CSSS 2008 Beijing-Readings-Week-One

CSSS 2008 Beijing Home Faculty Participants Highlights Photos 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

Dave Feldman

Lecture Notes

• Some Foundations in Complex Systems: Entropy, Information, Computation, and Complexity. Complete set of slides from all five lectures.

Additional Reading

• David Feldman, Carl McTague, James Crutchfield, The Organization of Intrinsic Computation: Complexity-Entropy Diagrams and the Diversity of Natural Information Processing. An examination of the relationships between complexity and entropy for many different model systems. I covered this material on the last day of my lectures.

• 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.

• 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.

• 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.

• 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

Miguel Fuentes

Laplace's Deterministic Paradise Lost

Hao Bailin

Lecture Notes

A Brief Introduction to Written Chinese

Will Tracy

Lecture Notes

• Computational Complexity in the Social Sciences I
• Computational Complexity in the Social Sciences II

Jon Wilkins

Lecture Notes

Lecture 1: Monday, June 30

• Adaptationism and the Adaptive Landscape

Lecture 2: Wednesday, July 2

• Geneologies I: Introduction to Coalescent Theory

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 Early Civilizations: First Steps.

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
• Urbanization Within a Dynamic Environment T.J. Wilkinson, J.H. Christiansen, J. Ur, M. Widell, and M. Altaweel
• Figures to Accompany "Urbanization Within a Dynamic Environment" T.J. Wilkinson, J.H. Christiansen, J. Ur, M. Widell, and M. Altaweel

Richard Callahan

Download SIENA

• Go to http://stat.gamma.rug.nl/stocnet/ to download StOCHNET, the Graphical User Interface that houses SIENA. StOCHNET comes built in with last year's version of SIENA. Download the .zip file for version 1.8 and run the executable.

• There's also a brand-new version of SIENA that came out on Monday that you can download from http://stat.gamma.rug.nl/siena.html. You should just have to switch the executables for SIENA that unpack with StOCHNET with these newer ones. Apologies but I haven't yet done this myself, so I can't verify that the process works as it should.

Data

• Looks like I couldn't upload a .zip file to the Wiki, so you can find the data for this workshop on my Web site at http://students.washington.edu/rjcal/links.shtml.

Lecture Notes

• Introduction to Dynamic Social Network Analysis with SIENA
• Sample Mandarin Dialogues to Practice! Most of these slides came from Will Tracy's talk last year.

Additional Reading

• Link to http://stat.gamma.rug.nl/siena.html and click on 'Literature'. Also useful (but copyrighted, so you have to get it from your library unfortunately): Robins, Snijders, Wang, Handcock and Pattison, "Recent Developments in Exponential Random Graph Models for Social Networks", Social Networks 29(2007): 192-215.