http://www.biomag.helsinki.fi/images-mri.html
- LBS 492 (§8)-

Evolutionary Design

Michigan State University
Spring 2019
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

 

• Extra credit option: Eric Berling PhD defense. "Evolutionary Explanations of Morality"
Time: Friday, April 26, 10 am.
Location: 503 S. Kedzie Hall (Philosophy Dept seminar room)

• Extra credit option: David Sloan Wilson online Science Salon interview "This View of Life"
https://www.skeptic.com/science-salon/this-view-of-life-completing-darwinian-revolution/
For up to 1% extra credit, submit (in class by April173rd) a 1 1/2 to 2-page reflective write up about the interview, focusing on some specific topic most relevant to our class.

• Extra credit option Friday, March 29th, 5 pm: Brews and Views "How would you like that prepared? In a Petri Dish please!"
Location: IQ Atrium (775 Woodlot Drive). OR Join by Zoom information: from PC, Mac, iOS or Android: https://msu.zoom.us/j/355150721
For up to 1% extra credit, submit (in class by April 3rd) a 1 1/2 to 2-page reflective write up about the session, connecting it to the topics of our class as best you can.

• Homework assignment for Mon., April 1: Find a primary source article about an application of evolutionary design. This could be (i) an example of an evolutionary explanation of some pattern of adaptation / design as it is seen in nature, medicine, or society; or (ii) an example of how evolutionary science (e.g., Darwin's Law) is applied for some practical purpose (e.g. in agriculture, medicine, computer technology, engineering). Write it up following the model of evolutionary application vignette as describe here. Submit on line at our Turnitin.com page before class.

• Homework assignment for Wed., March 20


Course Info

Room: Holmes W40

Time: MW 5:20 pm – 7:10 pm

Course Description:

The complex, adaptive designs that we observe in the biological world were produced by evolution. We are now able to harness that power of evolutionary design by implementing Darwin’s law in computational environments. Combining biology, computer science and philosophy of science, this course will examine the workings of evolutionary design in natural and artificial systems. Questions to be considered include: How does Darwin’s law created functional designs? Why are evolutionary explanations critical not just in general biology, but also in specific fields like medicine? How can evolutionary processes be modeled and tested using computers? How can evolutionary design be used for practical purposes, such as to solve complex engineering problems?

This course will be conducted primarily in seminar format, emphasizing class discussion and student-led presentations. We will work to develop skills of effective group discussion and oral presentation. Students will also work in teams on a hands-on project experimenting with digital evolution in an artificial life system. Finally, as in all capstone courses, students will write and defend a thesis in a major research paper.

 

Grading

- Attendance – 10% (minus 1% per absence)
- Regular, active class participation - 10%
- Two formal seminar presentations - 5% each
- Blog (Reading journal) –15%
- Mid-term exam –20%
- HW and exercises - 10%
- Research project/term paper proposal (5 pages) – 5%
- Research project/term paper (15 – 20 pages) - 20%

• 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 (10%, 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 for med school interviews, car breakdowns, family visits, or whatever. Thereafter, one percentage point is deducted for each unexcused absence. There are two sorts of excused absenses: 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.

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


Office:BPS 1441 and Holmes W-34
Office hours: Friday 4:30 - 5:30 pm (in BPS) or by appointment or by open door.
Phone: 432-7701

E-mail: pennock5[at]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
Darwin and Design cover
Sciences of the Artificial cover
Body by Darwin cover
 
 

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

The Sciences of the Artificial 2nd ed. by Herbert Simon. The MIT Press; (1981)

Body by Darwin: How Evolution Shapes Our Health and Transforms Medicine by Jeremy Taylor.  University of Chicago Press; 1 edition (2015)

Evolution for Everyone by David Sloan Wilson.  Delacorte Press.  (2007)

Darwin and Design: Does evolution have a purpose? by Michael Ruse.  Harvard University Press (2003)

 

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 1 Beginnings
Jan 7 Introductory Business
No readings
Jan 9

Ruse Introduction - Ch 1
Blog #1 due

Week 2
Jan 14 Ruse Ch 2 - 4
Blog #2 due
Jan 16

Ruse Ch 5 - 6
Blog #3 due

Week 3
Jan 21

MSU Holiday (No class)


Jan 23

Wilson Ch 1 - 3
Blog #4 due

Week 4
Jan 28

Wilson Ch 4 - 7
Blog #5 due

Jan 30

Wilson 8 - 13
Blog #6 due

Week 5
Feb 4

Taylor Introduction & Ch 1
Blog #7 due

Feb 6

Taylor Ch 1 & 2
Blog #8 due
Presenters: Kaylie Chiles & Jordan Gerras - Slides (Rescheduled to Feb 11)

Week 6
Feb 11

Taylor Ch 3, 4 & 5
Blog #9 due
Presenters: Abby Martin, Sarah Campbell - Slides (Rescheduled to Feb 13)

Feb 13

Taylor Ch 6 & 7
Blog #10 due
Presenters: Monty Frankfort & Diba Ossareh - Slides ( (Rescheduled to Feb 18)

Week 7
Feb 18

Levy: Prologue, Ch 1 & 2 (The Promised Land & Playing by the Rules)
Blog #11 due
Presenters: - Slides

Feb 20

Levy: Ch. 3 - 4 (Garage Band Science & God's Heart)
Blog #12 due
Presenters: Raveena Munnangi & Allison Loch - Slides

Week 8
Feb 25 Levy: Ch 5 (The Genetic Algorithm)
Blog #13 due
Feb 27 (MT) Mid-Term Exam
Mar 4 Spring Break
Mar 6 Spring Break
Week 9
Mar 11 Simon Ch 1 (Understanding the Natural and Artificial Worlds)
Blog #14 due
Mar 13 Simon Ch 2 - 3
Blog #15 due
Presenters: Sophia Viola - Slides
Week 10
Mar 18

Simon Ch 5 - 6
Blog #16 due
Presenters: - Slides

Mar 20

Simon Ch 7, Levy: Ch 6 (Alchemists and Parasites) & Ch 7 (Artificial Flora...)
Blog #17 due
Presenters: - Slides

Week 11
Mar 25

Levy: Ch 8 (Real Artificial Life ) & Ch 9 (The Strong Claim)
Blog #18 due
Presenters: - Slides

Mar 27

Wilson Ch 14 - 17

Research instruction at MSU Library (meet in library instruction room)

Week 12
Apr 1

Wilson 18 - 21 - Group Selection & Evolution of Altruism
Blog #19 due
Presenters: Abby Bryson & Allison Loch - Slides

Apr 3

Wilson Ch 21 - 24
Blog #20 due
Presenters: Jordan Gerras & Abby Bryson - Slides

Week 13
Apr 8

Wilson Ch 25 - 27
Term paper proposal due

Apr 10 Wilson Ch 28 - 30
Blog #21 due
Presenters: Sarah Campbell - Slides
Week 14
Apr 15

Wilson Ch 31 - 33
Blog #22 due
Presenters: Sophia Viola & Diba Ossareh - Slides

Apr 17

Wilson Ch 34 - 36
Blog #23 due
Presenters: Abey Martin & Monty Frankfort- Slides

Week 15
Apr 22 Ruse Ch 13 - 14
Blog #24 due
Presenters: Kaylie Chiles & Raveena Munnangi- Slides
Apr 24

Ruse Ch 15
Blog #25 due
Presenters: Abby Bryson -

Final Exam Week  
Mon, Apr. 29
8 - 10 pm

Term paper due through Turnitin.com by 5 pm.  Hard copy due at beginning of class.  You should be prepared to give a 5 minute explanation/defense of your thesis.

 

 

 

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.

  • Come prepared
  • Be respectful of others political/social beliefs/orientations
  • Keep things relevant
  • Avoid speaking too much
  • Keep an open mind to other's ideas
  • Don't cut others off
  • Don't hesitate to speak up
 

Additional Info

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 couple of paragraphs. They may be of varying levels of formality, depending upon one's audience.

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 three or four paragraphs for each reading. What that should come to is about a page and a half a week, if you were to print it out.

On the day blogs are due, you should submit them through Turnitin for the numbered blog for that day. The Turnitin Class ID is 20020792. I'll let you know the enrollment key on the first day of class.

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. (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 will be links to blogs of students in class who make their blogs public.

 

 

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.

• The heart as a pump: William Harvey's experiments on the circulation of the blood. Video.

• Oral presentation guidelines. And some good tips for any sort of public speaking.

• Avida-ED lab book.

• Conway's Game of Life online.

• Library reference guide for our class.

• David Sloan Wilson talk on "Compassion and Altruism from an Evolutionary Perspective"

 

 

Page created: 1/7/2019. Last updated: 4/22/2019
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