Ecology

02 Oct 2024 11:03

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"Ecology" is not a religion or a political movement but merely a science, and an impeccably materialist and reductionist one at that. (Actually, "ecology" is a word of three syllables, and it's ecology which is the science, but let's not get into that.) Some ecologists are confused about this, but I suggest they read John Holland, or Dawkins, or Dennett. I happen to think (moderate) environmentalism is a good idea, but that's a separate issue.

"Ecosystems" are not very good "systems". They have no real boundaries, they don't have steady states, they have all the homeostasis of a Rube Goldberg tooth-brush (except that they don't grind to a halt when you shove something into the works, which real systems tend to do). In short they resemble waterfalls or storms more than they do thermostats, guided missiles or organisms; and it seems we learn more about them by tracing the flow of chlorine than by contemplating the whole.

It was observed that a certain species of fish was much more resistant to disease in its natural habitat than in captivity, regardless of the steps that were taken to simulate the habitat. Upon investigation it proved that the fishes were secreting a chemical into the water which, when absorbed by another of the same species, stimulated the immune system, and that the captive populations were simply too small to keep the concentration of the substance to the necessary level. [From Odum's book, via memory.]

See also:
• Agent-Based Modeling
• Evolution
• Stability and Complexity in Ecosystems

Recommended, big picture, less technical:
• Wallace Arthur, The Green Machine [Argues very nicely for reductionist science and Green politics. Makes an interesting case that a suburban development does more damage to the environment than your average oil-tanker spill, since the development will be around for centuries.]
• Daniel Botkin
  • Discordant Harmonies [Dividing through for a lot of spirit-of-the-times bosh about "the machine age"]
  • Our Natural History
• Stephen Budiansky, Nature's Keepers: The New Science of Nature Management [Emphasis on the science, i.e., modern ecology. Review: Heaven and Earth Are Not Benevolent]
• John Harte
  • Consider a Spherical Cow
  • The Green Fuse
• Karl Sigmund, Games of Life: Explorations in Ecology, Evolution and Behavior [A very well-written popular book on mathematical biology]

Recommended, big picture, more technical:
• Robert M. May, Stability and Complexity in Model Ecosystems [An effective demolition of the idea that, ceteris paribus, complicated systems are more stable. In fact the reverse is true --- in general more complicated systems are less stable. This is good: it allows us to discard hypotheses "in general" and focus on the much smaller set which allow for both complexity and stability. May is yet another heart-warming "theoretical physicist makes good in biology" story.]
• Eugene Odum, Ecology [Was deservedly the standard ecology text for many years.]

Recommended, close-ups, more technical:
• Baltimore Ecosystem Study [Large-scale, long-term, rigorous study of a whole urban ecosystem, including economic and sociological effects]
• Carole Crumley (ed.), Historical Ecology: Cultural Knowledge and Changing Landscapes
• John A. Endler, Natural Selection in the Wild
• Gary King, A Solution to the Ecological Inference Problem: Reconstructing Individual Behavior from Aggregate Data [King mostly has human data in mind, but mutatis mutandis... Review]
• Cavan Reilly and Angelique Zeringue, "Improved predictions of lynx trappings using a biological model", pp. 297--308 in Andrew Gelman and Xiao-Li Meng (eds.), Applied Bayesian Modeling and Causal Inference from Incomplete-Data Perspectives [PDF. "Improved" compared to using standard time-series models with no biological content.]
• Max Rietkerk, Stefan C. Dekker, Peter C. de Ruiter and Johan van de Koppel, "Self-Organized Patchiness and Catastrophic Shifts in Ecosystems", Science 305 (2004): 1926--1929

To read, historical interest:
• A. J. Lotka, Elements of Physical Biology
• Robert H. MacArthur and Edward O. Wilson, The Theory of Island Biogeography
• George Oster and Edward O. Wilson, Caste and Ecology in the Social Insects
• William L. Thomas, Jr., et al. (eds.), Man's Role in Changing the Face of the Earth

To read, history and philosophy:
• Frances Hammerston, My Double Life: Memoirs of a Naturalist
• Sharon E. Kingsland, Modeling Nature: Episodes in the History of Population Ecology
• John Kricher, The Balance of Nature: Ecology's Enduring Myth
• Nancy G. Slack, G. Evelyn Hutchinson and the Invention of Modern Ecology [Review in Science]
• Nathan G. Swenson, Phylogenetic Ecology: A History, Critique, and Remodeling
• Donald Worster, Nature's Economy: A History of Ecological Ideas

To read, big picture:
• Dennis Chitty, Do Lemmings Commit Suicide?
• W. H. Drury, Chance and Change: Ecology for Conservationists
• Timothy E. Essington, Introduction to Quantitative Ecology: Mathematical and Statistical Modelling for Beginners

To read, close ups:
• Edward R. Abraham, "Sea urchin feeding fronts", q-bio.PE/0610004
• James Brown [not that one], Macroecology
• J. Camacho, R. Guimera and L. A. N. Amaral, "Robust Patterns in Food Web Structure," cond-mat/0103114
• J. Camacho, R. Guimera, D. B. Stouffer and L. A. N. Amaral, "Quantitative patterns in the structure of model and empirical food webs", q-bio.PE/0401023
• Robert Stephen Cantrell and Chris Cosner, Spatial Ecology via Reaction-diffusion Equations
• Marie-France Cattin, Louis-Felix Bersier, Carolin Banasek-Richter, Richard Baltensperger and Jean-Pierre Gabriel, "Phylogenetic constraints and adaptation explain food-web structure", Nature 427 (2004): 835--839
• Eric L. Charnov, Life History Invariants: Some Explorations of Symmetry in Evolutionary Ecology
• Francois Coppex, Michel Droz and Adam Lipowski, "Extinction dynamics of Lotka-Volterra ecosystems on evolving networks", q-bio.PE/0312030
• Roderick C. Deewar and Annabel Porte, "Statistical mechanics explains macroecological patterns", q-bio.PE/0703061
• Judy Diamond and Alan B. Bond, Kea, Bird of Paradox [Review by Danny Yee]
• Barbara Drossel, Alan McKane and Christopher Quince, "The impact of non-linear functional responses on the long-term evolution of food web structure", q-bio.PE/0401025
• Barbara Drossel, Paul G. Higgs and Alan J. McKane, "The Influence of Predator-Prey Population Dynamics on the Long-term Evolution of Food Web Structure," nlin.AO/0002032
• Michael M. Fuller, Tamara N. Romanuk and Jurek Kolasa, "Community Structure and Metacommunity Dynamics of Aquatic Invertebrates: a Test of the Neutral Theory", q-bio.PE/0406023
• Amatzia Genin, Jules S. Jaffe, Ruth Reef, Claudio Richter, Peter J. S. Franks, "Swimming Against the Flow: A Mechanism of Zooplankton Aggregation", Science 308 (2005): 860--862
• Godfray, Parasitoids: Behavioral and Evolutionary Ecology
• Volker Grimm and Steven F. Railsback, Individual-based Modeling and Ecology
• Volker Grimm, Eloy Revilla, Uta Berger, Florian Jeltsch, Wolf M. Mooij, Steven F. Railsback, Hans-Hermann Thulke, Jacob Weiner, Thorsten Wiegand, and Donald L. DeAngelis, "Pattern-Oriented Modeling of Agent-Based Complex Systems: Lessons from Ecology", Science 310 (2005): 987--991
• Alan Hastings, "Transients: the key to long-term ecological understanding?", Trends in Ecology and Evolution 19 (2004): 39--45
• Stephen P. Hubbell, The Unified Neutral Theory of Biodiversity and Biogeography
• Gail Jarrow and Paul Sherman, The Naked Mole Rat Mystery
• Henrik Jeldtoft Jensen, Elsa Arcaute, "Complexity, Collective Effects and Modelling of Ecosystems: formation, function and stability", arxiv:0709.2015
• Jerald B. Johnson and Kristian S. Omland, "Model selection in ecology and evolution", Trends in Ecology and Evolution 19 (2004): 101--108
• Colleen K. Kellya, Stephen J. Blundell, Michael G. Bowler, Gordon A. Fox, Paul H. Harvey, Mark R. Lomas, F. Ian Woodward, "The statistical mechanics of community assembly and species distribution", arxiv:1004.2271
• Richard Kingsford (ed.), Ecology of Desert Rivers
• Mark Kot, Elements of Mathematical Ecology
• N. Lanchier and C. Neuhauser, "A spatially explicit model for competition among specialists and generalists in a heterogeneous environment", math.PR/0610227 = Annals of Applied Probability 16 (2006): 1385--1410
• Simon A. Levin
  • Fragile Dominion: Complexity and the Commons
  • "The Problem of Pattern and Scale in Ecology: The Robert H. MacArthur Award Lecture", Ecology 73 (1992): 1943--1967 [JSTOR]
  • (ed.), The Princeton Guide to Ecology
• Michel Loreau, From Populations to Ecosystems: Theoretical Foundations for a New Ecological Synthesis
• Marc Mangel, The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology
• Brian A. Maurer, "Statistical mechanics of complex ecological aggregates", Ecological Complexity 2 (2005): 71--85
• Kevin S. McCann, Food Webs
• A. J. McKane and T. J. Newman, "Predator-Prey Cycles from Resonant Amplification of Demographic Stochasticity", Physical Review Letters 94 (2005): 218102
• Lorus and Margery Milne, Patterns of Survival
• Janice Moore, Parasites and the Behavior of Animals
• James P. O'Dwyer and Jessica L. Green, "Field Theory for Biogeography: A Spatially Explicit Model for Predicting Patterns of Biodiversity", Ecology Letters 13 (2010): 87--95 [Open access; commentary by Aaron Clauset]
• Mercedes Pascual and Jennifer A. Dunne (eds.), Ecological Networks: Linking Structure to Dynamics in Food Webs
• Eric Post, Ecology of Climate Change: The Importance of Biotic Interactions
• Peter Price, Evolutionary Biology of Parasites
• Christopher Quince, Paul Higgs and Alan McKane, "Deleting species from model food webs", q-bio.PE/0401037
• Steven F. Railsback and Bret C. Harvey, Modeling Populations of Adaptive Individuals
• Esa Ranta, Per Lundberg and Veijo Kaitala, Ecology of Populations
• Klaus Rohde, Nonequilibrium Ecology
• A. G. Rossberg, H. Matsuda, T. Amemiya and K. Itoh, "Food Webs: Experts Consuming Families of Experts", q-bio.PE/0508002
• Samuel M. Scheiner and Michael R. Willig (eds.), The Theory of Ecology
• Oswald J. Schmitz, Resolving Ecosystem Complexity
• Paul Sherman, Jennifer Jarvis and Richard Alexander, The Biology of the Naked Mole-Rat
• Ricard V. Solé and Jordi Bascompte, Self-Organization in Complex Ecosystems
• David Stephens and John Krebs, Foraging Theory
• Can Ozan Tan, Uygar Ozesmi, Meryem Beklioglu, Esra Per, Bahtiyar Kurt, "Statistical Predictive Models in Ecology: Comparison of Performances and Assessment of Applicability", q-bio.QM/0510031 [Even without reading it, I can tell you that the last sentence of the abstract is definitely correct: "for predictive modeling purposes, first a suitable, computationally inexpensive method should be applied to the problem at hand a good predictive performance of which would render the computational cost and efforts associated with complex variants unnecessary."]
• Horst R. Thieme, Mathematics in Population Biology
• David Tilman, "Niche tradeoffs, neutrality, and community structure: A stochastic theory of resource competition, invasion, and community assembly", PNAS (2004)
• Peter Turchin, Complex Population Dynamics
• John Vandermeer and Ivette Perfecto, "A Keystone Mutualism Drives Pattern in a Power Function", Science 311 (2006): 1000--1002 [I don't think their title is grammatical!]
• Geerat J. Vermeij
  • Evolution and Escalation: An Ecological History of Life
  • A Natural History of Shells
  • Nature: An Economic History [Review in American Scientist]
• Igor Volkov, Jayanth R, Banavar, Stephen P. Hubbell and Amos Maritan, "Neutral Theory and Relative Species Abundance in Ecology", q-bio.PE/0504018 = Nature 424 (2003): 1035--1037
• J. Timothy Wootton, "Field parametrization and experimental test of the neutral theory of biodiversity", Nature 433 (2005): 309--312
• Nicolas L. Ziebarth, Karen C. Abbott and Anthony R. Ives, "Weak population regulation in ecological time series", Ecology Letters 13 (2010): 21--31