CSSS 2007 Santa Fe-Readings

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Week One: Modeling/Nonlinear Dynamics

Modeling: Stephen Guerin, Owen Densmore, Josh Thorp
Stephen@Redfish.com, Owen@Redfish.com, Josh@Redfish.com
First of all, download the NetLogo 4.0 application: NetLogo Home
Then read the documents: NetLogo Docs which are also in the application under the Help menu.
Note that the documentation within the Netlogo application is preferred, being 4.0, but slightly "in process" due to being beta.

Homework: Run NetLogo and look at the documentation .. especially the Learning and Reference sections. Then run and look at the code for at least three of the Model Library examples which are under the File Menu -> Model Library.
Web: Several models we'll be using in the class, along with a pdf file of the slides are available on The Modeling Web Site

Week Two

Jennifer Dunne & Neo Martinez
Food Webs

Network structure and biodiversity loss in food webs: robustness increases with connectance
Food-web structure and network theory: The role of connectance and size
Simple rules yield complex food webs
Allometric scaling enhances stability in complex food webs
Stabilization of chaotic and non-permanent food web dynamics
The Network Structure of Food Webs

Week Three

Blake LeBaron
Finance
Agent-based Computational Finance
A Builder's Guide to Agent Based Financial Markets
Long-Memory in an Order-Driven Market

Week Four

Van Savage
Allometry

I recommend that all students look through the first couple of chapters of Reading 2. Otherwise, the students
should choose to read from among these based on what their interests and backgrounds are.

GENERAL LITERATURE ON BIOLOGICAL SCALING:

0. In the Beat of a Heart by John Whitfield (A recent popular science book about the history of and work on scaling relationships in biology.)

1. Chapters 2 and 3 of On Growth and Form by D'arcy Thompson (This is a seminal text for all mathematical biology.)

2. Scaling: Why is Animal Size so Important by Knut Schmidt-Nielsen (This is an extremely clear and fairly succinct explanation of scaling in biology up to the 1980's. This book focuses on physiology.)

3. The Ecological Implications of Body Size by R.H. Peters (This book discusses how scaling relationships are useful in ecology, and it has an incredibly useful set of appendices for scaling relationships.)

4. Size, Function, and Life History by W.A. Calder (Another good book on scaling and ecology.)

5. Scaling in Biology (SFI book), edited by J.H. Brown and G.B. West (This book is a collection of articles by the leaders in the field, and updates the literature in the scaling field, including numerous theoretical advances of great importance.)

PAPERS FOR ORIGINS OF SCALING LAWS:

6. "A General Model for the Origin of Allometric Scaling Laws in Biology", G.B. West, J.H. Brown, and B.J. Enquist 1997, Science (276) 122-126.
(This paper is a classic and puts forward the leading theory for an explanation of scaling relationships in biology.
The authors use a few simple assumptions about the structure and function of the cardiovascular system to construct the most powerfully predictive theory to date.)

7. V. M. Savage and G. B. West (2006). Biological scaling and physiological time: Biomedical applications. in Complex System Science in Biomedicine. Ed. T. S. Deisboeck and J. Y. Kresh, New York, Kluwer Academic. (The first part of this book chapter gives a more detailed account of the assumptions and derivations listed in Reading 6, and it also explains how biological rates and times depend on body temperature. This book contains several chapters by SFI faculty and alums and should provide interesting reading to those interested in the health sciences or an introduction to complex systems.)

PAPERS ON APPLYING SCALING RELATIONSHIPS TO ECOLOGY:

8. J. H. Brown, J. F. Gillooly, A. P. Allen, V. M. Savage, and G. B. West. (2004) Toward a metabolic theory of ecology (MacArthur award paper,), Ecology 85(7), 1771-1789. (This paper lays out a modern approach to applying scaling relationships to ecological systems.)

9. V. M. Savage, J. F. Gillooly, J. H. Brown, G. B. West, and E. L. Charnov, (2004). Effects of body size and temperature on population growth, The American Naturalist 163(3), 429-441. (This paper gives one of the first examples of explicitly building up from scaling relationships in individuals to those for populations.)

10. "Size and Scaling of Predator-Prey Dynamics" J Weitz and SA Levin Ecol. Lett. 2006, (9) 548-557.
(This paper represents one of the first attempts to combine scaling relationships for body body mass with species interactions.)

11. "A Mechanistic Approach for Modeling Temperature-Dependent Consumer Resource Dynamics", DA Vasseur and KS McCann AmNat 2005, (166) 184-198. (This paper look at species interactions and how they are affected by temperature, with possible implications for how global warming may affect biological systems.)

PAPERS APPLYING SCALING RELATIONSHIPS TO TISSUE- AND CELLULAR-LEVEL:

12. V. M. Savage and G. B. West, Towards a quantitative, metabolic theory of mammalian sleep, (2007) PNAS 104(3), 1051-1056. (This paper uses scaling relationships as a tool to better understand the function of sleep and whether it is a process for the brain or the whole body.)

13. V. M. Savage, A.P. Allen, J. F. Gillooly, A. B. Herman, J. H. Brown, and G. B. West, (2007) Scaling of number, size, and metabolic rate of cells with body size in mammals, PNAS, 104(11), 4718-4713. (This paper grapples with what the scaling relationships imply at the cellular level, and how that might impact our understanding of cellular studies and phenomena.)

BOOKS ON POWER LAWS, FRACTALS, NON-LINEAR DYNAMICS, ETC.:

14. Fractals, Chaos, and Power Laws by Manfred Schroeder (A good and playful introduction to these subjects.)

15. Nonlinear Dynamics and Chaos by Steven Strogatz (An extremely well written introduction to these subjects.)