everything.study
12.517

Geobiology: History of Life on Earth

3-0-9 units · Graduate

Introduces the processes by which biological and geological systems interact across Earth history, and the interpretation of the geochemical and paleontological record of these interactions. Surveys Earth history from the perspective of biological evolution, including major transitions in microbial and complex life, and corresponding ecological, environmental, and planetary changes. Topics include the early history of Earth and its ocean and atmosphere; biogeochemical cycles and microbial metabolisms; organismal evolutionary processes and the fossil record; the organic and inorganic biogeochemical record; snowball Earths and glacial periods; the history of climate changes, major mass extinctions and biodiversity. Students taking graduate version complete additional assignments.

Spring 2005 · Dynamics of Complex Systems: Biological and Environmental Coevolution Preceding the Cambrian Explosion

Topics

  • Geochemical Signals of the Proterozoic-Phanerozoic Transition
  • The Molecular Fossil Record
  • Early Animal Evolution
  • Molecular Clocks and the Divergence of Metazoans
  • Oxygenation
  • Glaciations
  • Chronology
  • Student Presentations

Readings

  • Logan, G. A., J. M. Hayes, G. B. Hieshima, and R. E. Summons. “Terminal Proterozoic Reorganization of Biogeochemical Cycles.” Nature 376 (1995): 53-56.
    Listed reading
  • Hayes, J. M., H. Strauss, and A. J. Kaufman. “The Abundance of C13 in Marine Organic Matter and Isotopic Fractionation in the Global Biogeochemical Cycle of Carbon during the Past 800 Ma.” Chemical Geology 161 (1999): 103-125.
    Listed reading
  • Rothman, D. H., J. M. Hayes, and R. E. Summons. “Dynamics of the Neoproterozoic Carbon Cycle.” Proceedings of the National Academy of Sciences USA 100 (2003): 8124-8129.
    Listed reading
  • Fenchel, T. “Marine Plankton Food Chains.” Annual Review of Ecology and Systematics 19 (1988): 19-38.
    Listed reading
  • Summons, R. E., and M. R. Walter. “Molecular Fossils and Microfossils of Prokaryotes and Protists from Proterozoic Sediments.” American Journal of Science 290A (1990): 212-244.
    Listed reading
  • Summons, R. E., and J. J. Brocks. “Sedimentary Hydrocarbons, Biomarkers for Early Life.” In Treatise on Geochemistry. Vol. 8. Edited by H. D. Holland and K. Turekian. Elsevier, 2005, pp. 63-115. ISBN: 9780080446424.
    Listed reading
  • Volkman, J. K. “Sterols and other Triterpenoids: Source Specificity and Evolution of Biosynthetic Pathways.” Organic Geochemistry 36 (2005): 139-159.
    Listed reading
  • Porter, S. H. “The Fossil Record of Early Eukaryotic Diversification.” Paleontological Society Papers 10 (2004): 35-50.
    Listed reading
  • Knoll, A. H. “Proterozoic and Early Cambrian Protists: Evidence for Accelerating Evolutionary Tempo.” Proc Natl Acad USA 91 (1994): 6743-6750.
    Listed reading
  • Peterson, K., et al. “Estimating Metazoan Divergence Times with a Molecular Clock.” Proc Natl Acad USA 101 (2004): 6536-6541.
    Listed reading
  • Runnegar, B. “Precambrian Oxygen Levels Estimated from the Biochemistry and Physiology of Early Eukaryotes.” Paleogeography, Palaeoclimatology, Palaeoecology 97 (1991): 97-111. (Global and Planetary Change Section.)
    Listed reading
  • Betts, J. N., and H. D. Holland. “The Oxygen Content of Ocean Bottom Waters, the Burial Efficiency of Organic Carbon, and the Regulation of Atmospheric Oxygen.” Paleogeography, Palaeoclimatology, Palaeoecology 97 (1991): 5-18. (Global and Planetary Change Section.)
    Listed reading
  • Colman, A. S., and H. D. Holland. “The Global Diagenetic Flux of Phosphorus from Marine Sediments to the Oceans: Redox Sensitivity and the Control of Atmospheric Oxygen Levels.” In Marine Authigenesis: From Global to Microbial . Edited by C. R. Glenn, L. Prevot-Lucas, and J. Lucas. Tulsa, OK: SEPM (Society for Sedimentary Geology), 2000, pp. 53-75. SEPM Special Publication No. 66.
    Listed reading
  • Hoffman, P. F., and D. P. Schrag. “The Snowball Earth Hypothesis: Testing the Limits of Global Change.” Terra Nova 14 (2002): 129-155.
    Listed reading
  • Bowring, S. A., and M. D. Schmitz. “High-precision U-Pb Zircon Geochronology and the Stratigraphic Record.” Reviews in Mineralogy & Geochemistry 53 (2003): 305-326.
    Listed reading
  • Condon, D., et al. “U-Pb Ages from the Neoproterozoic Doushantuo Formation, China.” Science 308 (2005): 95-98.
    Listed reading
Spring 2001 · Dynamics of Complex Systems: Ecological Theory

Topics

  • Predator-prey Models
  • Supplemental Information Ecological Experiments
  • Supplemental Information Niche Theory
  • Stability of Complex Systems
  • Supplemental Information Competitive Exclusion
  • Chaotic Dynamics
  • Network Theory
  • Population Dispersal
  • Patchiness
  • Pattern and Scale
  • Spatial Models and Interacting Particle Systems
  • Lattice-gas Models
  • Plankton Patchiness
  • Supplemental Information Scaling from Trees to Forests
  • Evolution of Biodiversity
  • Supplemental Information Adaptation and Diversification
  • Artificial Life and Biological Complexity
  • Cycles
  • Reactivity, Stability, and Plankton (2 Presentations)
  • Theory of Productivity-Diversity Relationships
  • Evolution of Virulence in Host-Pathogen Systems
  • Renormalization Approach to Biological Systems
  • Directed Motion in Lotka-Volterra Models
  • Supplemental Information “Highly Optimized Tolerance” and Ecology
  • Theory of Vegetation Patterns

Readings

  • Lotka, A. Elements of Mathematical Biology . New York, NY: Dover Publications, Inc. 1925, Reprinted 1957. ISBN: 9780486603469.
    Listed reading
  • Volterra, V. “Fluctuations in the Abundance of a Species Considered Mathematically.” Nature 118 (1926): 558-560.
    Listed reading
  • ———. “Experimental Analysis of Vito Volterra’s Mathematical Theory of the Struggle for Existence.” Science 79 (1934b): 16-17.
    Listed reading
  • Hutchinson, G. E. Concluding Remarks. Cold Spring Harbor Symp. Quan Biol 22 (1957): 415-427.
    Listed reading
  • ———. “Homage to Santa Rosalia, Or Why Are There So Many Kinds of Animals?” American Naturalist 93 (1959): 254-259.
    Listed reading
  • May, R. M. Stability and Complexity in Model Ecosystems . Princeton, NJ: Princeton University Press, 2001. ISBN: 9780691088617.
    Listed reading
  • Kerner, E. H. “Why Are There So Many Species?” Bull Math Biol 36 (1974): 477-488.
    Listed reading
  • Armstrong, R. A., and R. McGehee. “Competitive Exclusion.” American Naturalist 115 (1980): 151-170.
    Listed reading
  • Cushing, J. M., et al. “A Chaotic Attractor in Ecology: Theory and Experimental Data.” Chaos Solitons and Fractals 12 (2001): 219-234.
    Listed reading
  • Krapivsky, P. L., and S. Redner. “Organization of Growing Random Networks.” Cond-mat/0011094, 2000.
    Listed reading
  • Strogatz, S. H. “Exploring Complex Networks.” Nature 410 (2001): 268-276.
    Listed reading
  • Skellam, J. G. “Random Dispersal in Theoretical Populations.” Biometrika 38 (1951): 196-216.
    Listed reading
  • MacArthur, R. H., and E. R. Pianka. “On Optimal Use of a Patchy Environment.” American Naturalist 100 (1966): 603-609.
    Listed reading
  • Levin, S. A. “The Problem of Pattern and Scale in Ecology.” Ecology 73 (1992): 1943-1967.
    Listed reading
  • Durrett, R. “Stochastic Spatial Models.” SIAM Review 41 (1994): 677-718.
    Listed reading
  • Satulovsky, J. E., and T. Tome. “Stochastic Lattice Gas Model for a Predator-prey System.” Phys Rev E 49 (1994): 5073-5079.
    Listed reading
  • Flierl, G., D. Grunbaum, S. Levin, and D. Olson. “From Individuals to Aggregations: The Interplay Between Behavior and Physics.” Journal of Theoretical Biology 196 (1999): 397-454.
    Listed reading
  • Plotkin, J. B., et al. “Predicting Species Diversity in Tropical Forests.” Proc Natl Acad Sci 97 (2000): 10850-10854.
    Listed reading
  • Signor, P. W., III. “Real and Apparent Trends in Species Richness Through Time.” In Phanerozoic Diversity Patterns . Edited by J. W. Valentine. Princeton, NJ: Princeton University Press, 1986, pp. 129-150. ISBN: 9780691083742.
    Listed reading
  • ———. “The Geologic History of Diversity.” Annu Rev Ecol Syst 21 (1990): 509-539.
    Listed reading
  • Lenski, R. E., and M. Travisano. “Dynamics of Adapatation and Diversification: A 10,000-generation Experiment with Bacterial Populations.” Proc Natl Acad Sci 91 (1994): 6808-6814.
    Listed reading
  • Adami, C., C. Ofria, and T. C. Collier. “Evolution of Biological Complexity.” Proc Natl Acad Sci 97 (2000): 4463-4468.
    Listed reading
  • Kauffman, S. “Metabolic Stability and Epigenesis in Randomly Constructed Genetic Nets.” Journal of Theoretical Biology 22 (1969): 437-467.
    Listed reading
Spring 2000 · Dynamics of Complex Systems: Complexity in Ecology

Topics

  • How many Species are there on Earth?
  • Introduction to Food Webs and Trophic Interactions
  • Empirical Examples and Critiques of the Cascade Model
  • Dynamical Models of Food Webs
  • What is the Relationship Between Complexity and Stability?
  • Evidence from Experiments
  • Diversity Stability Relationships: Statistical Inevitability or Ecological Consequence?
  • Diversity in Terrestrial Ecosystems
  • Perspectives on Biodiversity and Ecosystem Function
  • Island Biogeography
  • Theoretical Foundation: Log-normal Distributions of Species Abundance Power-law Species-area Curves
  • Spatial Models
  • What is the Role of Resource Availability in Species-area Relationships?
  • Empirical Tests of Species-energy Theory
  • Issues of Scale
  • Extinction Rates and Range Contraction of Endangered Species
  • Introduction to Body Size in the Context of Evolution and Ecology
  • Allometric Constraints, Resource Equipartitioning and Body Size
  • Cope’s Rule
  • Home Range Scaling and Statistical Artifacts in Abundance Sampling
  • Evolutionary Entropy and Body Size
  • Student Presentations

Readings

  • May, R. M. “How many Species are there on Earth?” Science 241 (1988): 1441-9.
    Listed reading
  • Cohen, J. E., and C. M. Newman. “A Stochastic Theory of Community Food Webs I. Models and Aggregated Data.” Proc R Soc Lond B 224 (1985): 421-48.
    Listed reading
  • Pimm, S. L., J. H. Lawton, and J. E. Cohen. “Food Web Patterns and their Consequences.” Nature 350 (1991): 669-74.
    Listed reading
  • Goldwasser, L., and J. Roughgarden. “Construction and Analysis of a Large Caribbean Food Web.” Ecology 74 (1993): 1216-33.
    Listed reading
  • Havens, K. “Scale and Structure in Natural Food Webs.” Science 257 (1992): 1107-9.
    Listed reading
  • Pimm, S. L., and J. H. Lawton. “Number of Trophic Levels in Ecological Communities.” Nature 268 (1977): 329-331.
    Listed reading
  • Post, W. M., and S. L. Pimm. “Community Assembly and Food Web Stability.” Mathematical Biosciences 64 (1983): 169-192.
    Listed reading
  • May, R. M. “Will a Large Complex System be Stable?” Nature 238 (1972): 413-414.
    Listed reading
  • Cohen, J. E., and C. M. Newman. “When will a Large Complex System be Stable?” J Theor Biol 113 (1985): 153-6.
    Listed reading
  • Solow, A. R., C. Costello, and A. Beet. “On an Early Result on Stability and Complexity.” American Naturalist 154 (1999): 587-588.
    Listed reading
  • Tilman, D. “Biodiversity: Population versus Ecosystem Stability.” Ecology 77 (1996): 350-363.
    Listed reading
  • Doak, D. F., et al. “The Statistical Inevitability of Stability Diversity Relationships in Community Ecology.” American Naturalist 151 (1998): 264-76.
    Listed reading
  • Tilman, D., C. L. Lehman, and C. E. Bristow. “Diversity Stability Relationships: Statistical Inevitability or Ecological Consequence?” American Naturalist 151 (1998): 277-82.
    Listed reading
  • Naeem, S., L. J. Thompson, S. P. Lawler, J. H. Lawton, and R. M. Woodfin. “Empirical Evidence that Declining Species Diversity may Alter the Performance of Terrestrial Ecosystems.” Phil Trans R Soc Lond B 347 (1995): 249-62.
    Listed reading
  • Grime, J. P. “Biodiversity and Ecosystem Function: The Debate Deepens.” Science 277 (1997): 1260-1.
    Listed reading
  • Wardle, D. A., O. Zackrisson, G. Hornberg, and C. Gallet. “The Influence of Island Area on Ecosystem Properties.” Science 277 (1997): 1296-1300.
    Listed reading
  • Tilman, D., J. Knops, D. Wedin, P. Reich, M. Ritchie, and M. Siemann. “The Influence of Functional Diversity and Composition on Ecosystem Processes.” Science 277 (1997): 1300-2.
    Listed reading
  • Hooper, D. U., and P. M. Vitousek. “The Effects of Plant Composition and Diversity on Ecosystem Processes.” Science 277 (1997): 1302-5.
    Listed reading
  • MacArthur, R. H., and E. O. Wilson. “An Equilibrium Theory of Insular Zoogeography.” Evolution 17 (1963): 373-387.
    Listed reading
  • May, R. M. “Patterns of Species Abundance and Diversity.” In Ecology and Evolution of Communities. Edited by M. L. Cody and J. M. Diamond. Cambridge, MA: Belknap Press, 1975, pp. 81-120. ISBN: 9780674224445.
    Listed reading
  • Durrett, R., and S. Levin. “Spatial Models for Species-area Curves.” Journal of Theoretical Biology 179 (1996): 119-127.
    Listed reading
  • Wright, D. H. “Species-energy Theory: An Extension of Species-area Theory.” Oikos 41 (1983): 4896-506.
    Listed reading
  • Currie. “Energy and Large-scale Patterns of Animal- and Plant-species Richness.” The American Naturalist 137 (1991): 27-49.
    Listed reading
  • Rosenzweig, M. L., and Z. Abramsky. “How are Diversity and Productivity Related?” In Diversity in Ecological Communities . Edited by R. E. Ricklefs and D. Schluter. Chicago, IL: University of Chicago Press, 1994, pp. 52-65. ISBN: 9780226718224.
    Listed reading
  • Wright, D. H., D. J. Currie, and B. A. Maurer. “Energy Supply and Patterns of Species Richness on Local and Regional Scales.” In Diversity in Ecological Communities . Edited by R. E. Ricklefs and D. Schluter. Chicago, IL: University of Chicago Press, 1994, pp. 66-74. ISBN: 9780226718224.
    Listed reading
  • Lawton, J. H. “Population Dynamics Principles.” In Extinction Rates . Edited by R. H. Lawton and R. M. May. New York, NY: Oxford University Press, 1995, pp. 147-63. ISBN: 9780198548294.
    Listed reading
  • Channel, R., and M. V. Lomolino. “Dynamic Biogeography and Conservation of Endangered Species.” Nature 403 (2000): 84-6.
    Listed reading
  • LaBarbera, M. “Analyzing Body Size as a Factor in Ecology and Evolution.” Annu Rev Ecol Sys 20 (1989): 97-117.
    Listed reading
  • Damuth, J. “Population Density and Body Size in Mammals.” Nature 290 (1981): 699-700.
    Listed reading
  • Enquist, B. J., J. H. Brown, and G. B. West. “Allometric Scaling of Plant Energetics and Population Density.” Nature 395 (1998): 163-5.
    Listed reading
  • Alroy, J. “Cope’s Rule and the Dynamics of Body Mass Evolution in North American Fossil Mammals.” Science 280 (1998): 731-4.
    Listed reading
  • Lindstedt, S. L., B. J. Miller, and S. W. Buskirk. “Home Range, Time and Body Size in Mammals.” Ecology 67 (1986): 413-8.
    Listed reading
  • Blackburn, T. M., and K. J. Gaston. “Abundance-body Size Relationships: the Area you Census tells you More.” Oikos 75 (1996): 303-9.
    Listed reading
  • Demetrius, L. “Directionality Principles in Thermodynamics and Evolution.” Proc Natl Acad Sci 94 (1997): 3491-8.
    Listed reading
  • ———. “Directionality Theory and the Evolution of Body Size.” (Unpublished, 2000).
    Listed reading

Prerequisites & course information

Subject meets with 12.107 Prereq: None G (Spring) 3-0-9 units

Sources