CSSS 2007 Beijing-Readings-Week-One

CSSS 2007 Beijing Home Faculty Participants Schedule Readings and Lecture Notes Week One Week Two Week Three Week Four Projects T-Shirt Chinese Visa Information Travel Details and Logistics Final Papers Forum

Dave Feldman

Lecture Notes

• Introduction
• Dynamical Systems and Chaos
• Introduction to Chaos: Part II
• Information Theory
• Information Theory: Part II, Applications to Stochastic Processes
• Extensions to Shannon Entropy
• A (Mostly) Informal Introduction to Computation Theory
• An Informal Introduction to Computability and Computational Complexity
• An Introduction to Computational Mechanics
• Some Thoughts on Complexity Measures
• Thoughts on the Subjectivity of Complexity
• Conclusion

Additional Reading

General Complex Systems

• James Crutchfield, What Lies between Order and Chaos?, in Art and Complexity, J. Casti, editor, Oxford University Press (2002). An interesting, non-technical essay discussing how new patterns are discovered, and how complexity arises from the interplay between order and chaos. This is an excellent introduction to the notions of complexity and emergence, and history of one strand of the study of complex systems.

• J.B. Rosser, On the Complexities of Complex Economic Dynamics. Journal of Economic Perspectives. 13:169-192. 1999. I've only read about half of this. It strikes me as a thorough, even-handed review of the applications of "complexity theory" to economics. Presents good spectrum of views, from those who think complexity is mostly hype, to those who believe it has contributed significant new understandings. Contains around 125 references. pdf format, for AEA members.

• Cosma Shalizi, Methods and Techniques of Complex Systems Science: An Overview. Chapter 1 (pp. 33--114) in Thomas S. Deisboeck and J. Yasha Kresh (eds.), Complex Systems Science in Biomedicine (New York: Springer, 2006.) This is an excellent, thorough review of the "field" -- to the extent that there is such a thing -- of complex systems. Covers many tools: statistical learning and model selection; time series analysis; cellular automata; agent-based models; the evaluation of complex-systems models; information theory; and ways of measuring complexity. Contains over 250 references. Also available here.

Entropy Rate, Excess Entropy

• J.P. Crutchfield and D. P. Feldman Regularities Unseen, Randomness Observed: Levels of Entropy Convergence. Chaos, 2003. 15: 25-54. 2003. cond-mat:0102181. This is a long paper discussing the entropy rate and excess entropy and including many different examples.
• Complexity Entropy Diagrams: Exploring the Relationships between Complexity and Randomness. Talk given in February 2006 at the Center for Computational Science and Engineering at UC Davis. Additional info on some of the ideas from Lecture 4.

Power Laws

• Aaron Clauset, Cosma Rohilla Shalizi, M. E. J. Newman, Power-law distributions in empirical data, E-print (2007). physics/0706.1062. An excellent review paper. Highly recommended. Matlab and R code is available here.

• M. E. J. Newman, Power laws, Pareto distributions and Zipf's law, Contemporary Physics 46, 323-351 (2005). Anohter excellent review.

Computational Mechanics

• C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors for Discrete Sequences", Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference (UAI 2004), pp. 504--511. Best description of the CSSR algorithm. cs.LG/0406011

• K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", Advances in Neural Information Processing Systems 18 (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). q-bio.NC/0506009

John Pepper

Lecture Notes

Agent-Based modeling

• A brief introduction to Agent-Based Modeling, Part 1
• Agent-Based Modeling, Part 2

Evolution

• Darwinian Evolution
• Natural Selection

Additional Reading

Evolution: Applications to cancer biology

• A recent review of somatic evolution in cancer: Merlo Pepper et al 2006
• My most recent work on the topic: Pepper et al. 2007

Jon Wilkins

Lecture Notes

Introduction to SFI: Monday, July 9

• Introduction to SFI

Lecture 1: Monday, July 9

• Introduction to Coalescent Theory

Lecture 2: Wednesday, July 11

• Adaptationism and the Adaptive Landscape

Lecture 3: Friday, July 13

• Statistical Inference in Complex Systems: Approximate Bayesian Computation

Additional Reading

Coalescent Theory:

Here are two different introductions to coalescent theory. One is a review article written by Magnus Nordborg:

• Nordborg Review

The other is a chapter from John Wakeley's book called Coalescent Theory

• Wakeley Review

If you are interesed in learning a lot more about the subject, I recommend the rest of the book as well

Genomic Imprinting:

Here are a couple of review articles that talk about the evolution of genomic imprinting

• Wilkins & Haig Imprinting Review Nature Reviews Genetics, 2003
• Wilkins Imprinting Review Trends in Genetics, 2005

Here are some modeling papers on imprinting. The first two are the models that I used as an example in Wednesday's lecture

• Game-Theoretic model of imprinting evolution Wilkins & Haig, Proc. R. Soc. B, 2002
• Population-Genetic model of imprinting evolution Spencer, Clark & Feldman, Genetics, 1998

These are some papers that look at what happens when there are more than two "players" or "genetic factions" that are co-evolving

• Genetic conflicts in genomic imprinting Burt & Trivers, Proc. R. Soc. B, 1998
• Somatic reactivation of imprinted gene expression Wilkins, J. Theor. Biol., 2006
• Competitive signal discrimination in imprinting Wilkins, J. Theor. Biol., 2006

Also, here is a paper that talks about how the level of analysis in evolutionary problems affects how you perceive the role of natural selection in evolution It is now out it the Blackwell Companion to the Philosophy of Biology. It is the article entry on "Adaptationism" I don't have the final PDF with me, though, so I have attached the final draft that we sent to the publishers. I suspect that it is similar, though.

• Adaptationism Godfrey Smith and Wilkins, Blackwell Companion to the Philosophy of Biology, 1997

Approximate Bayesian Computation

Here are a few papers that describe the basic ideas of Approximate Bayesian Computation. In these papers, the applications are specifically population genetic. One warning: the techniques used in these papers to deal with the issues of correlations among statistics, etc. are completely ad hoc. The procedure that I outlined on Friday is somewhat less ad hoc. Soon, I hope to post something that provides a written description of what I talked about. Conceivably, even some code to implement these steps.

Henry Wright

Lecture Notes

• Modeling Food Gatherers

Additional Reading

Foragers and the Emergence of Agriculture

• Brief Syllabus of Sources on the “Forager” Project
• PowerPoint presentation of Part 1 (Updated 21 July 2006)
• Talk Outline (Updated 09 July 2007)
• Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach. Martin Wobst.
• Archaological Systems Theory and Early Mesoamerica, Kent V. Flannery. In Anthropological Archaeology in the Americas. The Anthropological Society of Washington. 1968.
• The Research Problem, Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed.
• Guila Naquitz in Spacial, Temporal, and Cultural Context, Kent V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
• The Physical Environment of the Guila Naquitz Cave Group, Kirkby, M. J., A. V. Whyte, and K. V. Flannery. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Ken V. Flannery, ed..
• The Modeling of Foraging Strategy: An Introduction to Part IV, Robert Reynolds. In Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico, Kent V. Flannery, ed.
• Jared Diamond's Overview of the Emergence of Food Production

Villages and the Emergernce of Tribal Alliance Systems

• Brief Syllabus of Sources on the “Village” Project
• Revised PowerPoint presentation of Part 2 (Updated 21 July 2006)
• Talk Outline (Updated 21 July 2006)
• Simulating Ancient Societies Kohler, T. A., G.J. Gumerman and R.G. Reynolds
• Long House Valley Simulation
• Agent-Based Modeling of Prehistoric Settlement Systems in the Northern American Southwest Kohler, T. A., C. R. Van West, E. P. Carr and C. G. Langton
• Cultural Algorithms: A Tutorial Robert G. Reynolds (PowerPoint)
• Cultural Algorithms: A Tutorial Robert G. Reynolds (PDF)
• A Multi-Agent Simulation Using Cultural Algorithms: The Effect of Culture on the Resilience of Social Systems Kobti, Z., R. G. Reynolds, and T. A. Kohler
• The Effects of Generalized Reciprocal Exchange on the Resilience of Social Networks: An Example from the Prehispanic Mesa Verde Region Reynolds, R. G., T. A. Kohler and Z. Kobti
• The Effect ofKinship Cooperation Learning Stategy and culture on the Resilience of Social Systems in the Village Mulit-Agent Simulation Kobti, Z., R. G. Reynolds, and T. A. Kohler
• Agent-Based Modeling of Cultural Change in Swarm Using Cultural Algorithms Kobti, Z., R. G. Reynolds, and T. A. Kohler
• Unraveling Ancient Mysteries: Reimagining the Past Using Evolutionary Computation in a Complex Gaming Environment Reynolds, R. G., Z. Kobti, T. A. Kohler, and L. Y. L. Yap
• Web Access to Kohler's VILLAGE and Lansings BALI

Raising Civilizations

• Brief Syllabus of Sources on the “States” Project
• PowerPoint presentation of Part 3
• Talk Outline (Updated 21 July 2006)
• A Theory of the Origin of the State Robert L. Carneiro
• Recent Research on the Origin of the State Henry T. Wright
• The Changing Organization of Uruk Administration on the Susiana Plain Gregory A. Johnson. In The Archaeology of Western Iran, Frank Hole, ed.
• Uruk States in Southwestern Iran Henry T. Wright. In Archaic States, Gary M. Feinman and Joyce Marcus, eds.
• Cultural Action in the Uruk World Henry T. Wright. In Uruk Mesopotamia & Its Neighbors, Mitchell S. Rothman, ed.
• Settlement Patterns, Chiefdom Variability, and the Development of Early States in North China Li Liu
• Regional survey and the development of complex societies in southeastern Shandong, China Underhill, A. P., G. M. Feinman, L. M. Nicholas, G. Bennett, H. Fang, F. Luan, H. Yu and F. Cai
• control strategies and polity competition in the lower Yi-Luo Valley, North China Yun Kuen Lee
• System-dependent Selection, Ecological Feedback and the Emergence of Functional Struction in Ecosystems Lansing, S. J., J. N. Kremer, and B. B. Smuts
• Digitizing 'Development' Stefan Helmreich
• Foucault and the Water Temples Steve Lansing