https://wiki.santafe.edu/api.php?action=feedcontributions&user=Hgintis&feedformat=atomSanta Fe Institute Events Wiki - User contributions [en]2022-01-19T14:29:05ZUser contributionsMediaWiki 1.32.0https://wiki.santafe.edu/index.php?title=CSSS_2006_Beijing-Readings&diff=4370CSSS 2006 Beijing-Readings2006-07-23T16:26:13Z<p>Hgintis: </p>
<hr />
<div>{{CSSS 2006 Beijing}}<br />
<br />
<br />
__FORCETOC__<br />
<br />
<br />
Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further. <br />
<br />
<br />
<br />
== Readings Associated with Particular Lecturers ==<br />
<br />
=== Week One ===<br />
<br />
<br />
'''Andreas Wagner'''<br />
<br />
[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS. <br />
<br />
<br />
'''Henry Wright'''<br />
<br />
[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 1 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:<br />
<br />
'''Part One-''' Foragers and the Emergence of Agriculture<br />
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]<br />
*[http://hornacek.coa.edu/dave/Wright/csss_foragers1_rev_06.ppt PowerPoint presentation of Part 1] (Updated 21 July 2006)<br />
*[[Media:Foragrs_talk.doc|Talk Outline]] (Updated 21 July 2006)<br />
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.<br />
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In <i>Anthropological Archaeology in the Americas</i>. The Anthropological Society of Washington. 1968. <br />
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Ken V. Flannery, ed.<br />
*[[Media:ch3-1.pdf|Guila Naquitz in Spacial, Temporal, and Cultural Context]], Kent V. Flannery. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Ken V. Flannery, ed..<br />
*[[Media:ch4.pdf|The Physical Environment of the Guila Naquitz Cave Group]], Kirkby, M. J., A. V. Whyte, and K. V. Flannery. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Ken V. Flannery, ed..<br />
*[[Media:Reynolds_introduction_to_model.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Robert Reynolds. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Kent V. Flannery, ed. <br />
*[[Media:Diamond_Nature_02.pdf| Jared Diamond's Overview of the Emergence of Food Production]]<br />
<br />
'''Part Two-''' Villages and the Emergernce of Tribal Alliance Systems<br />
*[[Media:Modeling_Villages.doc|Brief Syllabus of Sources on the “Village” Project]]<br />
*[http://hornacek.coa.edu/dave/Wright/csss_villages2_rev_06.ppt Revised PowerPoint presentation of Part 2] (Updated 21 July 2006)<br />
*[[Media:Villages_talk.doc|Talk Outline]] (Updated 21 July 2006)<br />
*[[Media:Kohleretal_SimAncntSocs_SciAm05.pdf|Simulating Ancient Societies]] Kohler, T. A., G.J. Gumerman and R.G. Reynolds<br />
*[[Media:Gumerman_etal_.pdf|Long House Valley Simulation]]<br />
*[[Media:Kohler_etal_Agent_Based_Mdling_SFI96.doc|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<br />
*[[Media:Reynolds_Algorithms_2002.ppt|Cultural Algorithms: A Tutorial]] Robert G. Reynolds<br />
*[[Media:Kobti_Reynolds_Kohler_Resilience_IEEE03.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<br />
*[[Media:Reynolds_Kohler_Kobti_Resilience_CMOT04.pdf|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<br />
*[[Media:Kobti_Reynlds_Kohler_Kinship_IEEE04.pdf|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<br />
*[[Media:Kobti_etal_SwarmFest_Cultural_Algorithms_04.pdf|Agent-Based Modeling of Cultural Change in Swarm Using Cultural Algorithms]] Kobti, Z., R. G. Reynolds, and T. A. Kohler<br />
*[[Media:Reynolds_etal_Gaming_IEEE05.pdf|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<br />
*[[Media:VILLAGE_and_BALI_URLs.doc|Web Access to Kohler's VILLAGE and Lansing''s BALI]]<br />
<br />
'''Part Three-''' Raising Civilizations<br />
*[[Media:Modeling_States.doc|Brief Syllabus of Sources on the “States” Project]] <br />
*[[Media:CSSS_Wright3_States.ppt|PowerPoint presentation of Part 3]] <br />
*[[Media:States_talk_06.doc|Talk Outline]] (Updated 21 July 2006)<br />
*[[Media:Carneiro 1970.pdf|A Theory of the Origin of the State]] Robert L. Carneiro<br />
*[[Media:Wright 1977.pdf|Recent Research on the Origin of the State]] Henry T. Wright<br />
*[[Media:Johnson_Uruk_Administration copy.pdf|The Changing Organization of Uruk Administration on the Susiana Plain]] Gregory A. Johnson. In ''The Archaeology of Western Iran'', Frank Hole, ed.<br />
*[[Media:Wright_UrukStates.pdf|Uruk States in Southwestern Iran]] Henry T. Wright. In ''Archaic States'', Gary M. Feinman and Joyce Marcus, eds.<br />
*[[Media:Wright_UrukWorld.pdf|Cultural Action in the Uruk World]] Henry T. Wright. In ''Uruk Mesopotamia & Its Neighbors'', Mitchell S. Rothman, ed.<br />
*[[Media:Liu_LongShan_96.pdf|Settlement Patterns, Chiefdom Variability, and the Development of Early States in North China]] Li Liu<br />
*[[Media:Underhill_etall_02.pdf|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<br />
*[[Media:Lee_Erlitou.pdf|control strategies and polity competition in the lower Yi-Luo Valley, North China]] Yun Kuen Lee<br />
*[[Media:System-dependent Selection.pdf|System-dependent Selection, Ecological Feedback and the Emergence of Functional Struction in Ecosystems]] Lansing, S. J., J. N. Kremer, and B. B. Smuts<br />
*[[Media:Digitizing_Devpmnt.pdf|Digitizing 'Development']] Stefan Helmreich<br />
*[[Media:Foucault.pdf|Foucault and the Water Temples]] Steve Lansing<br />
<br />
<br />
<br />
'''Dave Feldman'''<br />
<br />
[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.<br />
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]], [[Media:chaos.1.4.pdf|Part I]], [[Media:Chaos.2.4.pdf|Part II]]<br />
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]], [[Media:Info.2.4.slides.pdf|Part II]]<br />
* Lecture 3: Computation Theory. [[Media:Comp.1.4.pdf|Automata and Computation Theory]], [[Media:Comp.theory.2.4.pdf|Computability and Computational Complexity]]<br />
* Lecture 4: Measures of Complexity. [[Media:Comp.mech.4.pdf|Computational Mechanics]], [[Media:Complexity.measures.4.pdf|Measures of Complexity]], [[Media:Conclusion.slides.4.pdf|Conclusion]]<br />
<br />
Further reading<br />
<br />
*J.P. Crutchfield and D. P. Feldman Regularities Unseen, Randomness Observed: Levels of Entropy Convergence. Chaos, 2003. 15: 25-54. 2003. [http://arxiv.org/abs/cond-mat/0102181 cond-mat:0102181]. This is a long paper discussing the entropy rate and excess entropy and including many different examples. <br />
*[[Media:Comp.ent.diagrams.4.pdf|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.<br />
<br />
<br />
'''Cosma Shalizi'''<br />
<br />
* Lecture 1: [[Media:Shalizi-CSSS06-1-power-laws.pdf|Power Laws, What They Mean, How to Tell If You Have One]]<br />
<br />
M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.<br />
<br />
* Lecture 2: [[Media:Shalizi-CSSS06-2-inference.pdf|Statistical Inference for Complex Systems Models]]<br />
<br />
See also:[[Media:Shalizi.overview.pdf|Methods and Techniques of Complex Systems Science: An Overview]], [http://arxiv.org/abs/nlin.AO/0307015 nlin.AO/0307015].<br />
<br />
* Lecture 3: [[Media:Shalizi-CSSS06-3-model-discovery.pdf|Optimal Prediction, Model Discovery and Self-Organization]]<br />
<br />
C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors<br />
for Discrete Sequences", <cite>Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference</cite> (UAI 2004), pp. 504--511. Best description of the CSSR algorithm; helpful for third lecture. [http://arxiv.org/abs/cs.LG/0406011 cs.LG/0406011]<br />
<br />
K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", <cite>Advances in Neural Information Processing Systems 18</cite> (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). [http://arxiv.org/abs/q-bio.NC/0506009 q-bio.NC/0506009]<br />
<br />
=== Week Two ===<br />
<br />
<br />
'''Li Shuzhuo & Marcus W.Feldman ''July 17, Morning '''''<br />
<br />
[[Media:Population dynamics introduction.pdf|Population dynamics introduction]].<br />
<br />
'''Marcus W.Feldman & Li Shuzhuo ''July 17, Afternoon '''''<br />
<br />
[[Media:Rural-urban Migration in China Social Networks and Socio-demography.pdf|Rural-urban Migration in China Social Networks and Socio-demography]].<br />
<br />
'''Marcus W.Feldman ''July 18, Morning '''''<br />
<br />
[[Media:Niche construction A new dimension for biological and cultural evolution.pdf|Niche construction A new dimension for biological and cultural evolution]].<br />
<br />
<br />
'''Jim Crutchfield'''<br />
<br />
Background for lecture two:<br />
* O. Goenernup and J. P. Crutchfield, [http://cse.ucdavis.edu/~cmg/papers/hsofps.pdf Hierarchical Self-Organization in the Finitary Process Soup], Proceedings of Artificial Life X (2006) submitted.<br />
* J. P. Crutchfield and Olof Görnerup, [http://cse.ucdavis.edu/~cmg/papers/otmo.pdf Objects That Make Objects: The Population Dynamics of Structural Complexity].<br />
<br />
=== Week Three ===<br />
<br />
'''Hao Bai-lin'''<br />
<br />
*[[Media:Asd_hao.pdf|Applied Symbolic Dynamics: From 1D to 2D to ODEs]]<br />
<br />
<br />
'''Lee Altenberg'''<br />
<br />
'''Slides'''<br />
*[[Media:AltenbergAnalysis.4up.pdf|Spectral Analysis of Evolutionary Dynamics]]<br />
<br />
'''Background and Additional Reading'''<br />
<br />
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems. <br />
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.<br />
*Altenberg, L. , 1994. [http://dynamics.org/Altenberg/PAPERS/STPT/ The Schema Theorem and Price's Theorem] delves into the claims about schema processing as the source of power in genetic algorithms, and recasts the Schema Theorem (Holland 1975) by using Price's Theorem (1970). It is shown that the Schema Theorem says nothing about a GA's power, but a modification with a different measurement function produces a theorem about evolvability that is a local measure of GA power. The concept of rugged landscapes is also deconstructed in terms of operator-defined distance.<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 24 & 25, 10:30-11:45 '''''<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_notes.pdf Notes to Lectures 1 and 2].<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_bibliography.pdf Bibliography to Lectures 1 and 2].<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 26, 10:30-11:45 '''''<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_intro.pdf Introduction to Lectures 3 to 5].<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_bib.pdf Bibliography to Lectures 3 to 5].<br />
<br />
Lecture 3: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_acquisition.pdf Modeling the ontogenetic emergence of language using recurrent neural networks].<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 27, 10:30-11:45 '''''<br />
<br />
Lecture 4: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_4_emergence.pdf Modeling the phylogenetic emergence of language using agent-based modeling].<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 28, 10:30-11:45 '''''<br />
<br />
Lecture 5: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_5_competition.pdf Modeling language competition and death using differential equations and agent-based modeling].<br />
<br />
=== Week Four ===<br />
<br />
<br />
'''Herbert Gintis'''<br />
<br />
Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper. The rest will be based on various papers available from his[[http://www-unix.oit.umass.edu/~gintis web site.]]<br />
<br />
<br />
<br />
<br />
== General Background ==<br />
<br />
<br />
James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|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.<br />
<br />
[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc 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. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].<br />
<br />
Cosma Shalizi, [[Media:Shalizi.overview.pdf|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 [http://arxiv.org/abs/nlin.AO/0307015 here].</div>Hgintishttps://wiki.santafe.edu/index.php?title=CSSS_2006_Beijing-Readings&diff=4369CSSS 2006 Beijing-Readings2006-07-23T16:24:52Z<p>Hgintis: </p>
<hr />
<div>{{CSSS 2006 Beijing}}<br />
<br />
<br />
__FORCETOC__<br />
<br />
<br />
Below are some readings that can provide some background for some of the lectures and/or that you can read after the lecturers to pursue some ideas further. <br />
<br />
<br />
<br />
== Readings Associated with Particular Lecturers ==<br />
<br />
=== Week One ===<br />
<br />
<br />
'''Andreas Wagner'''<br />
<br />
[[Media:WagnerCSSS06.pdf|Genome-scale Biological Networks]]. These are the slides that Andreas will use for his lectures. We will make hard copies available at the CSSS. <br />
<br />
<br />
'''Henry Wright'''<br />
<br />
[[Media:Modeling_Villages.doc|This file]] introduces you to the web resources for Part 1 of Henry Wright's Presentation at the 2006 CSSS in Beijing. Here are some other readings associated with Henry Wright's talks:<br />
<br />
'''Part One-''' Foragers and the Emergence of Agriculture<br />
*[[Media:Modeling_Foragrs.doc|Brief Syllabus of Sources on the “Forager” Project]]<br />
*[http://hornacek.coa.edu/dave/Wright/csss_foragers1_rev_06.ppt PowerPoint presentation of Part 1] (Updated 21 July 2006)<br />
*[[Media:Foragrs_talk.doc|Talk Outline]] (Updated 21 July 2006)<br />
*[[Media:Wobst_BoundaryConditions_.pdf|Boundary Conditions for Paleolithic Social Systems: A Simultaion Approach]]. Martin Wobst.<br />
*[[Media:ArchSysThry68.pdf|Archaological Systems Theory and Early Mesoamerica]], Kent V. Flannery. In <i>Anthropological Archaeology in the Americas</i>. The Anthropological Society of Washington. 1968. <br />
*[[Media:Guila_Naquitz_A.pdf|The Research Problem]], Kent V. Flannery. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Ken V. Flannery, ed.<br />
*[[Media:ch3-1.pdf|Guila Naquitz in Spacial, Temporal, and Cultural Context]], Kent V. Flannery. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Ken V. Flannery, ed..<br />
*[[Media:ch4.pdf|The Physical Environment of the Guila Naquitz Cave Group]], Kirkby, M. J., A. V. Whyte, and K. V. Flannery. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Ken V. Flannery, ed..<br />
*[[Media:Reynolds_introduction_to_model.pdf|The Modeling of Foraging Strategy: An Introduction to Part IV]], Robert Reynolds. In <i>Guila Naquitz: Archaic Foraging and Early Agriculture in Oaxaca, Mexico</i>, Kent V. Flannery, ed. <br />
*[[Media:Diamond_Nature_02.pdf| Jared Diamond's Overview of the Emergence of Food Production]]<br />
<br />
'''Part Two-''' Villages and the Emergernce of Tribal Alliance Systems<br />
*[[Media:Modeling_Villages.doc|Brief Syllabus of Sources on the “Village” Project]]<br />
*[http://hornacek.coa.edu/dave/Wright/csss_villages2_rev_06.ppt Revised PowerPoint presentation of Part 2] (Updated 21 July 2006)<br />
*[[Media:Villages_talk.doc|Talk Outline]] (Updated 21 July 2006)<br />
*[[Media:Kohleretal_SimAncntSocs_SciAm05.pdf|Simulating Ancient Societies]] Kohler, T. A., G.J. Gumerman and R.G. Reynolds<br />
*[[Media:Gumerman_etal_.pdf|Long House Valley Simulation]]<br />
*[[Media:Kohler_etal_Agent_Based_Mdling_SFI96.doc|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<br />
*[[Media:Reynolds_Algorithms_2002.ppt|Cultural Algorithms: A Tutorial]] Robert G. Reynolds<br />
*[[Media:Kobti_Reynolds_Kohler_Resilience_IEEE03.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<br />
*[[Media:Reynolds_Kohler_Kobti_Resilience_CMOT04.pdf|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<br />
*[[Media:Kobti_Reynlds_Kohler_Kinship_IEEE04.pdf|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<br />
*[[Media:Kobti_etal_SwarmFest_Cultural_Algorithms_04.pdf|Agent-Based Modeling of Cultural Change in Swarm Using Cultural Algorithms]] Kobti, Z., R. G. Reynolds, and T. A. Kohler<br />
*[[Media:Reynolds_etal_Gaming_IEEE05.pdf|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<br />
*[[Media:VILLAGE_and_BALI_URLs.doc|Web Access to Kohler's VILLAGE and Lansing''s BALI]]<br />
<br />
'''Part Three-''' Raising Civilizations<br />
*[[Media:Modeling_States.doc|Brief Syllabus of Sources on the “States” Project]] <br />
*[[Media:CSSS_Wright3_States.ppt|PowerPoint presentation of Part 3]] <br />
*[[Media:States_talk_06.doc|Talk Outline]] (Updated 21 July 2006)<br />
*[[Media:Carneiro 1970.pdf|A Theory of the Origin of the State]] Robert L. Carneiro<br />
*[[Media:Wright 1977.pdf|Recent Research on the Origin of the State]] Henry T. Wright<br />
*[[Media:Johnson_Uruk_Administration copy.pdf|The Changing Organization of Uruk Administration on the Susiana Plain]] Gregory A. Johnson. In ''The Archaeology of Western Iran'', Frank Hole, ed.<br />
*[[Media:Wright_UrukStates.pdf|Uruk States in Southwestern Iran]] Henry T. Wright. In ''Archaic States'', Gary M. Feinman and Joyce Marcus, eds.<br />
*[[Media:Wright_UrukWorld.pdf|Cultural Action in the Uruk World]] Henry T. Wright. In ''Uruk Mesopotamia & Its Neighbors'', Mitchell S. Rothman, ed.<br />
*[[Media:Liu_LongShan_96.pdf|Settlement Patterns, Chiefdom Variability, and the Development of Early States in North China]] Li Liu<br />
*[[Media:Underhill_etall_02.pdf|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<br />
*[[Media:Lee_Erlitou.pdf|control strategies and polity competition in the lower Yi-Luo Valley, North China]] Yun Kuen Lee<br />
*[[Media:System-dependent Selection.pdf|System-dependent Selection, Ecological Feedback and the Emergence of Functional Struction in Ecosystems]] Lansing, S. J., J. N. Kremer, and B. B. Smuts<br />
*[[Media:Digitizing_Devpmnt.pdf|Digitizing 'Development']] Stefan Helmreich<br />
*[[Media:Foucault.pdf|Foucault and the Water Temples]] Steve Lansing<br />
<br />
<br />
<br />
'''Dave Feldman'''<br />
<br />
[[Media:Csss.bibliography.pdf|Annotated bibliography]] to accompany Dave's lectures. In addition to references specific to the lecture topics, there are also a number of general complex systems references.<br />
* Lecture 1: Introduction to Chaos. [[Media:intro.4.pdf|Introductory Comments]], [[Media:chaos.1.4.pdf|Part I]], [[Media:Chaos.2.4.pdf|Part II]]<br />
* Lecture 2: Information Theory [[Media:info.1.4.pdf|Part I]], [[Media:Info.2.4.slides.pdf|Part II]]<br />
* Lecture 3: Computation Theory. [[Media:Comp.1.4.pdf|Automata and Computation Theory]], [[Media:Comp.theory.2.4.pdf|Computability and Computational Complexity]]<br />
* Lecture 4: Measures of Complexity. [[Media:Comp.mech.4.pdf|Computational Mechanics]], [[Media:Complexity.measures.4.pdf|Measures of Complexity]], [[Media:Conclusion.slides.4.pdf|Conclusion]]<br />
<br />
Further reading<br />
<br />
*J.P. Crutchfield and D. P. Feldman Regularities Unseen, Randomness Observed: Levels of Entropy Convergence. Chaos, 2003. 15: 25-54. 2003. [http://arxiv.org/abs/cond-mat/0102181 cond-mat:0102181]. This is a long paper discussing the entropy rate and excess entropy and including many different examples. <br />
*[[Media:Comp.ent.diagrams.4.pdf|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.<br />
<br />
<br />
'''Cosma Shalizi'''<br />
<br />
* Lecture 1: [[Media:Shalizi-CSSS06-1-power-laws.pdf|Power Laws, What They Mean, How to Tell If You Have One]]<br />
<br />
M. E. J. Newman, [[Media:Newman.powerlaws.pdf|Power laws, Pareto distributions and Zipf's law]], ''Contemporary Physics'' '''46''', 323-351 (2005). An excellent paper. Good background for Cosma's lecture on power laws.<br />
<br />
* Lecture 2: [[Media:Shalizi-CSSS06-2-inference.pdf|Statistical Inference for Complex Systems Models]]<br />
<br />
See also:[[Media:Shalizi.overview.pdf|Methods and Techniques of Complex Systems Science: An Overview]], [http://arxiv.org/abs/nlin.AO/0307015 nlin.AO/0307015].<br />
<br />
* Lecture 3: [[Media:Shalizi-CSSS06-3-model-discovery.pdf|Optimal Prediction, Model Discovery and Self-Organization]]<br />
<br />
C. R. Shalizi and K. L. Klinkner, "Blind Construction of Optimal Nonlinear Recursive Predictors<br />
for Discrete Sequences", <cite>Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference</cite> (UAI 2004), pp. 504--511. Best description of the CSSR algorithm; helpful for third lecture. [http://arxiv.org/abs/cs.LG/0406011 cs.LG/0406011]<br />
<br />
K. L. Klinkner, C. R. Shalizi and M. F. Camperi, "Measuring Shared Information and Coordinated Activity in Neuronal Networks", <cite>Advances in Neural Information Processing Systems 18</cite> (NIPS 2005), pp. 667--674. Using CSSR to measure information sharing in networks (not just neural ones). [http://arxiv.org/abs/q-bio.NC/0506009 q-bio.NC/0506009]<br />
<br />
=== Week Two ===<br />
<br />
<br />
'''Li Shuzhuo & Marcus W.Feldman ''July 17, Morning '''''<br />
<br />
[[Media:Population dynamics introduction.pdf|Population dynamics introduction]].<br />
<br />
'''Marcus W.Feldman & Li Shuzhuo ''July 17, Afternoon '''''<br />
<br />
[[Media:Rural-urban Migration in China Social Networks and Socio-demography.pdf|Rural-urban Migration in China Social Networks and Socio-demography]].<br />
<br />
'''Marcus W.Feldman ''July 18, Morning '''''<br />
<br />
[[Media:Niche construction A new dimension for biological and cultural evolution.pdf|Niche construction A new dimension for biological and cultural evolution]].<br />
<br />
<br />
'''Jim Crutchfield'''<br />
<br />
Background for lecture two:<br />
* O. Goenernup and J. P. Crutchfield, [http://cse.ucdavis.edu/~cmg/papers/hsofps.pdf Hierarchical Self-Organization in the Finitary Process Soup], Proceedings of Artificial Life X (2006) submitted.<br />
* J. P. Crutchfield and Olof Görnerup, [http://cse.ucdavis.edu/~cmg/papers/otmo.pdf Objects That Make Objects: The Population Dynamics of Structural Complexity].<br />
<br />
=== Week Three ===<br />
<br />
'''Hao Bai-lin'''<br />
<br />
*[[Media:Asd_hao.pdf|Applied Symbolic Dynamics: From 1D to 2D to ODEs]]<br />
<br />
<br />
'''Lee Altenberg'''<br />
<br />
'''Slides'''<br />
*[[Media:AltenbergAnalysis.4up.pdf|Spectral Analysis of Evolutionary Dynamics]]<br />
<br />
'''Background and Additional Reading'''<br />
<br />
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/OPSAED/ Open Problems in the Spectral Analysis of Evolutionary Dynamics] presents a mathematical framework for evolutionary optimization and some of its unsolved problems. <br />
*Altenberg, L. , 2004. [http://dynamics.org/Altenberg/PAPERS/MESLLQ/ Modularity in Evolution: Some Low Level Questions] deconstructs the concept of modularity in terms of spaces of variation, and discusses properties needed for modularity to enhance evolvability.<br />
*Altenberg, L. , 1994. [http://dynamics.org/Altenberg/PAPERS/STPT/ The Schema Theorem and Price's Theorem] delves into the claims about schema processing as the source of power in genetic algorithms, and recasts the Schema Theorem (Holland 1975) by using Price's Theorem (1970). It is shown that the Schema Theorem says nothing about a GA's power, but a modification with a different measurement function produces a theorem about evolvability that is a local measure of GA power. The concept of rugged landscapes is also deconstructed in terms of operator-defined distance.<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 24 & 25, 10:30-11:45 '''''<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_notes.pdf Notes to Lectures 1 and 2].<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_1_to_2_bibliography.pdf Bibliography to Lectures 1 and 2].<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 26, 10:30-11:45 '''''<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_intro.pdf Introduction to Lectures 3 to 5].<br />
<br />
[http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_to_5_bib.pdf Bibliography to Lectures 3 to 5].<br />
<br />
Lecture 3: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_3_acquisition.pdf Modeling the ontogenetic emergence of language using recurrent neural networks].<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 27, 10:30-11:45 '''''<br />
<br />
Lecture 4: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_4_emergence.pdf Modeling the phylogenetic emergence of language using agent-based modeling].<br />
<br />
<br />
'''William S-Y. Wang & James W. Minett, ''July 28, 10:30-11:45 '''''<br />
<br />
Lecture 5: [http://www.ee.cuhk.edu.hk/~jminett/minett_files/SFI_Lectures_5_competition.pdf Modeling language competition and death using differential equations and agent-based modeling].<br />
<br />
=== Week Four ===<br />
<br />
<br />
'''Herbert Gintis'''<br />
<br />
Herbert Gintis, [[Media:Unity-bbs.pdf|A Framework for the Unification of the Behavioral Sciences]]. ''Behavioral and Brain Sciences'', forthcoming 2006. Parts of Herb's lectures will be based on this paper. The rest will be based on various papers available from his [[web site. http://www-unix.oit.umass.edu/~gintis]]<br />
<br />
<br />
<br />
<br />
== General Background ==<br />
<br />
<br />
James Crutchfield, [[Media:Crutchfield.order.and.chaos.pdf|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.<br />
<br />
[http://cob.jmu.edu/rosserjb/ J.B. Rosser], [http://cob.jmu.edu/rosserjb/GENERIC.CPX.doc 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. [http://ideas.repec.org/a/aea/jecper/v13y1999i4p169-192.html pdf format, for AEA members].<br />
<br />
Cosma Shalizi, [[Media:Shalizi.overview.pdf|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 [http://arxiv.org/abs/nlin.AO/0307015 here].</div>Hgintishttps://wiki.santafe.edu/index.php?title=CSSS_2006_Beijing-Public_Lectures&diff=4367CSSS 2006 Beijing-Public Lectures2006-07-23T16:18:37Z<p>Hgintis: </p>
<hr />
<div>{{CSSS 2006 Beijing}}<br />
<br />
== James Crutchfield == <br />
<br />
<b>Wednesday 19 July. 19:30.</b><br />
<br />
James Crutchfield. (Professor of Physics, Computational Science & Engineering Center University of California, Davis. External Faculty, Santa Fe Institute.)<br />
<br />
<b>Is Anything Ever New?</b><br />
<br />
We are confronted, as never before, with an explosion in the size of databases: from data-mining the web to dynamical brain imaging, the various genome projects, and near-real-time skymaps for dynamical cosmology. These datasets are so vast that there is no conceivable way humans can directly examine all of the data. What has been an intuitive and very human discovery process---hypothesizing structures and building predictive theories about the systems that produce them---must now be automated. But do we understand the notions of structure and pattern well enough that we can teach machines to discover them? How do we build theories that capture patterns in useful and predictive ways? I will review recent results on automated pattern discovery and theory building for nonlinear systems. The lessons hint at what a future "artificial" science might look like.<br />
<br />
<br />
== Herbert Gintis ==<br />
<br />
<b>Monday 31 July. 19:30.</b><br />
<br />
Herbert Gintis. (External Professor, Santa Fe Institute, Professor of Economics, Central European University, Budapest. Visiting Professor, University of Siena, Italy. )<br />
<br />
<b>Structural Conflicts among the Behavioral Disciplines: A Way Forward</b><br />
<br />
The various behavioral disciplines model human behavior in distinct and incompatible ways. Yet, recent theoretical and empirical developments have created the conditions for rendering coherent the areas of overlap of the various behavioral disciplines, as outlined in this paper. The analytical tools deployed in this task incorporate core principles from several behavioral disciplines. The proposed framework recognizes evolutionary theory, covering both genetic and cultural evolution, as the integrating principle of behavioral science. Moreover, if decision theory and game theory are broadened to encompass other-regarding preferences, they become capable of modeling all aspects of decision making, including those normally considered "psychological," "sociological" or "anthropological." The mind as a decision-making organ then becomes the organizing principle of psychology.</div>Hgintishttps://wiki.santafe.edu/index.php?title=CSSS_2006_Beijing-Faculty&diff=4366CSSS 2006 Beijing-Faculty2006-07-23T16:17:10Z<p>Hgintis: </p>
<hr />
<div>{{CSSS 2006 Beijing}}<br />
[[Lee Altenberg]] University of Hawaii at Manoa<br />
<br />
<br />
[[Xiaosong Chen]] Institute of Theoretical Physics<br />
<br />
<br />
[[Jim Crutchfield]] UC Davis<br />
<br />
<br />
[[Raissa D'Souza]] UC Davis<br />
<br />
<br />
[[Dave Feldman]] College of the Atlantic<br />
<br />
<br />
[[Marc Feldman]] Stanford University<br />
<br />
<br />
[[Herb Gintis]] Santa Fe Institute<br />
<br />
<br />
[[Michelle Girvan]] Santa Fe Institute<br />
<br />
<br />
[[Jing Han]] Academy of Mathematics and Systems Science<br />
<br />
<br />
[[Bailin Hao]] The Institute of Theoretical Physics, Chinese Academy of Sciences<br />
<br />
<br />
[[Shuzhuo Li]] Xian Jiaotong University<br />
<br />
<br />
[[Bernhard Meister]] Renmin University of China<br />
<br />
<br />
[[James Minett]] The Chinese University of Hong Kong<br />
<br />
<br />
[[Van Savage]] Harvard University<br />
<br />
<br />
[[Cosma Shalizi]] Carnegie Mellon University<br />
<br />
<br />
[[Andreas Wagner]] University of New Mexico<br />
<br />
<br />
[[William Wang]] The Chinese University of Hong Kong<br />
<br />
<br />
[[Jon Wilkins]] Santa Fe Institute<br />
<br />
<br />
[[Henry Wright]] University of Michigan</div>Hgintis