12.007 | Spring 2013 | Undergraduate




[Stanley] = Stanley, Steven M. Earth System History. W. H. Freeman, 2008. ISBN: 9781429233491.

[Kump] = Kump, Lee R., James F. Kasting, and Robert G. Crane. The Earth System. Prentice Hall, 2003. ISBN: 9780131420595.

Madigan, Martinko, and F. Parker. Brock Biology of Microorganisms. Benjamin Cummings, 2008. ISBN: 9780132324601.

[Hering and Morel] = Morel, M. M., and J. Hering. Principles and Applications of Aquatic Chemistry. Wiley-Interscience, 1993. ISBN: 9780471548966.

Wills, Christopher, and Jeffrey Bada. The Spark of Life: Darwin And The Primeval Soup. Basic Books, 2000. ISBN: 9780738201962. [Preview with Google Books]

Cesare, Emiliani. Planet Earth: Cosmology, Geology and the Evolution of Life and Environment. Cambridge University Press, 1992. ISBN: 9780521409490. [Preview with Google Books]

[Brock] = Broecker, Wallace S. How to Build a Habitable Planet. Columbia Univ Trustees, 1998. ISBN: 9780961751111.

Additional readings provided for some lectures.

Weekly Reading Assignments

1 Overview of course; What is life? Can it be defined? Brief history of paleontology and geobiology; Life as a geological agent. Sedimentary environments and processes; Stratigraphy (John Smith??); Isostasy; Plate tectonics; Water and life; Habitable zone; Radiative balance; Greenhouse gases. Faint Young Sun.

[Stanley] Chapters 1 and 2.

[Kump] pp. 187–95.

2 Time scales of major events in formation of Universe and Solar System; Abundance of elements. Geochronology; Introduction to geological processes, rocks and minerals. Planetary accretion and differentiation. Introduction to the geological timescale and major transitions in Earth history. [Stanley] pp. 129–51 and 177–97.
3 Evolution of other terrestrial planets (Mars)

Valley, John W. “Early Earth.” Elements 2, no. 4 (2006): 201–4.

Woese, Carl R., and George E. Fox. “Phylogenetic structure of the prokaryotic domain: The primary kingdoms.” Proceedings of the National Academy of Sciences of the United States of America 74, no. 11 (1977): 5088–90.

4 Prebiotic chemistry, Nucleic acids, Amino Acids and Chirality, Origins of life, Panspermia; Luca and the three domains; Universal tree of life.

[Kump] pp. 195–204 and 383–90.

[Stanley] pp. 103–27.

Hayes, John M. “Practice and Principles of Isotopic Measurements in Organic Geochemistry.” (PDF) (2002).


Isotopes; isotopic nomenclature; definition of atm%, ratio, α, δ, ε; how to do simple isotopic calculations including mass balance; CHNOS standards, what they are and the forms that are prepared for analysis; what processes cause isotopic fractionation including C, H and N in OM and C and O in limestones; S in pyrite and sulfate; ballpark δ values of C, O, S in main reservoirs and biomass.

Isotope paper: Des Marais C-cycle

[Stanley] pp. 221–44.

Hayes, John M. “Fractionation of the Isotopes of Carbon and Hydrogen in Biosynthetic Processes.” (PDF)

6 More about fractionated isotopes; S in pyrite and sulfate; How H&O are fractionated in the hydrological cycle; How (roughly) C&H fractionation occurs in lipids. Biogeochemical carbon cycle.

[Kump] pp. 147–72.

[Stanley] pp. 273–88.

Marais, David J. Des. “Isotopic evolution of the biogeochemical carbon cycle during the Proterozoic Eon.” Organic Geochemistry 27, no. 5–6 (1997): 185–93.

7 Discussion of isotope papers. Fike seminar in EAPS.

Edmonda, John M., and Youngsook Huh. “Non-steady state carbonate recycling and implications for the evolution of atmospheric PCO2.” Earth and Planetary Science Letters 216, no. 1–2 (2003): 125–39.

Ridgwell, Andy, and Richard E. Zeebe. “The role of the global carbonate cycle in the regulation and evolution of the Earth system.” Earth and Planetary Science Letters 234, no. 3–4 (2005): 299–315.

8 Redox processes [Hering and Morel] pp. 421–77.
9 Redox processes II, examples from various environments. Anaerobic metabolisms. [Hering and Morel] pp. 421–77.
10 Anoxygenic and oxygenic photosynthesis; BIF; Evidence for early life on Earth; Stromatolites; Microfossils. Microbial sediments. [Stanley] pp. 245–70.
11 Geological evidence of photosynthesis and oxygenation. Early atmosphere. Oxygenation of the ocean/atmosphere system. Anbar and Knoll. Redox transitions.

[Kump] pp. 207–20 and 230–44.

[Stanley] pp. 273–88.

Anbar, Ariel D., and A. H. Knoll. “Proterozoic Ocean Chemistry and Evolution: A Bioinorganic Bridge?Science 297, no. 5584 (2002): 1137–42.

 Anbar, Ariel D., Yun Duan, et al. “A Whiff of Oxygen Before the Great Oxidation Event?Science 317, no. 5846 (2007): 1903–6.

12 Geological evidence of photosynthesis and oxygenation, Part II. Early atmosphere. Oxygenation of the ocean/atmosphere system. Anbar and Knoll. Redox transitions.

[Kump] pp. 207–20 and 230–44.

[Stanley] pp. 273–88.

Hoffman, Paul F., and Daniel P. Schrag. “The snowball Earth hypothesis: testing the limits of global change.” Terra Nova 14, no. 3 (2002): 129–55.

———. “Snowball Earth.” Scientific American 282 (2000): 68–75.

  Midterm exam Schink, Bernhard, and Michael Friedrich. “Bacterial metabolism: Phosphite oxidation by sulphate reduction.” Nature 406, no. 37 (2000).
13 Neoproterozoic carbon cycle and environmental oscillations. Snowball Earth.

Keeling, Patrick J., Gertraud Burger, et al. “The tree of eukaryotes.” Trends in Ecology & Evolution 20, no. 12 (2005): 670–6.

Delwiche, Charles F. “Tracing the Thread of Plastid Diversity through the Tapestry of Life.” The American Naturalist 154 (1999): 164–77.

Janouškoveca, Jan, Aleš Horák, et al. “A common red algal origin of the apicomplexan, dinoflagellate, and heterokont plastids.” Proceedings of the National Academy of Sciences of the United States of America 107, no. 24 (2010): 10949–54.

14 Evolution and Radiation of Photosynthetic Organisms; Successions of plankton in the ocean. Radiation of vascular plants.

Keeling, Patrick J., Gertraud Burger, et al. “The tree of eukaryotes.” Trends in Ecology & Evolution 20, no. 12 (2005): 670–6.

Heckman, Daniel S., David M. Geiser, et al. “Molecular Evidence for the Early Colonization of Land by Fungi and Plants.” Science 293, no. 5532 (2001): 1129–33.

Narbonne, Guy M. “The Ediacara Biota: Neoproterozoic Origin of Animals and Their Ecosystems.” Annual Review of Earth and Planetary Sciences 33 (2005): 421–42.

Marshall, Charles R. “Explaining The Cambrian “Explosion” Of Animals.” Annual Review of Earth and Planetary Sciences 34 (2006): 355–84.

15 Ediacaran fauna. Evolution and radiation of animals. Evidence for early animals. Animal body plans. Sponges. Deadline to decide on the problem to write about for the final blog piece. Chirata, Régis, Derek E. Moultonb, et al. “Mechanical basis of morphogenesis and convergent evolution of spiny seashells.” Proceedings of the National Academy of Sciences of the United States of America 110, no. 15 (2013): 6015–20.
16 Reefs and carbonate precipitation through time: evidence for changes in ocean chemistry and biology. Impact of biomineralization on carbon cycle.

Bambach, Richard K. “Phanerozoic Biodiversity Mass Extinctions.” Annual Review of Earth and Planetary Sciences 34 (2006): 127–155.

Payne, Jonathan L., and Matthew E. Clapham. “End-Permian Mass Extinction in the Oceans: An Ancient Analog for the Twenty-First Century?Annual Review of Earth and Planetary Sciences 40 (2012): 89–111.

17 Biomineralization and biominerals. Ray Pierrehumbert seminar in EAPS.

Schulte, Peter, Laia Alegret, et al. “The Chicxulub Asteroid Impact and Mass Extinction at the Cretaceous-Paleogene Boundary.” Science 327, no. 5970 (2010): 1214–8.

D’Hondt, Steven. “Consequences Of The Cretaceous/Paleogene Mass Extinction For Marine Ecosystema.” Annual Review of Ecology, Evolution, and Systematics 36 (2005): 295–317.

McInerney, Francesca A., and Scott L. Wing. “The Paleocene-Eocene Thermal Maximum: A Perturbation of Carbon Cycle, Climate, and Biosphere with Implications for the Future.” Annual Review of Earth and Planetary Sciences 39 (2011): 489–516.

18 Mass Extinctions including Permian-Triassic event  Rothschild, Lynn J., and Rocco L. Mancinelli. “Life in extreme environments.” Nature 409 (2001): 1092–101.
19 Mesozoic time. Geology and biology. K-T boundary, LPTM. Volcanism, carbon cycle perturbation or impact?

DeLong, Edward F. “The microbial ocean from genomes to biomes”. Nature 459 (2009): 200–6.

Zehr, Jonathan P., John B. Waterbury, et al. “Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean.” Nature 412 (2001): 635–8.

20 Life in extreme environments  
21 Molecular microbiology and paleontology. PCR, genomics, trees. Modern microbially-dominated ecosystems.  
22 Class discussion of a paper related to environmental microbiology

Milucka, Jana, and Timothy G. Ferdelman, et al. “Zero-valent sulphur is a key intermediate in marine methane oxidation.” Nature 491 (2012): 541–6.

Valentine, David L. “Adaptations to energy stress dictate the ecology and evolution of the Archaea.” Nature Reviews Microbiology 5 (2007): 316–23.

23 Student presentations of blog pieces (extended to recitation time)  
  Oral exam  
  Exam week (no written final, blog pieces due)  

Course Info

Learning Resource Types
assignment_turned_in Problem Sets with Solutions
notes Lecture Notes