Introduction to Complexity
Lead instructor: Santiago Ortolano Guisasola
Video Zip Files:

Lecture Slides: 
NetLogo:
 Download NetLogo
 Hints for downloading NetLogo (if you're having problems)
 Getting started with NetLogo (pdf)
 Netlogo Users Manual
 NetLogo Behavior Space Tutorial
Unit 1 Models:
Unit 2 Models:
 SimplePopulationGrowth.nlogo
 LogisticModel.nlogo
 LogisticMap.nlogo
 SensitiveDependence.nlogo
 LogisticMapBifurcationDiagramExplorer.nlogo
 SineMap.nlogo
Unit 3 Models:
 KochCurve.nlogo
 ExamplesOfFractals.nlogo
 BoxCountingDimension.nlogo
 BoxCountingApplied.zip
 LSystems.nlogo
Unit 4 Models:
 SlotMachine.nlogo
 CoinFlipInformationContent.nlogo
 TextInformationContent.nlogo
 LogisticMapInformationContent.nlogo
Unit 5 Models:
 RobbyGA.nlogo
 CommonSelectionMethods.pdf (for AdvancedLevel Homework)
Unit 6 Models:
 MiniLife.nlogo (note that this version does not show the "green" updates shown in the vidoes)
 GameOfLife.nlogo
 ElementaryCAs.nlogo
 Link to Edge of Chaos Applet
Unit 7 Models:
 Note that the Flocking, Fireflies, and Ants NetLogo models are in the Models Library: go to the Biology section.
 FirefliesWithEntropy.nlogo
 FlockingWithEntropy.nlogo
Unit 8 Models:
Unit 9 Models:
 SmallWorldNetworks.nlogo
 preferentialattachment.nlogo (from the NetLogo Models Library)
 ZipfsLaw.nlogo
Unit 10
Optional Readings:
General:
 M. Mitchell, Complexity: A Guided Tour. Parts of the course will roughly follow this book. The book is a useful companion to the course, but is not required for taking this course.
Unit 1: What is Complexity?
 W. Weaver, Science and complexity. American Scientist, 36: 536544, 1948. A classic article by an influential 20th century scientists/mathematician, on why science should focus on complex systems.
 S. Lloyd, Measures of complexity: A nonexhaustive list. IEEE Control Systems Magazine, 78, August, 2001. A list of some mathematical measures of complexity, though without much explanation of what they mean.
Unit 2: Dynamics and Chaos
 L. Kadanoff, Chaos: A view of complexity in the physical sciences. In From Order to Chaos: Essays: Critical, Chaotic, and Otherwise, 1993. A relatively nontechnical discussion of the logistic map, and other issues in the study of chaos.
 M. Feigenbaum, Universal behavior in nonlinear systems. Los Alamos Science, 1, 1980, pp. 427. A more thorough and technical, though very readable, discussion of the logistic map and related systems by the scientist who made many of the discoveries described here.
 J. Garland and L. Bradley, On the importance of nonlinear modeling in computer performance prediction
Unit 3: Fractals
 Fractal Explorer. An online book and other resources for learning about fractals. Make sure to have Flash enabled.
 B. Mandelbrot, The Fractal Geometry of Nature, W.H. Freeman and Co. New York (1983).
 N. LesmoirGordon and R. Edney, et al. Introducing Fractal Geometry, Icon Books Ltd. (2000).
 M. Schroeder, Fractals, Chaos, Power Laws. W. H. Freeman and Co. (1991)
 C. Brown and L. Liebovitch, Fractal Analysis, Series: Quantitative Applications in the Social Sciences, Sage Publications Inc. (2010).
Unit 4: Information, Order, and Randomness
 Shannon, C.E. (1948), A Mathematical Theory of Communication, Bell System Technical Journal, 27, pp. 379–423 & 623–656, July & October, 1948. Shannon's original article is tough going in places but is available online here.
 R.V.L. Hartley, Transmission of Information, Bell System Technical Journal, July 1928
 J. L. Lebowitz, Boltzmann's entropy and time's arrow. A semipopular article for people who want to read further about the issues in Unit 4.
 S. Carroll, From Eternity to Here: The Quest for the Ultimate Theory of Time. A fascinating (if long) book that will bring you uptodate on current views in physics about the nature of time.
 T. D. Schneider, Information Theory Primer. A nice, brief primer on Shannon information; readable if you are comfortable with exponents, logarithms, summation signs, and such. Geared towards biologists, so uses genetics as an example.
 James Gleick, The Information: A History, a Theory, a Flood, New York: Pantheon, 2011. For general audiences.
 Thomas M. Cover, Joy A. Thomas. Elements of information theory. New York: WileyInterscience, 1991. A more advanced textbook on information theory.
Unit 5: Genetic Algorithms
 There are many excellent online tutorials on genetic algorithms, and several good free software packages.
 Chapter 9 in Complexity: A Guided Tour, covers some of the same material covered in the lectures for this unit.
 Robby the Robot code in C.
 Link to Karl Sims' papers on evolving computer graphics and virtual creatures.
 J. H. Holland. Adaptation in Natural and Artificial Systems. MIT Press, 1992. John Holland's classic book, originally published in 1975, that sets out the theoretical basis for genetic algorithms.
 K. De Jong, Evolutionary Computation. MIT Press, 2002. Somewhat technical textbook on genetic algorithms and other evolutionary computation techniques.
 M. Mitchell, An Introduction to Genetic Algorithms. MIT Press, 1996. Older, fairly short textbook on genetic algorithms
Unit 6: Cellular Automata
 J. Conway, "What is Life?" Chapter 25 in Berlekamp, E. R.; Conway, J. H.; and Guy, R. K., Winning Ways for Your Mathematical Plays, Vol. 2: Games in Particular
 W. Poundstone, The Recursive Universe: Cosmic Complexity and the Limits of Scientific Knowledge. An entertaining and enlightening popular science book that tackles big questions about the universe by looking at Conway's Game of Life.
 Elementary Cellular Automaton from mathworld.wolfram.com
 Website for A New Kind of Science
 M. Mitchell, Review of A New Kind of Science
 M. Mitchell, Computation in Cellular Automata: A Selected Review
 Mitchell, M., Crutchfield, J. P., and Das, R. Evolving cellular automata to perform computations: A review of recent work
Unit 7: Models of SelfOrganization
 S. Camazine et al., SelfOrganization in Biological Systems. Princeton University Press, 2001.
 S. Strogatz, Sync: How Order Emerges From Chaos In the Universe, Nature, and Daily Life. Hyperion, 2003.
 E. Yong, How the science of swarms can help us fight cancer and predict the future. Wired, 03.19.13.
 C. W. Reynolds, Flocks, herds, and schools: A distributed behavioral model. ACM SIGGRAPH Computer Graphics, 1987.
 D. M. Gordon, The regulation of foraging activity in Red Harvester ant colonies.
 D. M. Gordon, Interaction patterns and task allocation in ant colonies.
Unit 8: Models of SelfOrganization and Cooperation in Social Systems
 R. Axlerod, The Evolution of Cooperation. New York: Basic Books, 1984.
 R. Axelrod, The Complexity of Cooperation. Princeton University Press, 1997.
 M. Nowak, Five rules for the evolution of cooperation.
 B. Hayes, New dilemmas for the prisoner. American Scientist
 D. Jessie and D. Saari, Strategic and Behavioral Decomposition of Games. IIASA Interim Report, 2015.
 T. C. Schelling, Dynamic models of segregation.
 B. Hayes, The math of segregation.
 W. B. Arthur, Inductive reasoning and bounded rationality (the El Farol problem).
 W. B. Arthur, Complexity economics: A different framework for economic thought.
 J. D. Farmer, Economics needs to treat the economy as a complex system.
Unit 9: Networks
 D. J. Watts and S. H. Strogatz, Collective dynamics of 'smallworld' networks.
 A. L. Barabasi and R. Albert, Emergence of scaling in random networks.
 M. E. J. Newman, Networks: An Introduction.
 M. E. J. Newman, Structure and function of complex networks.
 D. Easley and J. Kleinberg, Networks, Crowds, and Markets.
 D. J. Watts, Six degrees: The science of a connected age.
 A. L Barabasi, Linked: The new science of networks.
 D. J. Watts, "Too complex to exist", Boston Globe, June 14, 2009.
Unit 10: Scaling in Biology and Society
 M. E. J. Newman, Power laws, Pareto distributions, and Zipf's law.
 G. B. West and J. H. Brown, The origin of allometric scaling laws in biology from genomes to ecosystems: Towards a quantitative unifying theory of biological structure and organization.
 G. B. West et al., The fourth dimension of life: Fractal geometry and allometric scaling of organisms.
 P. S. Agutter and D. N. Wheatley, Metabolic scaling: Consensus or controversy?
 Mathbench, The 3/4 Law (Very nice, relatively nontechnical overview)
 L. M. A. Bettencourt et al., Growth, innovation, scaling, and the pace of life in cities.
 L. M. A. Bettencourt, The origins of scaling in cities.
 P. Ball, Decoding deep similarities (Review of Geoffrey West's book, Scale)