Gene in a Bottle
Philosophy of Biological Science
Dr. Robert T. Pennock
TABLE OF CONTENTS
- Course information
- Meeting time and location
- Instructor contact info
- Important Dates
- Required textbooks
- Tentative Reading Assignments
- Grading system
- Attendance & Other Policies
- Scholastic dishonesty policy
- Study, Paper & Exam Tips
- Discussion Guidelines
- Additional information
- Useful Links
- Announcements (Last Updated)-
Check here periodically for late-breaking news.
Extra Credit option: SimBio Evolution Exercises on-line
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 https://www.nescent.org/media/NABTSymposium2011.php or contact email@example.com.
To view the live, free webcast, simply go to http://dukeuniversity.acrobat.com/nabt2011 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 firstname.lastname@example.org.)
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.
Meeting time and location
Days: Mondays and Wednesdays.
Time: 10:20 am to 11:40
Place: 1455A BPS (BEACON seminar room)
Instructor Contact Info.
Name: Dr. Robert T. Pennock.
Office: Holmes Hall
Office hours: Monday 9 - 10 am (BPS 1446) or by appointment
or by open door.
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
Also, please NEVER send me any attachment to an e-mail unless we
have specifically arranged it in advance.
- Michael Ruse, Philosophy of Biology. 2nd edition. Prometheus Press (2007)
- 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.
|| Introductory Business - No readings
||University Closed (No class); Aristotle "Generation of Animals" (RPB 63-66)
|| Haldane "What is Life?" (RPB 67-69); Orgel "The Origin of Life" (RPB 71-81)
Dennett "Preface" & "Tell Me Why" (DDI Preface & Ch.1); Paley -"Natural Theology" (RPB 83-86)
Blog #1 due
Darwin Origin of Species excerpt (RPB 87-91) Dennett "An Idea is Born" (DDI Ch 2)
Blog #2 due
||Denton "Beyond the Reach of Chance" (RPB 93-108); Dawkins "Accumulating Small Change" (RPB 109-116)
Blog #3 due
Evolutionary computation research project assigned
||Bethall "Darwin's Mistake" (RPB 133-140) & Gould "Darwin's Untimely Burial" (RPB 141-146)
Blog #4 due
Mayr "Cause and Effect in Biology" (RPB 49-62)
Blog #5 due
Evolutionary computation project presentations
Dennett "Universal Acid" (DDI Ch 3)
Blog #6 due
Due: Evolutionary computation research project write-up
• Student Presentation - Dan Lewandowski
Dennett "The Tree of Life" (DDI Ch 4) & Mayr "Species Concepts and their Applications" (RPB 203-214)
Blog #7 due
• Student presentation - Margie White
Richards "Solving the Species Problem" (RPB 215-228)
Blog #8 due
• Student presentation - Jon Walters
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
Dennett "Priming Darwin's Pump" (DID Ch 7)
Blog #10 due
• Student Presentation - Taylor Hagerty
Dennett "Biology is Engineering" (DID Ch 8) & Action Potential explanation
• Student presentation - Evan Rudman (switched to later)
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
Gould "Darwinism and the Expansion of Evolutionary Theory" (RPB 147-166) & Score One for Punk Eek
Blog #12 due
Student presentation - Kaitlin Scharra
Dennett "Bully for Brontosaurus" (DID Ch 10) & Gould "The Pleasures of Pluralism"
Blog #13 due
Student presentation - Lawrence Mouton
Dennett "Controversies Contained" (DID Ch 11) & How Did Life Begin?
Blog #14 due
Student presentation - Meghan Miotto
Ruth Hubbard "Have Only Men Evolved" and Sandra Harding, "Rethinking Standpoint Epistemology: What is "Strong Objectivity?""
Sandra Harding guest lecture
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
Dennett "Losing Our Minds to Darwin" (DID Ch 13)
Blog #16 due
Student presentation - Erika Chant
Gould "Sociobiology and the Theory of Natural Selection" (RPB 251-262)
Student presentation - Colby Brooks
Dennett "The Evolution of Meanings" (DID Ch 14)
Research Proposal Due
Dennett "The Emperor's New Mind…" (DID Ch 15)
Blog #17 due
Student presentation - Chris Klerkx
Dennett "On the Origin of Morality" (DID Ch 16) & Pennock "Moral Darwinism"
Blog #18 due
Student presentation - Sha'Toirea Drew
Dennett "Redesigning Morality" (DID Ch 17) & TBA?
Blog #19 due
Student presentation - Evan Rudman
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
- 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
- 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
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
and thought about the assigned material. Be prepared to answer
questions I may ask about the reading and to engage in thoughtful,
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.
- Paper formatting guidelines
may be found within the section titled Study,
Paper & Exam Tips
- Oral presentation guide
• 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
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
- 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
- Cut the text from your document and paste it into the body of the email
message to send to me. <email@example.com>
- 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
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
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
Here are the guidelines that you generated in class. Please also read
my comments about discussion in the Study,
Paper & Exam Tips section.
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.