Schedule and Resources

WEEK 1 (1/22/13): Introduction to course, complex adaptive systems, and Gaia theory.
Lecture, discussion, and demonstration

Optional reading:

  • Levin, S. A. 1998. Ecosystems and the biosphere as complex adaptive systems. Ecosystems 1:431-436. Link
  • Dise, N. B. 2009. Peatland response to global change. Science 326:810-811. Link
  • Lenton, T. M. and M. van Oijen. 2002. Gaia as a complex adaptive system. Phil. Trans. R. Soc. Lond. B. 357:683-395. Link


  • NSF web page on Complex Environmental Systems: Synthesis for Earth, Life, and Society in the 21st Century: Link
  • StarLogo simulation software: Link
  • Interview with James Lovelock about Gaia theory: Link

WEEK 2 (1/29/13): Nonlinear dynamics, chaos, and the language of complexity.
Lecture and discussion

Required reading:

  • Sole and Bascompte, pp. 1-64: Link

WEEK 3 (2/5/13): Turing instabilities and pattern formation.
Lecture and discussion

Required reading:

  • Sole and Bascompte, pp. 65-84: Link
  • Rietkerk, M. and J. van de Koppel. 2008. Regular pattern formation in real ecosystems. Trends in Ecology & Evolution 23:169-175. Link


  • Bascompte, J. and R. V. Sole. 1998. Spatiotemporal patterns in nature. Trends in Ecology and Evolution 13:173-174. Link

WEEK 4 (2/11/13): Alternative stable states.

Required reading:

  • Suding, K. N., K. L. Gross, and G. R. Houseman. 2004. Alternative states and positive feedbacks in restoration ecology. Trends in Ecology & Evolution 19:46-53. Link
  • Didham, R. K. and C. H. Watts. 2005. Are systems with strong underlying abiotic regimes more likely to exhibit alternative stable states? Oikos 110:409-416. Link

Plus, one of the following (to be divided up and assigned in class):

  • Didham, R. K. and D. A. Norton. 2007. Alternative logical states. A reply to N. W. H. Mason, J. B. Wilson and J. B. Steel. Oikos 116:358-360. Link
  • Mason, N. W. H., J. B. Wilson, and J. B. Steel. 2007. Are alternative stable states more likely in high stress environments? Logic and available evidence do not support Didham et al. 2005. Oikos 116:353-357. Link
  • Fukami, T., and W. G. Lee (2006), Alternative stable states, trait dispersion and ecological restoration, Oikos, 113(2), 353-356. Link
  • Didham, R. K., and D. A. Norton (2006), When are alternative stable states more likely to occur?, Oikos, 113(2), 357-362. Link


  • Heffernan, J. B. 2008. Wetlands as an Alternative Stable State in Desert Streams. Ecology 89:1261-1271. Link
  • Lansing, J. S. 2012. Alternate stable states in a social-ecological system. Working Papers of the Santa Fe Institute. Link

WEEK 5 (2/18/13): Self-organized criticality, highly optimized tolerance, and power laws
Lecture and discussion.

Required reading (read the Bak and Chen first):

  • Bak, P., and K. Chen (1991), Self-organized criticality, Scientific American, 264(1), 46-53. Link
  • Brown, J. H., V. K. Gupta, B.-L. Li, B. T. Milne, C. Restrepo, and G. B. West. 2002. The fractal nature of nature: power laws, ecological complexity and biodiversity. Phil. Trans. R. Soc. Lond. B. 357:619-626. Link
  • Carlson, J. M. and Doyle, J (2000), Highly optimized tolerance: robustness and design in complex systems, Phys Rev Lett, 84(11), 2529-2532. Link
  • Frigg, R. (2003), Self-organised criticality: what it is and what it isn’t, Studies in History and Philosophy of Science Part A, 34(3), 613-632. Link

Optional (in particular, the section at the end on “Highly optimized tolerance features of ecological systems):

  • Carlson, J. M. and J. Doyle. 1999. Highly optimized tolerance: A mechanism for power laws in designed systems. Physical Review E 60:1412-1427. Link


  • Zinck, R. D. and V. Grimm. 2009. Unifying wildfire models from ecology and statistical physics. The American Naturalist 174:E170-E185. Link
  • Jameson, A. R. and A. B. Kotinski. 2002. Spurious power-law relations among rainfall and radar parameters. Q. J. R. Meteorol. Soc. 128:2045-2058. Link
  • Touboul, J., and A. Destexhe (2010), Can Power-Law Scaling and Neuronal Avalanches Arise from Stochastic Dynamics?, PLoS ONE, 5(2), e8982. Link
  • Farber, D. A. (2003), Probabilities behaving badly: Complexity theory and environmental uncertainty, Environs: Environmental Law and Policy Journal, 37, 145-174. Link

WEEK 6 (2/26/13): Predicting catastrophic shifts.

Required reading:

  • Sornette, D. (2002), Predictability of catastrophic events: Material rupture, earthquakes, turbulence, financial crashes, and human birth, Proceedings of the National Academy of Sciences of the United States of America, 99(Suppl 1), 2522-2529. Link
  • Scheffer, M., J. Bascompte, W. A. Brock, V. Brovkin, S. R. Carpenter, V. Dakos, H. Held, E. H. van Nes, M. Rietkerk, and G. Sugihara. 2009. Early-warning signals for critical transitions. Nature 461:53-59. Link
  • Peters, D. P. C., R. A. Pielke, B. T. Bestelmeyer, C. D. Allen, S. Munson-McGee, and K. M. Havstad (2004), Cross-scale interactions, nonlinearities, and forecasting catastrophic events, Proceedings of the National Academy of Sciences of the United States of America, 101(42), 15130-15135. Link

Optional reading:

  • Scheffer, M., et al. (2012), Anticipating Critical Transitions, Science, 338(6105), 344-348. Link
  • Rietkerk, M., S. C. Dekker, P. C. de Ruiter, and J. van de Koppel. 2004. Self-organized patchiness and catastrophic shifts in ecosystems. Science 305:1926-1929. Link


  • Kefi, S., M. Rietkerk, C. L. Alados, Y. Pueyo, V. P. Papanastasis, A. ElAich, and P. C. de Ruiter. 2007. Spatial vegetation patterns and imminent desertification in Meditteranean arid ecosystems. Nature 449:213-218. Link

WEEK 7 (3/5/13): Resilience.

Required reading:

  • Allen, C., L. Gunderson, and A. R. Johnson (2005), The Use of Discontinuities and Functional Groups to Assess Relative Resilience in Complex Systems, Ecosystems, 8(8), 958-966. Link
  • Hirota, M., M. Holmgren, E. H. Van Nes, and M. Scheffer (2011), Global Resilience of Tropical Forest and Savanna to Critical Transitions, Science, 334(6053), 232-235. Link
  • Holling, C. S. (2001), Understanding the Complexity of Economic, Ecological, and Social Systems, Ecosystems, 4(5), 390-405. Link

Optional reading:

  • Folke, C. (2006), Resilience: The emergence of a perspective for social‚Äìecological systems analyses, Global Environmental Change, 16(3), 253-267. Link

WEEK 8 (3/12/13): Hierarchy theory.
Lecture and discussion

Required reading:

  • Lane, D. (2006), Hierarchy, Complexity, Society, in Hierarchy in Natural and Social Sciences, edited by D. Pumain, pp. 81-119, Springer, Netherlands. Link
  • Wu, J. and J. L. David. 2002. A spatially explicit hierarchical approach to modeling complex ecological systems: theory and applications. Ecological Modelling 153:7-26. Link

WEEK 9 (3/19/13): Signals and noise.
Lecture and discussion

Required reading:

  • Freitas, U. S., and C. Letellier (2009), Using a nonlinearity detection as a prior step for global modeling, paper presented at ICCSA 2009. Link
  • Jerolmack, D. J. and C. Paola. 2010. Shredding of environmental signals by sediment transport. Geophysical Research Letters 37:L19401, doi:19410.11029/12010GL044638. Link
  • Glass, L. (2009), Introduction to Controversial Topics in Nonlinear Science: Is the Normal Heart Rate Chaotic?, Chaos: An Interdisciplinary Journal of Nonlinear Science, 19(2), 028501-028504. Link (skim)


  • Wondzell, S. M., M. N. Gooseff, and B. L. McGlynn (2007), Flow velocity and the hydrologic behavior of streams during baseflow, Geophysical Research Letters, 34(24). Link

WEEK 10: Spring break!

WEEK 11 (4/2/13): Visualizing and resolving process networks.
Lecture and discussion

Required reading:

  • Ruddell, B. L. and P. Kumar. 2009. Ecohydrologic process networks: 1. Identification. Water Resources Research 45:W03419, doi:03410.01029/02008WR007279. Link
  • Zanin, M., and S. Boccaletti (2011), Complex networks analysis of obstructive nephropathy data, Chaos: An Interdisciplinary Journal of Nonlinear Science, 21(3), 033103-033105. Link
  • Also read popular summary of Zanin and Boccaletti here: Link

Optional reading:

  • Larsen, L. G. and J. W. Harvey. 2010. How vegetation and sediment transport feedbacks drive landscape change in the Everglades and wetlands worldwide. The American Naturalist 176:E66-E79. Link
  • Moffatt, A. M., C. Beckstein, G. Churkina, M. Mund, and M. Heimann. 2010. Characterization of ecosystem responses to climatic controls using artificial neural networks. Global Change Biology 16:2737-2749. Link


  • Smirnov, D. A., and I. I. Mokhov (2009), From Granger causality to long-term causality: Application to climatic data, Phys Rev E, 80(016208), doi: 10.1103/PhysRevE.1180.016208. Link

WEEK 12 (4/9/13): Modeling and uncertainty.
Lecture and discussion

Required reading;

  • Grimm, V., E. Revilla, U. Berger, F. Jeltsch, W. F. Mooij, S. F. Railsback, H.-H. Thulke, J. Weiner, T. Wiegand, and D. L. DeAngelis. 2005. Pattern-oriented modeling of agent-based complex systems: Lessons from ecology. Science 310:987-991. Link
  • Hornberger, G. M. and R. C. Spear. 1981. Approach to the preliminary analysis of environmental systems. Journal of Environmental Management 12:7-18. Download from course website.
  • Beven, K. (1996), Equifinality and uncertainty in geomorphological modelling, in The Scientific Nature of Geomorphology: Proceedings of the 27th Binghampton Symposium in Geormophology held 27-29 September 1996, edited by B. L. Rhoads and C. E. Thorn, pp. 289-313, John Wiley & Sons. Link

Case study:

  • Eppinga, M. B., P. C. de_Ruiter, M. J. Wassen, and M. Rietkerk (2009), Nutrients and Hydrology Indicate the Driving Mechanisms of Peatland Surface Patterning, The American Naturalist, 173(6), 803-818. Link

WEEK 13 (4/16/13): Game theory.
Games and discussion

Required reading:

  • Santos, F. C., M. D. Santos, and J. M. Pacheco (2008), Social diversity promotes the emergence of cooperation in public goods games, Nature, 454(7201), 213-216. Link
  • Allesina, S., and J. M. Levine (2011), A competitive network theory of species diversity, Proceedings of the National Academy of Sciences, 108(14), 5638-5642. Link
  • Hasson, R., A. Lofgren, and M. Visser (2010), Climate change in a public goods game: Investment decision in mitigation versus adaptation, Ecological Economics, 70(2), 331-338. Link


  • Kerr, B., M. A. Riley, M. W. Feldman, and B. J. M. Bohannan (2002), Local dispersal promotes biodiversity in a real-life game of rock-paper-scissors, Nature, 418(6894), 171-174. Link
  • Hauert, C., S. De Monte, J. Hofbauer, and K. Sigmund (2002), Volunteering as Red Queen Mechanism for Cooperation in Public Goods Games, Science, 296(5570), 1129-1132. Link

WEEK 14 (4/23/13): Agents in complex environmental systems.
Lecture and discussion

Required reading:

  • Rounsevell, M. D. A., D. T. Robinson, and D. Murray-Rust. 2012. From actors to agents in socio-ecological systems models. Phil. Trans. R. Soc. Lond. B. 367:259-269. Link
  • Axtell, R. L., J. M. Epstein, J. S. Dean, G. J. Gumerman, A. C. Swedlund, J. Harburger, S. Chakravarty, R. Hammond, J. Parker, and M. Parker (2002), Population growth and collapse in a multiagent model of the Kayenta Anasazi in Long House Valley, Proceedings of the National Academy of Sciences of the United States of America, 99(Suppl 3), 7275-7279. Link
  • Manson, S. M., and T. Evans (2007), Agent-based modeling of deforestation in southern Yucatan, Mexico, and reforestation in the Midwest United States, Proceedings of the National Academy of Sciences, 104(52), 20678-20683. Link

Optional reading:

  • Bonabeau, E. (2002), Agent-based modeling: Methods and techniques for simulating human systems, Proceedings of the National Academy of Sciences of the United States of America, 99(Suppl 3), 7280-7287. Link

WEEK 15 (4/30/13): Complex systems and climate science.
Guest lecture (Norman Miller) and discussion

Required reading:

  • Randall, D.A., R.A. Wood, S. Bony, R. Colman, T. Fichefet, J. Fyfe, V. Kattsov, A. Pitman, J. Shukla, J. Srinivasan, R.J. Stouffer, A. Sumi and K.E. Taylor, 2007: Climate Models and Their Evaluation. In: Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Solomon, S., D. Qin, M. Manning, Z. Chen, M. Marquis, K.B. Averyt, M.Tignor and H.L. Miller (eds.)]. Cambridge University Press, Cambridge, United Kingdom and New York, NY, USA. Download from course website.

READING AND RECITATION WEEK (5/7/13): Synthesis and wrap-up.
Synthesis discussion
Pop-up presentations


  • NSF Advisory Committee for Environmental Research and Education (2009), Transitions and Tipping Points in Complex Environmental Systems. Link