I709: Complex Systems Seminar II
Spring 2008
Instructor: Luis M. Rocha, Complex Systems Group, School of Informatics and Cognitive Science Program, Indiana University
Class Location and Time: Tuesdays and Thursdays, 4:00PM - 5:15PM, Room: Informatics Building, 001
Course Description
Instructor: Luis M. Rocha, Complex Systems Group, School of Informatics and Cognitive Science Program, Indiana University
Class Location and Time: Tuesdays and Thursdays, 4:00PM - 5:15PM, Room: Informatics Building, 001
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
- Tuesdays: 2:00om – 3:30pm, Eigenmann Hall, Room #905
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.
- Systems Science
- Beer, S. [1965], "The World, The Flesh and The Metal: The Prerogatives of Systems". Nature 205:223 - 231.
- 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.
- 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.
- 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.
- Autopoiesis
- Beer, S. [1974], Designing Freedom. John Wiley & Sons.
- 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.
- 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.
- Von Foerster, H. [1993]. "On Gordon Pask". Systems Research, 10(3):35-42.
- Complex Systems
- 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
- 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.
- Human-computer conversation, Society and the Global Brain
- Arthur, W.B. [1999]. "The End of Certainty in Economics". Einstein Meets Magritte, D. Aerts, J. Broekaert, E. Mathijs, (Eds.), Kluwer Academic Publishers.
- Clark, A. [1999]. "Leadership and Influence: The Manager as Coach, Nanny and Artificial DNA".The Biology Of Business: De-Coding The Natural Laws Of Enterprise, J. Clippinger (Ed.), Jossey-Bass.
- Clippinger, J. and D. Bollier [2005]. "A Renaissance of the Commons: How the New Sciences and Internet Are Framing A New Global Identity and Order".Code: Collaborative Ownership and the Digital Economy, Ghosh, R.A. (Ed.), MIT Press.
- 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.
- Pangaro, Paul [2001]. "THOUGHTSTICKER 1986: A personal history of conversation theory in software, and its progenitor, Gordon Pask". Kybernetes, 30 (5-6): 790-806.
- Patel, A., B. Scott, and Kinshuk [2001]. "Intelligent tutoring: from SAKI to Byzantium ". Kybernetes, 30 (5-6): 807 - 819.
- Rocha, L.M. [2001]. "Adaptive recommendation and open-ended semiosis". Kybernetes, 30 (5-6): 821 - 854.
- Stark, D. [1999]. "Heterarchy: Distributing Authority and Organizing Diversity".The Biology Of Business: De-Coding The Natural Laws Of Enterprise, J. Clippinger (Ed.), Jossey-Bass, 153-179.
- Part II: Current Research
- Evolution of Cooperation
- Hauert, Ch. [2006] "Cooperation, Collectives Formation and Specialization", Adv. Complex Systems 9, 315-335.
- Hauert, Ch., Traulsen, A., Brandt, H., Nowak, M. A. & Sigmund, K. [2007] "Via freedom to coercion: the emergence of costly punishment", Science 316, 1905-1907.
- Langer, P., Nowak, M. A. & Hauert, Ch. [2008] "Spatial Invasion of Cooperation", J. theor. Biol. 250, 634-641.
- Collective Choice
- D. Richards, W. Richards and B.D.McKay. [1999] "Collective Choice and Mutual Knowledge Structures", Adv. Complex Systems 1, 221–236.
- W. Richards, B.D.McKay, and D. Richards. [2002] "Probability of Collective Choice with Shared Knowledge Structures", Jrl. Math. Psych. 46, 338-351.
- W. Richards and S. Seung. [2006] "Neural Voting Machines", Neural Networks 19, 1161-1167.
- Network Inference
- 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.
- C. Christensen, J. Thakar, and R. Albert [2007] "Systems-level insights into cellular regulation: inferring, analyzing and modeling intercellular networks", IET Systems Biology. 1, 61-77.
- U. Alon [2007] "Network motifs: theory and experimental approaches.", Nat Rev Genet. 8(6), 450–461
- Computation and Representation in Distributed Networks
- M. Mitchell. [2006] "Complex systems: Network thinking.", Artificial Intelligence. 170,(18):1194–1212
- W. Hordijk, J. P. Crutchfield, and M. Mitchell. [1998] "Mechanisms of emergent computation in automata", Proceedings of the Fifth International Problem Solving From Nature—PPSN V. In A. E. Eiben, editor, , New York, 1998. Springer.
- Rocha, Luis M. and W. Hordijk [2005] "Material Representations: From the Genetic Code to the Evolution of Cellular Automata", Artificial Life. 11(1-2), 189 - 214
- D. Peak, J.D. West, S.M. Messinger, and K.A. Mott. [2004] "Evidence for complex, collective dynamics and distributed emergent computation in plants.", PNAS. 101(4): 918–922
- T. Helikar, J. Konvalina, J. Heidel, and J.A. Rogers [2008] "Emergent decision-making in biological signal transduction networks.", PNAS. 105(6): 1913-1918
- Other Topics
- C. Barrett, S. Eubank and M. Marathe [2006] "Modeling and Simulation of Large Biological, Information and Socio-Technical Systems: An Interaction Based Approach .", Interactive Computation: The New Paradigm . D. Goldin, S.A. Smolka and P. Wegner (Eds.), pp. 353-392
- C. Barrett, B. W. Bush, S. Kopp, H. S. Mortveit, C. M. Reidys [2000] "Sequential Dynamical Systems and Applications to Simulations.", Proceedings of the 33rd Annual Simulation Symposium , pp. 245
- 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
- Mattick, J.S. and M.F. Mehler [2008] "RNA editing, DNA recoding and the evolution of human cognition", Trends Neurosci In Press.
- Medina, E. [2006] "Designing Freedom, Regulating a Nation: Socialist Cybernetics in Allende's Chile.", Journal of Latin American Studies 38, 571-606
- Stewart J, Coutinho A. [2004] "The affirmation of Self: A New Perspective on the Immune System", Artificial Life. 10(3), 261 - 276
- J. Timmis, P. Andrews, N. Owens and E. Clark [2008] "An interdisciplinary perspective on artificial immune systems ", Evolutionary Intelligence 1(1), 5-26




