Schedule and Resources

WEEK 1 (1/21/14): 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
  • Lenton, T. M. and M. van Oijen. 2002. Gaia as a complex adaptive system. Phil. Trans. R. Soc. Lond. B. 357:683-395. Link

Resources:

  • 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 (1/28/14): Nonlinear dynamics and chaos.
Lecture and discussion

Required reading:

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

Optional:

  • 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

WEEK 3 (2/4/14): Spatial complexity: role of dispersal and diffusion.
Lecture and discussion

Required reading:

  • Sole and Bascompte, pp. 65-84: 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
  • 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

WEEK 4 (2/10/14): Spatial pattern formation.
Lecture and discussion

Required reading:

  • Rietkerk, M. and J. van de Koppel. 2008. Regular pattern formation in real ecosystems. Trends in Ecology & Evolution 23:169-175. Link
  • DeAngelis, D. L. 2012. Self-organizing processes in landscape pattern and resilience: a review. ISRN Ecology, doi:10.5402/2012/274510. Link
  • Weerman, E. J., J. van de Koppel, M.B. Eppinga, F. Montserrat, Q. X. Liu, and P. M. J. Herman. 2010.  Spatial self-organization on intertidal mudflats through biophysical stress divergence. The American Naturalist 176:doi:10.1086/652991. Link

Optional:

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

WEEK 5 (2/17/14): Alternate stable states.
Lecture and discussion

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
  • 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

Case-studies:

  • 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 6 (2/25/14): Self-organized criticality and power laws.
Lecture and discussion

Required reading:

  • 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
  • Sapozhnikov, V.B. and Foufoula-Georgiou, E. 1996. Do the current landscape evolution models show self-organized criticality? Water Resources Research 32:1109-1112. Link
  • Sapozhnikov, V.B. and Foufoula-Georgiou, E. 1999. Horizontal and vertical self-organization of braided rivers toward a critical state. Link

Case-studies:

  • 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 7 (3/4/14): Predicting catastrophic shifts.
Lecture and discussion

Required reading:

  • Batt, R. D., S. R. Carpenter, J. J. Cole, M. L. Pace, and R. A. Johnson. 2013. Changes in ecosystem resilience detected in automated measures of ecosystem metabolism during a whole-lake manipulation. Proc. Nat. Acad. Sci. 110: 17398-17403. 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
  • Scheffer, M., et al. (2012), Anticipating Critical Transitions, Science, 338(6105), 344-348. Link

Optional reading:

  • 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
  • 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

Case-studies:

  • 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
  • Dai, L., D. Vorselen, K. S. Korolev, and J. Gore. 2012. Generic indicators for loss of resilience before a tipping point leading to population collapse. Link

WEEK 8 (3/11/14): Resilience.
Lecture and discussion

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-ecological systems analyses, Global Environmental Change, 16(3), 253-267. Link

WEEK 9 (3/18/14): 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
  • D’Odorico, P., F. Laio, and L. Ridolfi. 2005. Noise-induced stability in dryland plant ecosystems. Proc. Nat. Acad. Sci. 102: 10819-10822. Link

WEEK 10: Spring break!

WEEK 11 (4/1/14): Approaches to modeling complex systems. Lecture, discussion, and guest lecture

Required reading:

  • Rozier, O. and C. Narteau. 2014. A real-space cellular automaton laboratory. Earth Surf.Process. Landforms 39: 98-109. Link
  • Gross, T. and B. Blasius. 2008. Adaptive coevolutionary networks: a review. J. R. Soc. Interface 5: 259-271. Link
  • O’Sullivan. 2009. Changing neighborhoods – neighborhoods changing: A framework for spatially explicit agent-based models of social systems. Sociological Methods Research 37: 498-529. Link

Optional:

  • 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
  • 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

Case studies:

  • Epstein, J.M. 2002. Modeling civil violence: An agent-based computational approach. Proc. Nat. Acad. Sci. 99:7243-7250. 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
  • 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 12 (4/8/14): Hierarchies and hierarchical modeling. Lecture, discussion, and guest lecture

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

Guest lecture on hierarchical modeling in climate science. Associated reading TBD.

WEEK 13 (4/15/14): Big-data (top-down) approaches to understanding complex systems.
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
  • Kirchner, J. and C. Neal. 2014. Universal fractal scaling in stream chemistry and its implications for solute transport and water quality trend detection. Proc. Nat. Acad. Sci. doi:10.1073/pnas130428110. Link
  • Boers, N., B. Bookhagen, N. Marwan, J. Kurths, and J. Marengo. 2013. Complex networks identify spatial patterns of extreme rainfall events of the South American Monsoon System. Geophys. Res. Letters 40:4386-6392. Link

Case-study:

  • 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
  • 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
  • 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

WEEK 14 (4/22/14): Sensitivity and uncertainty analyses.
Lecture and discussion

Required 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
  • Spear, R. C. 1997. Large simulation models: calibration, uniqueness, and goodness-of-fit. Environmental Modelling & Software 12:219-229. Link
  • 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
  • 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

Optional:

  • 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.

Case studies:

  • Eppinga, M.B., M. Rietkerk, W. Borren, E. D. Lapshina, W. Bleuten, and M. J. Wassen. 2010. Regular surface patterning of peatlands: Confronting theory with field data. Ecosystems 11: 520-526. Link

WEEK 15 (4/29/14): Presentation of NSF proposals.

Proposals due for peer review

READING AND RECITATION WEEK (5/6/14): Mock NSF panel meeting, synthesis, and wrap-up