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Syllabus2009FallCSCS 501 -- readings for Fall 2009Books you probably should purchase include:
Barabasi: Linked.
Those (and other) books are in the CSCS Lab, for reading at CSCS. Reading assignments, Discussion leaders:Wed 9 Sept --- Organizational meeting. Handout in class today -- general course intro, grading, etc.
Books to get NOW:
Waldrop -- Complexity
Flake -- Computational Beauty of Nature
Holland -- Hidden Order
Kelly -- Out of Control (optional, since its online!)
Sole and Goodwin -- Signs of Life
Mon 14 Sept --- What are Complex Adaptive Systems?
Waldrop: Complexity, Preface: "Visions of the Whole"; Chapter 1, 2;
Flake: The Computational Beauty of Nature, p1-8. pdf of these pages
Bar-Yam: Section 0, Overview: The Dynamics of Complex Systems, pp 1-15 (online version here)
Suggestion: trawl the web for other views/definitions of
complex (adaptive) systems, think about them, compare to what
you think are complex [adaptive] systems.
Discussion Leaders: Jason, Craig
Wed 16 Sept Some more history of ideas from early days at SFI Waldrop: Chapter 3, 4,
Discussion Leaders: Colin, Irem
Mon 21 Sept --- Some basics: CAs, Chaos; More ideas -- Edge of Chaos Flake Chapter 15 (CA = Cellular Automata)
Flake: Chapters 10,11 (Chaos)
Waldrop Chapter 6 (Edge of Chaos)
Semi-Optional --- be sure to read sometime soon!
Flake Chapters 2-3 (Numbers, Computation, Computability)
Optional -- but highly recommended.
Mathematical Fallacies and Paradoxes, Bryan Bunch.
A very nice little book -- i recommend the whole book!
But for this class, two good chapters are here:
Optional - a bit challenging, but may be of interest:
G.J. Chaitan: Computers, Paradoxes and the Foundation of Mathematics.
Discussion Leaders: Trevor, Do Kyeong
Wed 23 Sept --- SFI III - Holland ; Kelly's Biologically Inspired Approach Waldrop, Chapter 5.
Kelly: Out of Control, Chapter 1-2,4-6. online here
Discussion Leaders: Ashwini, Sunit
Mon 28 Sept --- More big ideas - SFI III Waldrop Chapters 7-9
Whitfield: Survival of the Likeliest? Plos Biology 5(5): e142 (May 2008)
Farmer: Review of Into the Cool: Energy Flow, Thermodynamics and Life (Schneider and Sagan), in Nature 436 (4 August 2005)
Optional
Morowitz and Smith: Energy flow and the organization of life Complexity 13(1): 51-59 (2007)
Kelly, Chapter 21 (Rising Flow)
Discussion Leaders: Vijay, Avinash
Wed 30 Sept --- Attend Public Event in honor of John Holland If you can, reading the material listed under next Monday (Oct 5) before these talks might lead to a better understanding of the talks. But hearing the talks before reading will be ok. Annenberg Auditorium - UM Ford School of Public Policy 4pm-6pm
Refreshments will be served
Speakers
Mon 5 Oct --- Readings related to the Holland Fest Talks Holland, Hidden Order Chapter 1,2
West and Brown. Life's Universal Scaling Laws. Phys. Today 2004
Discussion Leaders: Vijay, Jason
Wed 7 Oct --- Adaptation: GAs, Classifier systems Flake Chapters 20-21 (GA and classifier systems);
Flake Chapter 23: Postscript -- Adaptation
Riolo, Survival of the Fittest Bits
Optional Koza, "Evolving Inventions" Sci Amer Feb 2003
Flake Chapter 22: Neural Nets
Flake, Chapter 4 (Computation Postscript)
Discussion Leaders: craig , sunit
Mon 12 Oct --- Holland and CAS (cont): Echo Holland, Hidden Order, Chapters 3-5
Optional Find something on the web about Holland's echo model,
eg. followup papers, related work, etc.
Discussion Leaders: Irem, Dokyeong
Wed 14 Oct --- From Chaos and equation-based models to Agent Based Modeling Flake Chapter 14 (Producer-Consumer Dynamics)
Flake Chapter 16 (Autonomous Agents and Self-Organization)
Scott Page: Agent Based Models, From The New Palgrave Dictionary of Economics
Dan Brown: Agent Based Models
Optional Sole and Goodwin Chapter 6 (Ants, Brains and Chaos)
Flake 14 (Chaos Epilogue)
Discussion Leaders: Colin, Jason
Mon 19 Oct -- Fall break! No class! Wedn 21 Oct: Misc CAS/evolution/ecology topics. Jacob, Evolution and Tinkering, Science 196(4295): 1161-1166 (10 june 1977)
Kelly, Chapter 17 (open universe), Chapter 18 (Structure of organized change),
Kelly, Chapter 19 (post darwinism), Chapter 21 (Rising Flow)
Flake Chap 19 (Postscript -- Complex Systems)
Optional R.Sole and B.Goodwin Signs of Life: Chapter 7.
Flake Chap 17 (Competition and Cooperation);
Discussion Leaders: Ashwina, avinash
Mon 26 Oct: Paper presentations Presenters: Trevor, Jason, Vijay, Do Kyeong, Ashwina
Wed 28 Oct: Paper presentations Presenters: Irem, Colin, Avinash, Sunit, Craig
Mon 2 Nov: Papers due.''' No class!
Wed 4 Nov: Hierarchy, Modularity. These first two are truly "classics"!
Anderson: More is Different. Science 177, 393 (1972)
Simon: The Architecture of Complexity. A chapter of Sciences of the Artificial.
George Ellis: Physics, complexity and causality. Nature 435 (9 June 2005): p743.
Optional (but it has some good history): Corning: The Re-emergence of "Emergence": A Venerable Concept in Search of a Theory.
Discussion Leaders: Vijay, Sunit
Mon 9 Nov: Coupled Human and Natural Systems (CHNS) Jane Jacobs, The Death and Life of Cities, Chapter 22 (pdf version)
Lui etal: Complexity of Coupled Human and Natural Systems. Science 317: 1513-1516 (2007 Sept 14).)
Helbing. Managing Complexity in Socio-Economic Systems. European Review 17(2): 423-428 (2009).
Ostrom: A General Framework for Analyzing Sustainability of Social-Ecological Systems. Science 325 (24 July 2009): 419-422.
Optional Steven Manson. Complexity Theory in the study of space and place.
Environment and Planning A 38: 677-692 (2006). Discussion Leaders: Trevor, Irem
Wed 11 Nov: CHNS II -- Resilience, Adaptive Capacity, etc. Holling. Understanding the Complexity of Economic, Ecological and Social Systems. Ecosystems 4: 390-405 (2001).
Walker, Holling, Carpenter, Kinzig: Resilience, Adaptability and Transformability in Social–ecological Systems Ecology and Society: 9(2)
Gallopin. Linkages between vulnerability, resilience and adaptive capacity. Global Environment Change 16: 293-303 (2006).
Discussion Leaders: Ashwina, Irem
Mon 16 Nov -- Cellular Automata -- Cities, emergence Cities: Batty. Cellular Automata and Urban Form: A primer. J.Amer.Planning Assoc 63(2): 266-274 (1997).
Batty. The Size, Scale and Shape of Cities. Science 319 (8 Feb 2008): 769-771.
Sharaf and Shan. Cellular Automata Urban Growth Simulation and Evaluation - A Case Study of Indianapolis. Proc 8th Int. Conf on GeoComputation (2005)
Emergence: James P. Crutchfield, Melanie Mitchell, and Rajarshi Das.
Evolving Cellular Automata with Genetic Algorithms: A Review of Recent Work. Optional Batty. Cities as Complex Systems. Encyl.Complexity and System Science (2008)
Thomas Bäck etal. Modeling urban growth by cellular automata. Parallel Problem Solving from Nature — PPSN IV, Springer Lecture Notes in Computer Science (1996).
James P. Crutchfield, Melanie Mitchell, and Rajarshi Das.
The Evolutionary Design of Collective Computation in Cellular Automata (long version). Discussion Leaders: Do Kyeong, Jason
Wed 18 Nov: SOC and HOT systems. SOC Readings for Per Bak's How Nature Works
Sole and Goodwin, Chap 10
HOT Mark Newman. The Power of Design.
Carlson, JM & Doyle, J. Complexity and Robustness Proc. Nat. Acad. Sci. 99 , 2538-2545 (2002)
Marie Csete and John Doyle. Reverse Engineering of Biological Complexity.
Optional: Brunk: Understanding SOC as a Statistical Process.
Complexity, v5 (3): 26-33 (2000). Raup: A Breakthrough Book? Review of How Nature Works.
Complexity, v2 (6): 772-773 (1997). Per Bak and Kim Sneppen.
Punctuated equilibrium and criticality in a simple model of evolution.
Phys.Rev.Lett., 71(24): 4083-4086, 1993. (near the bottom of the page)
Carlson, JM & Doyle, J (2000) Phys. Rev. Lett. 84, 2529-2532.
(See Carlson's complexity pagesfor more HOT papers...)
Moritz etal. Wildfires, Complexity and Highly Optimized Tolerance
Proc. Nat. Acad. Sci.102, 17912-17917
Reynolds, D, Carlson, JM & Doyle, J (2002) Phys. Rev. E 66.
Discussion Leaders: Craig, Ashwina
Mon 23 Nov: Networks and CAS. Duncan Watts: Six Degrees, the Science of a Connected Age (2003).
Chapters 2, 3, 4 and 6. (Other chapters are fun, too.)
Duncan J. Watts and Steven H. Strogatz.
Collective Dynamics of 'Small Worlds' Networks. Nature 393: pp440-442 (1998)
(See also the News and Views article 409-410.)
Barabsi. Scale-Free Networks: A Decade and Beyond. Science 325 (24 Jul 2009): 412-413.
Butts. Revisiting the Foundations of Network Analysis. Science 325 (24 Jul 2009): 414-416.
Optional From Barabasi's book, Linked: Chpts 1-7, 10, 13, 14. (In the lab, or buy a copy -- its worth it!)
Chapter 9 of Strogatz's Sync is his view on his work with his student, Duncan Watts.
Barabesi and Albert. Emergence of Scaling in Random Networks. Science 286: 509-512 (1999)
Discussion Leaders: Trevor, Craig
Wed 25 Nov: Thanksgiving break -- no class. Mon 30 Nov: Kauffman: At Home in the Universe Kauffman chapters: 1, 3-5, 8,9.
Sole and Goodwin, Chapters 3, 8.
Discussion Leaders: Vijay, Sunit
Wed Dec 2: Kauffman and variations. Kauffman: At Home in the Universe. Chapters: 10, 11.
Sole and Goodwin, Chapter 9.
Pick at least one (or more!) of the following to read -- each uses On the Use of multi-species NK models to explore ecosystem development. Swanack etal. Ecological Modeling 218: 367-374 (2008), Neutrality in Technological Landscapes.
Lobo, Miller. Fontana.
Epochal Evolution Shapes the Phylodynamics of Interpandemic Influenza A (H3N2) in Humans Katia Koelle etal. Science 314 (5807), 1898 (22 December 2006). (A paper by two former cscs501 students which uses an extension of Kaufmann's NK-model) Landscape Design: Designing for Local Action in Complex Worlds. Levinthal and Warglien. Organization Science, 10(3): 342-357. (1999) Avoiding Complexity Catastrophe in Coevolutionary Pockets: Strategies for Rugged Landscape. W.McKelvey. Organization Science 10(3): 294-321 (1999). (See Bill's page of publications for this and related papers.) Understanding and Attenuating the Complexity Catastrophe in Kauffman's NK Model of Genome Evolution. Solow, D. etal. Complexity 5(1): 53-66 (1999). Evolutionary Consequences of Selected Locus-specific Variations in Epistasis and Fitness Contribution in Kauffman's NK-Model. Solow, D. etal. J. Theor. Biol., 196, pp181-196 (1999). Discussion Leaders: Avinash, Colin
Mon 7 Dec: Systems Dynamics approaches to Complex Systems. General System Dyanamics. The Beer Game-- another classic!
Arquitt etal. A systems dynamics analysis of boom and bust in the shrimp acquiculture industry. Systems Dynamics Review Vol 21 (4): 305-324 (Winter 2005)
This one is not just about systems dynamics models: Sterman. Learning from Evidence in a Complex World. Amer. J. Public Health 96(3): 505-514 (2006).
System Dynamics in human motion/cognition: Ester Thelan. Motor Development: A New Synthesis.
From American Psychologist 50(2): 79-95 (1995).
Optional Sole and Goodwin, Chapter 5.
Esther Thelen and Linda B. Smith (1994). From A Dynamical Systems Approach to the
Development of Cognition and Action: Introduction, Chaps 1,2,3 and pp71-83,121-125 of Chp.4. (e-reserves)
Tim Van Gelder (and a host of commentators). The dynamical hypothesis in cognitive science. Behavioral and Brain Sciences 21 (5): 615-665. (1998)
from An Introduction to Systems Thinking, Barry Richmond.
(Note: In Richmond translate "Stella" -> "system dynamics" to generalize beyound Stella.)
Discussion Leaders: Trevor, Do Kyeong
Wed 9 Dec: CAS and Cognition -- Copycat, etc Douglas Hofstadter: Metamagical Themas (1996) In e-reserves.
Who shoves whom around in the careenium? pp. 604-630.
Waking up from the Boolean dream, or, Subcognition as computation. pp. 631-665.
Melanie Mitchell and Douglas Hofstadter. (1995)
The Copycat Project, Chapter 5 in Fluid Concepts and Creative Analogies.
Computer Models of the Fundamental Mechanisms of Thought. (e-reserves)
Melanie Mitchell.
In L. Segel and A. Cohen (editors), Design Principles for the
Immune System and Other Distributed Autonomous Systems.
Discussion Leaders: Vijay, Avinash
Mon 14 Dec: Recap. CAS -- various lists of broad characteristics.''' Kelly, Chap2 23-24.
Johnson, Emergence pp77-79 (embedded in Chapter 2, here as pdf)
(e-reserves has most of the first chapter, too) Levin, Fragile Dominion Chapter 9
Flake Chapter 24: Epilogue: Duality and Dichotomy
Review Holland's list of CAS properties, etc.
Optional Chu etal: Theories of Complexity. Complexity: 8(3): 19-30 (2003).
Clash of Cultures. Evelyn Fox Keller. Nature 445 (8 Feb 2007): 603.
More Optional' Excerpts from "Complexity: Metaphors, Models and Reality":
pp 1-45. (e-reserves -- note this is in three parts, spread around the e-reserves pages.
Be sure to read the discussion transcripts after these articles:
Steven Manson. Simplifying Complexity: a review of complexity theory.
Morowitz: The Emergence of Everything: How the World Became Complex. (2003)
pp 1-38, 179-184. At the e-reserves site.
The CSCS lab library has copies if you want to read other parts of the book!)
Discussion Leaders: Colin, ?
18 Dec: Papers due. Things we didn't get to this term' These could be starting points for your second paper. Emergence of Entities/Laws at new levels. Walter Fontana (1996): On Organization
John Maynard Smith and E. Szathmary. Readings from their book The Origins of Life:
Chapters 1, 2 (e-reserves)
Another short, compressed version of their ideas:
E. Szathmary and John Maynard Smith. The Major Evolutionary Transitions.
Optional (but recommended): Maynard Smith and Szathmary: (e-reserves)
Two astounding steps in the evolution: Chap 9 (symbiosis), Chap 9 (multicellularity)
Walter Fontana and Leo Buss. Extra-Highly recommended!
pp1-27,40-51. From Barriers and Boundries, J. Casti and A. Karlqvist (eds), 1996.
James Crutchfield: Is Anything Ever New? Considering Emergence.
More Cellular Automata (CAs) James P. Crutchfield, Melanie Mitchell, and Rajarshi Das.
The Evolutionary Design of Collective Computation in Cellular Automata. (Really cool and use of CAs to generate "emergent" behaviors!) Excerpts from Wolfram's book, A New Kind of Science:
intro: 1-16 51-60
randomness: 223-231 299-305 315-326 (interesting issues raised there)
univ computation: 642-643 674-678 690-696 (needed for the next bit)
compuational equivalence: 715-753 (this is one of his key claims)
Melanie Mitchell: Doing Science: Is the Universe a Universal Computer. Science 298 (5591): 65-68 (2002 Oct 4).
Weinberg: Is the Universe a Computer? NYRevBooks 49(16) (2002 Oct 24).
Optional: P. Bhattacharyya. Cellular Automata: Wolfram's Metaphors for Complex Systems.
arXiv:nlin/0404003v2
CAS and the origin and evolution of living systems; A tiny intro to Fractals Kelly's view: chapters 14,15,17-20 --
Do web or wiki searches to read more about topics he covers.
Bedau: Artificial Life: organization, adaptation and complexity from the bottom up.
Trends in Cognitive Science: 7(11): 505-512 (2003).
Alon: Simplicity in Biology. Nature 446: p497 (20
H.Morowitz and E.Smith: Energy flow and the organization of life.
Optional -- but do at least scan. (Some may want to read the details.) Flake Chapters 5,6,9 (Fractals, L-Systems)
You might look at this article, too:
Fractalmania: How Jackson Pollock and the Bakuba discovered complexity
John Casti.
Optional
Emergent dynamics -- "Sync" Stephen Strogatz. Sync: The Emerging Science of Spontaneous Order
Chapters 1 (Fireflies), 2 (Brain Waves), 3 (Sleep), 7 (Chaos), and 10 (Humans-Fads,Traffic,etc). Epilogue.
(Chapters 9 on networks will be useful later in the term.)
Optional, but very interesting: John Vandermeer: Oscillating Populations and Biodiversity Maintenance.
Bioscience 56(12): 967-975 (2006).
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