I709: Complex Systems Seminar II
Spring 2011
Instructor: Luis M. Rocha, Center for Complex Networks and Systems Research, School of Informatics and Computing and Cognitive Science Program, Indiana University
Class Location and Time: Tuesdays, 01:45P-04:30PM, Room: Informatics East Building, 122
Course Description
Instructor: Luis M. Rocha, Center for Complex Networks and Systems Research, School of Informatics and Computing and Cognitive Science Program, Indiana University
Class Location and Time: Tuesdays, 01:45P-04:30PM, Room: Informatics East Building, 122
A complex system is any system featuring a large number of interacting components (agents, processes, etc.) whose aggregate activity is nonlinear (not derivable from the summations of the activity of individual components) and typically exhibits hierarchical self-organization under selective pressures. This definition applies to systems from a wide array of scientific disciplines. Indeed, the sciences of complexity are necessarily based on interdisciplinary research. Almost all interesting processes in nature are highly cross linked. In many systems, however, we can distinguish a set of fundamental building blocks, which interact nonlinearly to form compound structures or functions with an identity that requires more explanatory devices than those used to explain the building blocks. This process of emergence of the need for new, complementary, modes of description is known as hierarchical self-organization, and systems that observe this characteristic are defined as complex. Examples of these systems are gene networks that direct developmental processes, immune networks that preserve the identity of organisms, social insect colonies, neural networks in the brain that produce intelligence and consciousness, ecological networks, social networks comprised of transportation, utilities, and telecommunication systems, as well as economies. The field of complex systems studies the general characteristics of all these systems. Its goal is to identify and model the laws and behaviors common to various classes of complex systems.
Aims: This seminar is designed to present and discuss the history, methodology and impact of complex systems; we cover key literature as well as recent advances in the field.
Course Evaluation
Students are expected to read and annotate the materials presented, as well as present a few of the key readings. Students will also work on a term paper.
Office Hours
- Luis Rocha
- Thursdays 10:00am– 12:00pm, Informatics East, Room #301
Course Materials and Readings
Printed Resources are available to students in OnCourse: Class Folder. Readings below are updated weekly.
- Part I: History of the Field
- Cybernetics
- Heims, S.G. [1991]. The Cybernetics Group. MIT Press. Chapters: 1,2, 11, and 12.
- McCulloch, W. and W. Pitts [1943], "A Logical Calculus of Ideas Immanent in Nervous Activity". Bulletin of Mathematical Biophysics 5:115-133.
- Searls, David B. [2010]. "The Roots of Bioinformatics". PLoS Computational Biology 6(6): e1000809. doi:10.1371/journal.pcbi.1000809
- Systems Science
- Klir, G.J. [2001]. Facets of systems Science. Springer. Chapters: 1,2,3, 8, and 11.
- Rosen, R. [1986]. "Some comments on systems and system theory". Int. J. of General Systems, 13: 1—3.
- Weaver, W. [1948]. "Science and Complexity". American Scientist, 36(4): 536-44. (PMID: 18882675)
- Self-Organizing Systems
- Ashby, W.R.[1956]. An Introduction to Cybernetics, Chapman & Hall, London, Chapter 1. Full book available electronically.
- Ashby, W.R.[1962]. "Principles of the self-organizing system". In: Principles of Self-Organization: Transactions of the University of Illinois Symposium. H. Von Foerster and G. W. Zopf, Jr. (eds.), Pergamon Press: London, UK, pp. 255-278.
- Cariani, P. [1992]. "Some epistemological implications of devices which construct their own sensors and effectors". In: Towards a Practice of Autonomous Systems.In F. Varela and P. Bourgine (ed.), MIT Press, Cambridge, Massachusetts.
- Cariani, P. [1993]. "To evolve an ear. Epistemological implications of gordon pask's electrochemical devices". Systems Research, 10(3):19-33.
- Cariani P. [2009]. "On the Importance of Being Emergent. Extended Review of “Emergence and Embodiment: New Essays on Second-Order Systems Theory” edited by Bruce Clark and Mark B. N. Hanson.Duke University Press, Durham, 2009. Constructivist Foundations. 5(2):86-91.
- Autopoiesis and Second-Order Cybernetics
- Pask, G. [1992]. "Different kinds of Cybernetics". In: New Perspectives on Cybernetics. G. Van de Vijver (Ed.), Kluwer Academic Publishers. pp. 11-31.
- Rocha, Luis M. [1996]. "Eigenbehavior and Symbols". Systems Research, 13(3):371-384.
- Varela, Francisco J.; Maturana, Humberto R.; & Uribe, R. [1974]. "Autopoiesis: the organization of living systems, its characterization and a model". Biosystems 5(4): 187-196.
- Varela, F.J. [1996]. "The early days of autopoiesis". Systems Research, 13(3):407-416.
- Varela, F.J. [1997]. "Patterns of Life: Intertwining Identity and Cognition". Brain and Cognition, 34(1):72-87.
- Optional: Von Foerster, H. [1970]. "Molecular Ethology, an Immodest Proposal for Semantic Clarification". In Molecular Mechanisms in Memory and Learning, Georges Ungar (Hg.), Plenum Press, New York, pp. 213–248.
- Optional: Von Foerster, H. [1993]. "On Gordon Pask". Systems Research, 10(3):35-42.
- Organization of Complex Systems
- Jaimovich, A., R. Rinott, M. Schuldiner, H. Margalit, and N. Friedman. 2010. "Modularity and directionality in genetic interaction maps". Bioinformatics 26 (12): i228-i236. doi:10.1093/bioinformatics/btq197.
- Lazebnik, Y [2002]. "Can a biologist fix a radio?--Or, what I learned while studying apoptosis". Cancer Cell, 2(3):179-182.
- Pattee, H.H. [1973]. "The Physical Basis and Origin of Hierarchical Control". In: Hierarchy Theory: The Challenge of Complex Systems. H.H. Pattee (ed.) , New York: G. Braziller, pp.73-108.
- Pattee, H.H. [2007]. "Laws, Constraints, and the Modeling Relation - History and Interpretations". Chemistry & Biodiversity, 4(10):2272-2295.
- Prigogine, I. [1985]. "New Perspectives on Complexity". In: The Science and Praxis of Complexity (United Nations University Press: 1985) 107-118
- Optional: Randall, T.S. [2007]. "Robert Rosen in the Age of Systems Biology". Chemistry & Biodiversity, 4(10):2407 - 2414.
- Rosen, R. [1986]. "The Physics of Complexity". Systems Research, 2: 171.
- Rosen, R. [1987]. "On Complex Systems". European Journal of Operational Research, 30: 129-134.
- Simon, H.A. [1962]. "The Architecture of Complexity". Proceedings of the American Philosophical Society, 106: pp. 467-482.
- Part II: Current Research
- Evolutionary Systems
- Conrad, M. [1990]. "The geometry of evolution.". Biosystems 24: 61-81
- Draghi JA, Parsons TL, Wagner GP, Plotkin JB [2010]. "Mutational robustness can facilitate adaptation.". Nature 463 (7279):353-5
- Pigliucci M. [2008]. "Is evolvability evolvable?". Nature reviews. Genetics. 9 (1): 75-82
- Rocha LM, Hordijk W. [2005]. "Material representations: From the genetic code to the evolution of cellular automata.". Artificial Life. 11(1-2):189-214.
- Stadler, B.M.R., P.F. Stadler, G.P. WAGNER, and W. Fontana [2001]. "The topology of the possible: formal spaces underlying patterns of evolutionary change.". Journal of theoretical biology 213(2): 241-74.
- Vasas, Vera, Eors Szathmary, and Mauro Santos [2010]. " Lack of evolvability in self-sustaining autocatalytic networks: A constraint on the metabolism-first path to the origin of life. ". Proceedings of the National Academy of Sciences of the United States of America: 0912628107.
- Information, Complexity, and Evolution
- Feldman, David P., Carl S. McTague, and James P. Crutchfield [2008]. "The organization of intrinsic computation: Complexity-entropy diagrams and the diversity of natural information processing.". Chaos 18(4): 043106
- Krakauer, David C, James P Collins, Douglas Erwin, Jessica C Flack, Walter Fontana, Manfred D Laubichler, Sonja J Prohaska, Geoffrey B West, and Peter F Stadler. [2011]. "The challenges and scope of theoretical biology". Journal of theoretical biology. In Press.
- Prokopenko, Mikhail, Fabio Boschetti, and Alex J. Ryan. [2009]. "An information-theoretic primer on complexity, self-organization, and emergence. ". Complexity 15(1): 11-28
- Smith, David M. D., Jukka-Pekka Onnela, Chiu Fan Lee, Mark Fricker, and Neil F. Johnson [2007]. "Network Automata: Coupling structure and function in real-world networks". submitted. Preprint: arXiv: physics/0701307.
- Networks and Systems Biology
- Bornholdt S. [2010]. "Systems biology. Less is more in modeling large genetic networks". Science. 310(5747):449-51.
- M. Chaves, R. Albert and E.D. Sontag [2005] "Robustness and fragility of Boolean models for genetic regulatory networks", Journal of Theoretical Biology. 235, 431-449.
- Klamt S, Haus U-U, Theis F. [2010]. "Hypergraphs and cellular networks.". PLoS computational biology 5(5): e1000385
- T. Helikar, J. Konvalina, J. Heidel, and J.A. Rogers [2008] "Emergent decision-making in biological signal transduction networks.", PNAS. 105(6): 1913-1918
- Saadatpour A, Albert I, Albert R. [2010]. "Attractor analysis of asynchronous Boolean models of signal transduction networks". Journal of theoretical biology. 266(4):656-641.
- Modeling Human Behavior
- Arthur, W.B. [1999]. "The End of Certainty in Economics". Einstein Meets Magritte, D. Aerts, J. Broekaert, E. Mathijs, (Eds.), Kluwer Academic Publishers.
- Bettencourt, L.M.A., J.Lobo, D. Helbing, C. Kühnert, and G.B. West [2007]. "Growth, innovation, scaling, and the pace of life in cities.", PNAS 104(17), 7301-7306
- Bettencourt, L.M.A. and G.B. West [2010]. "A unified theory of urban living.", Nature 467(7318): 912-3
- Bollen, Johan, Huina Mao, and Xiaojun Zeng [2011]. "Twitter mood predicts the stock market.", Journal of Computational Science In Press. doi:10.1016/j.jocs.2010.12.007.
- M. D. Conover, J. Ratkiewicz, M. Francisco, B. Goncalves, A. Flammini, F. Menczer [2011]. "Political Polarization on Twitter", In: Proceedings of 5th International Conference on Weblogs and Social Media.
- Goel, S., J. M. Hofman, S. Lahaie, D. M. Pennock, and D. J. Watts [2010]. "Predicting consumer behavior with Web search.", Proceedings of the National Academy of Sciences 107(41): 17486-17490.
- W. Richards, B.D.McKay, and D. Richards. [2002] "Probability of Collective Choice with Shared Knowledge Structures", Jrl. Math. Psych. 46, 338-351.
- Shalizi, C.R. [2011]. "Scaling and Hierarchy in Urban Economies.", arxiv.org.
- Stark, David. [2009]. The sense of dissonance: accounts of worth in economic life. Princeton University Press. TOC and Chapter 1.
- Collective Behavior, Cooperation and Global Brain
- Conrad M. [1993]. "Adaptability theory as a guide for interfacing computers and human society". Systems Research: 10:1-23.
- Conradt L. [2011]. "Collective behaviour: When it pays to share decisions". Nature. 471(7336):40-41.
- Heylighen F. [2007]. "Accelerating Socio-Technological Evolution: from ephemeralization and stigmergy to the global brain".Globalization as an Evolutionary Process: Modeling Global Change, George Modelski, Tessaleno Devezas, and William Thompson (Eds.), Routledge, p.286-335.
- Hilbert M, Lopez P. [2011] "The World's Technological Capacity to Store, Communicate, and Compute Information". Science. 2011;332(6025):60-65.
- Moussaďd M, Perozo N, Garnier S, Helbing D, Theraulaz G. [2010] "The Walking Behaviour of Pedestrian Social Groups and Its Impact on Crowd Dynamics." PLoS ONE. 5(4):e10047.
- Nitschke G. [2005]. "Emergence of Cooperation: State of the Art". Artificial Life. 11(3):367.
- Szathmáry E, Számadó S. [2010]. "Being human: language: a social history of words". Nature. 456 (7218):40-1.
- Optional: De Silva, H., Hauert, Ch., Traulsen, A. & Sigmund, K. [2010] "Freedom, enforcement, and the social dilemma of strong altruism". J. Evol. Econ. 20: 203-217
- Optional: Hauert, Ch. [2006] "Cooperation, Collectives Formation and Specialization", Adv. Complex Systems 9, 315-335.