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
- Concurrent
biological processes
- Deborah
Gordon digs ants, video on TED.com
- A
Different Kind of Secret Code - ScienceNOW
- Environmental
Remediation Processes
- Robots at the Intelligent
Autonomous Systems Laboratory - contains link to Slugbot
- Life on
Earth
- Life-like
cells are made of metal, New Scientist, 14 September 2011
- Modelling E. coli, files from Prof. Vic
Norris’s lecture at Workshop on Systems Biology, Turku, Finland, 2004.
- Paul
Stamets on 6 ways mushrooms can save the world
- Systems
biology for beginners
- Transactions on Computational
Systems Biology
- Tutorial on E.
Coli Chemotaxis; Robustness of the Chemotaxis Circuit, U. Alon
- William L. Romey, SUNY Potsdam, Research in Grouping Behavior
- Roger
Alsing, Genetic Programming: Evolution of Mona
Lisa, weblog
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