr. Robert T. Pennock
Fall 2011


  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 option: SimBio Evolution Exercises on-line
  2. Proposal guidelines and research paper assignment
  3. Extra Credit option: Changing Humans in a Changing Environment
    Symposium on Human Evolution to be Webcast Live from NABT Conference in Anaheim on Friday, Oct. 14th, 2011 at 4:30 pm. Teachers and students are encouraged to tune in to all or part of the free webcast for an opportunity to hear internationally renowned researchers discuss their fascinating, cutting-edge work in human evolution. Classrooms all over the world will even be able to submit their questions online and have the speakers respond in real time!
    - For more information, including speaker names, talk titles and times, please see or contact
    - To view the live, free webcast, simply go to at 1:30 pm Pacific/4:30 pm Eastern and log in as a guest. (Note: We suggest you do this in advance to test the connection and make sure you can access the site without problems. When you log in successfully you'll see a "Congratulations" message. If you have problems, please contact
  4. Oral Presentation Guidelines
  5. Extra Credit option: Helen Veit "The Ethics of Aging in an Age of Youth: Rising Life Expectancy in the Early Twentieth-Century United States" Sept 7, Noon - 1 pm. C-102 East Fee Hall.

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: 10:20 am to 11:40 am
Place: 1455A BPS (BEACON seminar room)

Instructor Contact Info.

Name: Dr. Robert T. Pennock.
Office: Holmes Hall W-34
Office hours: Monday 9 - 10 am (BPS 1446) 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. 2nd edition. Prometheus Press (2007) - RPB
  • Daniel C. Dennett. Darwin's Dangerous Idea: Evolution and the Meanings of Life. Simon & Schuster (1996) - DDI
  • Various articles to be assigned individually

Tentative Reading Assignments

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

Week 1  
Aug 31 Introductory Business - No readings

Week 2  
Sept 5 University Closed (No class); Aristotle "Generation of Animals" (RPB 63-66)
Sept 7 Haldane "What is Life?" (RPB 67-69); Orgel "The Origin of Life" (RPB 71-81)
Week 3  
Sept 12

Dennett "Preface" & "Tell Me Why" (DDI Preface & Ch.1); Paley -"Natural Theology" (RPB 83-86)
Blog #1 due

Sept 14

Darwin Origin of Species excerpt (RPB 87-91) Dennett "An Idea is Born" (DDI Ch 2)
Blog #2 due

Week 4  
Sept 19 Denton "Beyond the Reach of Chance" (RPB 93-108); Dawkins "Accumulating Small Change" (RPB 109-116)
Blog #3 due
Evolutionary computation research project assigned
Sept 21 Bethall "Darwin's Mistake" (RPB 133-140) & Gould "Darwin's Untimely Burial" (RPB 141-146)
Blog #4 due
Week 5  
Sept 26

Mayr "Cause and Effect in Biology" (RPB 49-62)
Blog #5 due

Sept 28

Evolutionary computation project presentations


Week 6  
Oct 3

Dennett "Universal Acid" (DDI Ch 3)
Blog #6 due

Due: Evolutionary computation research project write-up

• Student Presentation - Dan Lewandowski

Oct 5

Dennett "The Tree of Life" (DDI Ch 4) & Mayr "Species Concepts and their Applications" (RPB 203-214)
Blog #7 due

• Student presentation - Margie White

Week 7  
Oct 10

Richards "Solving the Species Problem" (RPB 215-228)
Blog #8 due

• Student presentation - Jon Walters

Oct 12

Dennett "The Possible and the Actual (DID Ch 5) & "Threads of Actuality in Design Space" (DID Ch 6)
Blog #9 due

• Student presentation - Seth Elliott

Week 8  
Oct 17

Dennett "Priming Darwin's Pump" (DID Ch 7)
Blog #10 due

• Student Presentation - Taylor Hagerty

Oct 19

Mid-term exam.


Week 9

Oct 24

Dennett "Biology is Engineering" (DID Ch 8) & Action Potential explanation

• Student presentation - Evan Rudman (switched to later)

Oct 26*

Library Research Instruction w/ Librarian Holly Flynn (Meet in Main Library Information Desk then go to Beaumont Instruction Room.)

Dennett "Searching for Quality" (DID Ch 9)
Blog #11 due

Week 10  
Oct 31

Gould "Darwinism and the Expansion of Evolutionary Theory" (RPB 147-166) & Score One for Punk Eek
Blog #12 due

Student presentation - Kaitlin Scharra

Nov 2

Dennett "Bully for Brontosaurus" (DID Ch 10) & Gould "The Pleasures of Pluralism"
Blog #13 due

Student presentation - Lawrence Mouton

Week 11  
Nov 7

Dennett "Controversies Contained" (DID Ch 11) & How Did Life Begin?
Blog #14 due

Student presentation - Meghan Miotto

Nov 9

Ruth Hubbard "Have Only Men Evolved" and Sandra Harding, "Rethinking Standpoint Epistemology: What is "Strong Objectivity?""
Sandra Harding guest lecture

Week 12  
Nov 14

Dennett "The Cranes of Culture" (DID Ch 12) & E.O.Wilson "Heredity" (RPB 243-250)
Blog #15 due

Student presentation - Colette Ngana

Proposal and Research Paper assigned

Nov 16

Dennett "Losing Our Minds to Darwin" (DID Ch 13)
Blog #16 due

Student presentation - Erika Chant

Week 13  
Nov 21

Gould "Sociobiology and the Theory of Natural Selection" (RPB 251-262)

Student presentation - Colby Brooks

Nov 23

Dennett "The Evolution of Meanings" (DID Ch 14)

Research Proposal Due

Week 14  
Nov 28

Dennett "The Emperor's New Mind…" (DID Ch 15)
Blog #17 due

Student presentation - Chris Klerkx

Nov 30

Dennett "On the Origin of Morality" (DID Ch 16) & Pennock "Moral Darwinism"
Blog #18 due

Student presentation - Sha'Toirea Drew

Week 15  
Dec 5

Dennett "Redesigning Morality" (DID Ch 17) & TBA?
Blog #19 due

Student presentation - Evan Rudman

Dec 7

Dennett "The Future of an Idea" (DID Ch.18); Russow "Why Do Species Matter?"
Blog #20 due

Student presentation - NAME

Final Exam Week  
Thu., Dec. 15, 10 am -Noon 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

  • Attendance - 10% (minus 1% per absence)
  • Regular, active class participation - 10%
  • Two formal oral presentations & 2-3 page write-ups - 5% each
  • Evolutionary computation research project (in teams of two) - 10%
  • Blog - 15%
  • Mid-term exam - 20%
  • 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 10-12 minute oral presentations during the course, one time alone and one time in a team of two.
- The first will be a talk with your research partner on your evolutionary computation project.

- The second of these will involve the topic and readings for the particular period. You will have 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 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. Depending on the number of students in the course, presentations will begin in the fourth, fifth or sixth 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
  3. Blogs:
    What is a blog? The term "blog" is a contraction of "web log". A blog is essentially a journal of one's thoughts about some subject that is posted on a web page for the world to read. Blog entries are usually short, typically no more than a paragraph or two. They may be of varying levels of formality, depending upon one's audience. The Intersection is an example of a good science blog.

    For us, the subject is the course readings, so think of it as a reading journal. What I expect is that you will keep a regular log of your thoughts as you are doing the assigned reading. Try to write something about each reading. What I expect to see is evidence that you are thinking about what you are reading as you go along. In particular, I want to see that you are identifying and reflecting upon the philosophical issues that arise, posing questions that probe the ideas presented, drawing connections among our different readings, and so on. The purpose of the blogs is to make you engage the material and start to form your own views about the topics we will be discussing in class. Here is an example of an excellent student blog from a few years ago.

    What about length? These are not meant to be essays. I'm looking to see a paragraph or two for each reading. What that should come to is about a page a week, if you were to print it out.

    BLOG REQUIREMENTS: On the day blogs are due, you should send them to me by email in the following manner:
    - The subject line of the message should say: 484 - Blog # - Your Name. [E.g. "484 - Blog #1 - John Doe"]
    - Repeat that same information <484 - Blog # - Your Name> as the first line of the body of the message, in the same way you would submit a paper or assignment.
    - Cut the text from your document and paste it into the body of the email message to send to me. <>
    - DO NOT send your blog to me as an attachment. (5 pts off for doing that.)
    - As a check to see that your email was delivered, you should cc yourself.
    - Your blog must be emailed before you come to class on the day that it is due.

    Public posting is optional. If you do want to set up a real blog page with your thoughts so your fellow students (and the world!) can read them, you should do so on your AFL space or your own blog space. Send me the URL and I'll post that link on this web page. (However, do keep in mind that the blog is an official graded assignment, so the primary audience should be your professor--me--in the same way that other written assignments are. Even if you are doing a public blog, you must still submit your entries to me by email as described above.)

    Here are the links for students in our class who are making their blogs public:
    - Seth Elliott


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.

  • Be respectful of others
    Let others finish
    Clarify each other
    Be open to new ideas
    Read the material
    Stick to the topic
    Don’t take it personally
    Don’t let one person dominate the discussion
    Mind the facts when expressing opinions
    Be mindful of terminology
    Raise hand to be recognized.


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: 8/30/2011.  Updated: 11/14/2011
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