Ecology

"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.]

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.]
Baltimore Ecosystem Study [Large-scale, long-term, rigorous study of a whole urban ecosystem, including economic and sociological effects]
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]
Carole Crumley (ed.), Historical Ecology: Cultural Knowledge and Changing Landscapes
John A. Endler, Natural Selection in the Wild
John Harte
- Consider a Spherical Cow
- The Green Fuse
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]
Robert 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.]
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
Karl Sigmund, Games of Life: Explorations in Ecology, Evolution and Behavior [A very well-written popular book on mathematical biology]

Edward R. Abraham, "Sea urchin feeding fronts", q-bio.PE/0610004
James Brown [the other 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
Dennis Chitty, Do Lemmings Commit Suicide?
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
W. H. Drury, Chance and Change: Ecology for Conservationists
Christian W. Eurich, Andreas Thiel and Lorenz Fahse, "Distributed Delays Stabilize Ecological Feedback Systems", Physical Review Letters 94 (2005): 158104
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 [Blurb, chapter 1.]
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
Frances Hammerston, My Double Life: Memoirs of a Naturalist
Alan Hastings, "Transients: the key to long-term ecological understanding?", Trends in Ecology and Evolution 19 (2004): 39--45
C. S. Hollings, "Resilience and Stability of Ecological Systems", Annual Review of Ecology and Systematics 4 (1973): 1--23
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 [" We describe examples where combining statistical mechanics and ecology has led to improved ecological modelling and, at the same time, broadened the scope of statistical mechanics."]
Jerald B. Johnson and Kristian S. Omland, "Model selection in ecology and evolution", Trends in Ecology and Evolution 19 (2004): 101--108
James Justus, "Ecological and Lyapunov Stability", phil-sci/2987 ["Although Lyapunov stability adequately characterizes perturbation responses of systems typically studied in physics, it does not for ecological systems"]
Richard Kingsford (ed.), Ecology of Desert Rivers [Blurb]
Mark Kot, Elements of Mathematical Ecology [blurb]
John Kricher, The Balance of Nature: Ecology's Enduring Myth [Blurb, ch. 1]
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 Levin, Fragile Dominion: Complexity and the Commons
Robert H. MacArthur and Edward O. Wilson, The Theory of Island Biogeography
Marc Mangel, The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology [blurb]
Brian A. Maurer, "Statistical mechanics of complex ecological aggregates", Ecological Complexity 2 (2005): 71--85
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
George Oster and Edward O. Wilson, Caste and Ecology in the Social Insects
Mercedes Pascual and Jennifer A. Dunne (eds.), Ecological Networks: Linking Structure to Dynamics in Food Webs
Peter Price, Evolutionary Biology of Parasites
Christopher Quince, Paul Higgs and Alan McKane, "Deleting species from model food webs", q-bio.PE/0401037
Esa Ranta, Per Lundberg and Veijo Kaitala, Ecology of Populations ["how local births and deaths are tied to emigration and immigration processes, and how environmental variability at different scales affects population dynamics with stochastic processes and spatial structure. ... elementary analytical tools can be used to understand population fluctuations, synchrony, processes underlying range distributions and community structure and species coexistence ... spatial population dynamics models can be used to understand life history evolution and aspects of evolutionary game theory."]
Resilience Alliance
A. G. Rossberg, H. Matsuda, T. Amemiya and K. Itoh, "Food Webs: Experts Consuming Families of Experts", q-bio.PE/0508002 ["Here we show that observed topological features of predatory food webs can be reproduced to unprecedented accuracy by a mechanism taking into account only phylogeny, size constraints, and the heredity of the trophically relevant traits of prey and predators."]
Paul Sherman, Jennifer Jarvis and Richard Alexander, The Biology of the Naked Mole-Rat
Sitabhra Sinha and Sudeshna Sinha, "Evidence of universality for the May-Wigner stability theorem for random networks with local dynamics", nlin.AO/0402002
Ricard V. Solé and Jordi Bascompte, Self-Organization in Complex Ecosystems [Blurb, ch. 1]
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."]
William L. Thomas, Jr., et al. (eds.), Man's Role in Changing the Face of the Earth
David Tilman, "Niche tradeoffs, neutrality, and community structure: A stochastic theory of resource competition, invasion, and community assembly", PNAS (2004) [Abstract: "Stochastic niche theory resolves many of the differences between neutral theory and classical tradeoff-based niche theories of resource competition and community structure. In stochastic niche theory, invading species become established only if propagules can survive stochastic mortality while growing to maturity on the resources left unconsumed by established species. The theory makes three predictions about community structure. First, stochastic niche assembly creates communities in which species dominate approximately equally wide 'slices' of the habitat's spatial heterogeneity. These niche widths generate realistic distributions of species relative abundances for which, contrary to neutral theory but consistent with numerous observations, there are strong correlations among species traits, species abundances, and environmental conditions. Second, slight decreases in resource levels are predicted to cause large decreases in the probability that a propagule would survive to be an adult. These decreases cause local diversity to be limited by the inhibitory effects of resource use by established species on the establishment (recruitment) of potential invaders. If resource pulses or disturbance allowed invaders to overcome this recruitment limitation, many more species could indefinitely coexist. Third, the low invasibility of high diversity communities is predicted to result not from diversity per se, but from the uniformly low levels of resources that occur in high-diversity communities created by stochastic competitive assembly. This prediction provides a potential solution to the invasion paradox, which is the tendency for highly diverse regions to be more heavily invaded."]
David Tilman, Peter B. Reich and Johannes M. H. Knops, "Biodiversity and ecosystem stability in a decade-long grassland experiment", Nature 441 (2006): 629--632
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

Notebooks

Ecology