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- LBS 492 -

Applied Darwinism: Theory & Practice of Evolutionary Design

Michigan State University
Fall 2003
Dr. Robert T. Pennock

Course Info | Grading | Professor Contact Info | Textbooks | Class Schedule
Study, Paper & Exam Tips | Academic Integrity | Discussion Guidelines
Additional Info | Useful Links | Blogs

- Announcements -
Check here periodically for late-breaking news

• LBS Frankenstein Book Debate. Sept. 17 (Wed) at 7 pm. Holmes Hall C-106.

• Extra-credit option: Dr. Louise Leakey talk: "Origins and Evolution: In Search of How We Became Human"
Thursday, October 30, 7:30 PM Wharton Center, Pasant Theater.

• Here is the link for the library resources page that Terry Link set up to help with your research.

• I am giving an extension on the research proposal. Instead of Monday, 10 November, it will now be due Wednesday, 12 November. Be sure to download a copy of the proposal guidelines.

• If you want to do the extra-credit write-up on the chapters from Holland I mentioned, you'll need to turn it in by Dec. 3rd in class.

• I have given an extension on the final due date for the research paper. Instead of being due on Monday, December 8th, it is now due during the scheduled "exam period" for the class: Thursday, December 11 at 10 am.


Course Info

Room: C-101 Holmes Hall

Time: MW 10:20 am to 12:10 p.m

Course Description:
Scientists are only very recently beginning to recognize the full power of the evolutionary mechanism that Darwin discovered, and to understand that it can be used in practical design applications. Darwinism should be not be understood as confined to biology; rather, the evolution of biological species is just one instance of a lawful process that can be instantiated in many domains. In this course, we will analyze the conceptual elements of evolutionary theory to evaluate the degree to which they can or cannot be generalized. We will consider the philosophical issues in light of recent scientific developments in which evolutionary theory is beginning to be applied in a wide variety of fields such as artificial life, Darwinian medicine, evolutionary computation, engineering, pharmaceutical and agricultural development, and cognitive science. We will also look at ways in which Darwinism has been misapplied, especially in ethics (as in so-called Social Darwinism). In the final stage of the course, students will choose a topic of personal interest from among those we have discussed to investigate in detail.

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.

 

Grading

- Attendance – 10% (minus 1% per absence)
- Regular, active class participation - 10%
- Two formal seminar presentations - 10% each
- Blog (Reading journal) – 5%
- Mid-term exam – 20%
- Research proposal (5 pages) – 10%
- Research project/essay (15 – 20 pages) - 20%
- Final oral thesis defense – 5%

• Grade scale: For your final course average, the 100 pt scale will be translated to grades as follows:
- 90 or above – 4.0; 85 to 90 – 3.5; 80 to 85 – 3.0; 75 to 80 – 2.5;
- 70 to 75 – 2.0; 65 to 70 – 1.5; 60 to 65 – 1.0; Below 60 – 0.0

• I do not round up averages that fall below a cut-off, but resolve borderline grades entirely on the basis of optional extra-credit assignments completed before the last class period. You may earn up to two (2) percentage points by such options, which I will announce periodically during the semester. A common extra-credit option is to attend some relevant university guest speaker talk and turn in a reflective paper about it.

• Late assignments will be accepted, but will be docked half a grade per day (e.g, from an equivalent of 4.0 to 3.5).

• As a seminar-style tutorial course, at least half of each period will be devoted to discussion of the material. Class participation means not only attendance (5%, see below), but also regular and active participation in class discussions, workshops, simulations etc. (10%). It is not possible to have a meaningful discussion or to get the most out of lectures 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.

• Academic Dishonesty: Your work should always be your own. The penalty for cheating or plagiarism will be a failing grade of 0.0 for the course. You are expected to have read MSU’s policies on academic integrity <www.vps.msu.edu/splife/rule32.htm> and the Briggs honor code.

• Attendance. Everyone is allowed one unexcused absence. Thereafter, one percentage point is deducted for each unexcused absence. Days missed due to sickness will be excused if you have a doctor's note. Days missed because of a team commitment or a religious holiday will be excused, but only if you let me know in advance. If for any reason you do miss a class, you are responsible for getting notes and assignments from a fellow student. 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 you are having problems, don't wait until the end of the course to do something about it. See me right away. Helping you learn how to learn is what I'm here for. Welcome to the course!

 

Professor Contact Info

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.


Office: Holmes Hall W-35.
Office hours: Mon. 9:15 am - 10:15 am & Wed. 2:30 - 3:30 pm, or by appointment or by open door.
Phone: 432-7701.

E-mail: pennock5@msu.edu
To prevent spread of viruses, NEVER send me any attachment to an e-mail unless we have specifically arranged it in advance.

 

Textbooks
 
 

Artificial Life: A Report from the Frontier Where Computers Meet Biology by Steven Levy. Vintage Books; Reprint edition (August 1993)

Digital Biology by Peter Bentley. Simon & Schuster; 1st edition (February 2002)

Emergence: From Chaos to Order (Helix Books) by John H. Holland. Perseus Books Group; (April 1999)

Creation: Life and How to Make It by Steve Grand. Harvard Univ Pr; (October 2001)

Out of Control: The New Biology of Machines, Social Systems and the Economic World by Kevin Kelly. Perseus Publishing; Reprint edition (May 1995)

 

Class Schedule

NOTE: This is a tentative reading list. Any changes will be announced in advance. Read the assigned selections before the class period.

Week I
Aug 25 Introductory Business – No readings
Aug 27 Darwin – Origin of Species – Ch 1 - 4
Available online at the Gutenberg Project.

Week II
Sept 1 Labor Day Holiday (No class)
Sept 3 Levy: Prologue, Ch 1 & 2 (The Promised Land & Playing by the Rules)

Week III
Sept 8 Levy: Ch. 3 - 4 (Garage Band Science & God's Heart)
Sept 10 - Levy: Ch 5 (The Genetic Algorithm)
Blog #1 due

Week IV
Sept 15 - Levy: Ch 6 (Alchemists and Parasites)
Sept 17 - Levy: Ch 7 (Artificial Flora...)

Week V
Sept 22 - Levy: Ch 8 & 9 (Real Artificial Life & The Strong Claim)
Sept 24 - Grand: Introduction, Ch 1 - 5

Week VI
Sept 29 - Bedau et. al. "Open Problems in Artificial Life" - Joint class with CSE 891 - Guest lecture by Dr. Charles Ofria about the above article.
Oct 1 - Grand: Ch 6 - 10:
Blog #2 due

Week VII
Oct 6 Grand: Ch 11 - 15; Presentation by Ben Doerr & Matt Horn
Oct 8 - Bentley Ch 1 - 3; Presentation by Brent Beldyga & Erika Boerman

Week VIII
Oct 13 - Bentley Ch 4 - 6; Presentation by E. Helmer & Christie Hemming
Oct 15 - Bentley Ch 7 - 9; Presentation by Lindsay Ferguson & Cal Kim

Week IX
Oct 20 - Kelly Ch 1 - 4 - Presentation by Meghan Drummond
Oct 22 - Mid-Term Exam

Week X
Oct 7 - Kelly 5 - 7; Presentation by Matt Horn
Blog #3 due
Oct 29 - Library instruction with Terry Link (Meet at main library instruction lab on first floor east)

Week XI
Nov 3 - Kelly 8 - 9; Presentation by Erika Boerman
Nov 5 - Kelly 10 - 11; Presentation by Lindsay Ferguson

Week XII
Nov 10 - Kelly 12 - 14; Presentation by Ben Doer
Research proposal due
Nov 12 - Kelly 15 - 16; Presentation by Cal Kim

Week XIII
Nov 17 - Kelly 17 - 19; Joint class with CSE 891
Nov 19- Kelly 20 - 21; Presentation by Brent Beldyga

Week XIV
Nov 24 - Kelly 22 - 24; Presentation by E Helmer
Blog #4 due
Nov 26 - Holland Ch 2 - 4; Presentation by Meghan Drummond

Week XV
Dec 1 - Holland Ch 5 - 7; Presentation by Christie Hemming
Dec 3 - Holland Ch 11 - 12

Week XVI - EXAM WEEK
Dec 12 - FINAL CLASS 10 am - Term paper due

 

Study, Paper & Exam Tips Philosophy courses can sometimes be intimidating for students who are used to standard courses where the task is to learn a bunch of facts. In philosophy, the key task is to learn how to improve one's thinking, so the focus is not so much on the conclusions themselves but rather on the arguments on which conclusions are based. This requires that you study in quite a different way than you might be used to. To help, I have written a short guide that you may find useful. Click here.  

Academic Integrity This is sufficiently important that it is worth repeating: Your work should always be your own. I expect that all students understand how to properly document sources; this is not something for which one may plead ignorance. If you are not sure what counts as plagiarism, find out before you turn in an assignment. The penalty for cheating or plagiarism will be a failing grade of 0.0 for the course. I expect you to have read MSU’s policies on academic integrity and the Briggs honor code.  

Discussion Guidelines

Here I will include the guidelines that you generated and we agree to govern ourselves by for class discussion.

 

Additional Info

What is a blog? It is a new form of written communication that has arisen out of internet technology. 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. Trying doing an search and check out some of the blogs that are starting to appear.

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. 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.

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.

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: Blog # - Your Name.
- Repeat that same information -- 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. <pennock5@msu.edu>
- 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. Send me the URL with your assignment and I'll post that link on this web page. You may do this as an extra-credit option to earn half a percentage point added to your final course average. (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.)

 

Blogs

Here is an example of a blog from a student in a previous class. Sarah Vinyard's Blog

Here are public blogs from students in our class:

Erika Boerman's blog

Meghan Drummond's blog

Elizabeth Helmer's blog.

Kyung-Hong "Cal" Kim's blog.

 

 

Useful Links

I'll put links here that are relevant to what we are discussing. If you come across items that you think would be worth sharing, send me the URL.

Here are six articles about creating artificial living cells:
1. Bill Joy, “Why the future does not need us.” Wired 8 (April 2000). Very influential futurist worries about wet artificial life and the Singularity.
2. Rodney Brooks, “The relationship between matter and life.” Nature 409 (2001), 409-411. Argues that wet artificial life is the future of artificial life and artificial intelligence.
3. Szostak, Bartell, and Luisi. “Synthesizing Life” Nature 409 (18 Jan 2001), 387 - 390. Outline of a bottom-up route to creating artificial cells.
4. Gillis, J., “Scientists planning to make new form of life”, Washington Post, (21 November 2002), A01. Press announcement of Venter’s plan to create artificial cells.
5. Mooney. “Nothing wrong with a little Frankenstein.” Washington Post (1 December 2002), B01. Editorial on Venter’s plan to create artificial cells.
6. Steen Rasmussen, et al. “Critical steps toward protocells.” Executive summary of a NASA astrobiology proposal to create artificial cells.

Larry Yeager's Home Page at Apple with link to PolyWorld information.

• Conway's Game of Life.

• Chris Langton's CA Loop (and others)

• A simple version of Richard Dawkins' Biomorphs program. Here is a somewhat better implementation. Neither of these lets you see how the genetics works, as in Dawkins' original program.

• Craig Renolds wrote the original boids, bird flocking simulation. His page gives a lot of background information. And since we talked about the animation of Finding Nemo in class, here are two variations of boids that simulate fish schooling: a basic one and a more recent sophisticated one from Digital Biology.

• Here is something about simulating plants using L-systems.

• A page on Karl Sims work on evolving virtual creatures and other evolved images.

Steve Grand's site. I pointed to the page on Creatures, but check other tabs for his recent reserach on Lucy.

• Mark Pauline's Survival Research Labs.

• Virtual tour of Biosphere 2.

• The Information Liberation Front takes on political issues now too.

• Speaking of computer viruses... could one be sent to earth by extraterrestrials?

Humanoid Robotics Lab at MIT

 

 

Page created: 8/30/03. Last updated: 11/24/03
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