BY659/CS659
FALL 2011


Lecturer: James F. Lynch
Office: SC-381
Telephone: 268-2374
email: jlynch@clarkson.edu
Office hours:  MWF 9:15AM–10:00AM, 11:00AM–12:00PM
Lecture hours: MF 8:00AM–915AM, SC-336 (COSI Lab)
Text:  There is no text.  We will read a variety of articles taken from books, journals, and websites.


GRADING

Grading will be based entirely on the readings and participation in discussions and experiments with software. There may be some problems assigned as homework, but there will be no exams or final.


READING

Steven Levy, The Promised Land, in Artificial Life, Pantheon Books, New York (1992), pp. 11-46.

Arthur W. Burks, Von Neumann’s Self-Reproducing Automata, in Essays on Cellular Automata, ed. A. W. Burks, University of Illinois Press, Urbana (1970), pp. 3-64.

W. Richard Stark and William H. Hughes, Asynchronous Irregular Automata Nets: The Path not Taken, BioSystems 55 (2000), pp. 107-117.

Jeremy M. Berg, John L. Tymoczko, and Lubert Stryker, Biochemistry, 5th Ed., W, H, Freeman and Company, New York (2002), Chapter 1, pp. 3-18.

Jeremy M. Berg, John L. Tymoczko, and Lubert Stryker, Biochemistry, 5th Ed., W, H, Freeman and Company, New York (2002), Chapter 2, pp. 19-40.

Steven Levy, Playing by the Rules, in Artificial Life, Pantheon Books, New York (1992), pp. 48-83.

Darren J. Wilkinson, Stochastic Modelling for Systems Biology, Chapman & Hall/CRC, Boca Raton, Florida (2006), Chapter 1, pp. 1–17.

Darren J. Wilkinson, Stochastic Modelling for Systems Biology, Chapman & Hall/CRC, Boca Raton, Florida (2006), Chapter 2, pp. 19–31.

Darren J. Wilkinson, Stochastic Modelling for Systems Biology, Chapman & Hall/CRC, Boca Raton, Florida (2006), Chapter 6, pp. 139–161.

Aviv Regev and Ehud Shapiro, Cells as Computation, Nature, 419 (2002), p. 343.

 


QUESTIONS FOR DISCUSSION

Monday, September 5

Monday, September 12

Friday, September 16

Thursday and Friday, September 22 and 23

Friday, September 30

Monday and Friday, October 10 and 14 (revised)

Monday, October 24

Monday, October 31

Monday and Friday, November 7 and 11

Monday and Friday, November 14 and 18

Monday, November 28

Friday, December 2


LINKS


 

Alife

Conferences and Workshops

Corporations

Research Groups and Institutes

Software


QUOTES

  • Biologists can be divided into two classes: experimentalists who observe things that cannot be explained, and theoreticians who explain things that cannot be observed. - Aharon Katzir-Katchalsky
  • [Ask] not what mathematics can do for biology but what biology can do for mathematics. - Stanislaw M. Ulam, paraphrasing a famous remark of John F. Kennedy