ECOL
446A/546A (also ANTH
446A/546A):
Complex
biological systems
Spring 2003
Students: For more resources, also see the POLIS web
page for this course .
Announcement
(2/25/2004):
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The
Santa Fe Institute has announced the tenth annual Graduate
Workshop in Computational Social Science Modeling and Complexity. The
workshop will bring together a group of advanced graduate students and a
small faculty for an intensive two week study of computational social
science modeling and complexity. The workshop will consist of lectures
by faculty, special topic seminars by members of the Santa Fe Institute,
and presentations of work in progress by graduate student participants.
The
primary goal of the summer workshop is to assist graduate students
pursuing research agendas which include a computational modeling
component. A
significant portion of the workshop will be devoted to analyzing and
improving research being conducted by the graduate student
participants.
Participation at the workshop will be limited to fifteen graduate
students.
Student travel (up to a reasonable limit), accommodations, and living
expenses will be supported by the workshop.
For further information about the workshop, including application
instructions, pleasevisit<http://zia.hss.cmu.edu/econ/announce04.html>.
The application deadline is 9 April 2004.
Please feel free to forward this annoucement to colleagues or students
who
may be interested in the workshop.
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INSTRUCTOR:
Dept of Ecology
and
Evolutionary Biology University of Arizona
Telephone:
626-0440
E-mail:
jpepper1@email.arizona.edu
Office location:
114/326
Biosciences West
Office hours: W
& F 11:00 – 12:15 or almost any
time by appointment
Meeting
times:
Lectures
Tuesdays 11:00-12:15 (EDUC 502)
Computer
Laboratory: Thursdays. 11:00-12:15 (Biology Learning Center, Koffler Building, Room 209)
Recommended
Primary Texts*:
Flake,
G. The
Computational beauty of nature.
Nicolis
&
Prigogine:,. Exploring Complexity
Suggested
Secondary texts*
Waldrop:
Complexity,
Gell-Mann:
The
Quark and the Jaguar
Casti:
Complexification
Casti:
would-be
worlds
Johnson:
Emergence
Belew
&
Mitchell 1996 Adaptive individuals in evolving population
Luck et al., eds.”Multi-Agent Systems and Applications". (ACAI'01
Summer School, Prague,
July 2001, Proceedings”
Bar-Yam: The Dynamics of Complex Systems
Holland,
Hidden
order : how adaptation
builds complexity
Cowan,
Pines,
& Meltzer:. Complexity: Metaphors, Models, and reality
Camazine et al.: Self-organization in Biological
Systems
* On
course
reserve
Other
readings
Listed by topic
Complete list
, GRADING POLICIES:
A 100 – 90%
B
89 – 80%
C
79 – 70%
D
69 – 60%
Breakdown of points/percentages
(subject to
change)
Undergraduate
Students:
|
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Discussion
participation
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40%
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|
Quizzes
|
20%
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Lab
assignments
|
40%
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|
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|
|
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Honors
and
Graduate Students:
|
|
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Discussion
participation
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20%
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Quizzes
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10%
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Lab
assignments
|
20%
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Project
proposal
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10%
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Independent
modeling project
|
40%
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Tentative
Lecture Schedule
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Date
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Topic
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Readings
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Jan
20th
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Introduction
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Jan
27th
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Discussion: What are “Complex Systems”?
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Bar-Yam Ch.
0.1 [link]
Johnson Ch. 1 [reserve]
Laughlin et al. 1999. [PDF]
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Feb
3
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Discussion:
Self-organization
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Flake
Ch. 16 [reserve]
Skår 2003 [PDF]
Coveney 2003 [PDF]
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Feb
10
|
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Pepper
& Hoelzer 2001 [PDF]
Camazine et al. Ch. 1 [reserve]
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Feb
17
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Lecture:
Thermodynamics refresher
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Lecture notes:
[htm][powerpoint]
[PDF]
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Feb
27
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Lecture:
Thermodynamics and self-organization
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Lecture notes:
[html] [powerpoint]
[PDF]
|
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Feb
24th
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Discussion:
project ideas
(& health survey)
|
|
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March
2
|
Guest
Lecture: Dr. William Shafer: Nonlinear Dynamics
In
Biology
|
supplemental
material [web]:
http://bill.srnr.arizona.edu/classes/195b.html
|
|
March
9
|
Nonlinear
Dynamics (con’t.)
|
supplemental
material [web]:
http://bill.srnr.arizona.edu/classes/195b.html
|
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March 16
|
Spring break - no
class
(wrong on syllabus handout)
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March
23
|
Guest Lecture by Dr. Jeff Dean: “Artificial Anasazi”
|
Gumerman et al. 2003
[PDF]
|
|
??
|
ABMS in Ecology and Evolution
|
Weigand et al. 2003 [PDF]
Grimm 1999 [PDF]
Judson 1994 [PDF]
Pepper & Smuts
2000 [PDF]
|
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March
30
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Guest Lecture by John Murphy. Biocomplexity: The Emergence of
Cooperation from Human-Environmental Interactions
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[web]:http://www.ic.arizona.edu/%7Elansing/biocomplexity_poster.htm
[web]:http://www.nsf.gov/sbe/nuggets/015/nugget.htm
Funding sources:
[web]:
http://www.nsf.gov/geo/ere/ereweb/fund-biocomplex.cfm
[web]:
http://www.nsf.gov/home/crssprgm/hsd/start.htm
Lansing 2002 [PDF]
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April
6
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Discussion: What are models (including
(ABMs) good for?
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Casti,
pp 13-36 [reserve],
Goel & Thompson Ch. 2 [reserve],
Roughgarden 1996
(Ch. 2
in Belew & Mitchell) [reserve]
|
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April
13
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(Project
proposals due)
Guest Lecture by John Murphy. Introduction to Repast
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[repast home page]:
http://repast.sourceforge.net/index.php
[Murphy tutoria]
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April
20
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Lecture: Can we believe what our models tell
us? (Verification And Validation)
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Lecture
notes:
Powerpoint (.ppt)
Adobe Acrobat (.pdf)
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April
27
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Student
Presentations*
|
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May
4
|
Student
Presentations*
(Course evaluations)
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May
11
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Finals
week - No class
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*
Anyone is welcome
to schedule their own presentation for sooner if they prefer.