Video Zip Files: |
Lecture Slides: |
Netlogo:
Quizzes and Homework: Note that homework is optional and ungraded. We will be posting solutions to selected homework assignments.
Unit 1:
Unit 2:
- SimplePopulationGrowth.nlogo
- LogisticModel.nlogo
- LogisticMap.nlogo
- SensitiveDependence.nlogo
- SineMap.nlogo
- Unit 2 test
Unit 3:
- KochCurve.nlogo
- ExamplesOfFractals.nlogo
- BoxCountingDimension.nlogo
- BoxCountingApplied.zip
- LSystems.nlogo
- Unit 3 test
Unit 4:
- SlotMachine.nlogo
- CoinFlipInformationContent.nlogo
- TextInformationContent.nlogo
- LogisticMapInformationContent.nlogo
Unit 5:
- Unit5Homework.pdf
- RobbyGA.nlogo
- CommonSelectionMethods.pdf (for Advanced-Level Homework)
Unit 6:
- Mini-Life.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:
- Unit7Homework.pdf
- Note that all the NetLogo models are in the Models Library: go to the Biology section.
Unit 8:
Unit 9
- Unit9Homework.pdf
- SmallWorldNetworks.nlogo
- SmallWorldNetworksMacOS10.8.nlogo (the version above doesn't work on OS 10.8; instead use this one)
- preferential-attachment.nlogo (from the NetLogo Models Library)
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: 536-544, 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 non-exhaustive list. IEEE Control Systems Magazine, 7-8, 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 non-technical 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. 4-27. 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 on-line book and other resources for learning about fractals.
- B. Mandelbrot, The Fractal Geometry of Nature, W.H. Freeman and Co. New York (1983).
- N. Lesmoir-Gordon 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 semi-popular 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 up-to-date 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, 1st Edition. New York: Wiley-Interscience, 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 Self-Organization
- S. Camazine et al., Self-Organization 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 Self-Organization 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
- 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 'small-world' 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.