12.007 Geobiology

Spring 2003

Biogeochemical Carbon Cycle. (Courtesy of Prof. Julian Sachs.)

Course Highlights

This course includes detailed lecture notes and reading lists, as well as sample exams.

Course Description

The interactive Earth system: biology in geologic, environmental and climate change throughout Earth history. Since life began it has continually shaped and re-shaped the atmosphere, hydrosphere, cryosphere and the solid earth. This course introduces the concept of 'life as a geological agent' and examines the interaction between biology and the earth system during the roughly 4 billion years since life first appeared.

Syllabus

Course Description

Overview of Course; Time Scales; The Big Bang; Origin and Compositions of the Solar System, Earth and Moon; Creation and Distribution of the Chemical Elements
Earth Segregation; Formation and Composition of Early Atmosphere; Characteristics of the 'Habitable Zone'
Geologic Evidence for Antiquity of Life
Theories about the Origin of Life
Anaerobic Metabolism, Energy Yields, Deep Biosphere
Oxygenic Photosynthesis; The Rise of Atmospheric O₂
Life's Three Domains; Evolution of Algae; Fossil and Biogeochemical Evidence for their Presence and Evolution through Geological Time
Biogeochemical Carbon Cycle
Proterozoic Ocean Chemistry
The Cambrian Explosion and the Evolution and Radiation of Metazoans
Long-Term Climate Cycles #1
Long-Term Climate Cycles #2
Mass Extinctions #1
Mass Extinctions and Re-radiation #2
Biogeochemical Tracers #1
Biogeochemical Tracers #2
Biogeochemical Tracers #3
The Fate of Buried Organic Carbon; Petroleum and Natural Gas Occurrence and Distribution
Biogeomorphology: Plants and the Landscape
Long-term Climate Cycles
Methane Hydrates; Formation, Distribution, Potential Role in C-cylce and Subsurface Ecosystems Dependent upon Them
Pleistocene Glaciations, Holocene Climate; Abrupt Climate Change; Anthropogenic Forcing of Climate

Grading

ACTIVITY	PERCENTAGE
Problem Sets	15%
Final Paper and Oral Presentation	20%
Midterm Exam	25%
Final Exam	40%

Textbook

Stanley, Steven M. Earth System History. New York: W. H. Freeman & Co., 1999. (On reserve in Lindgren Library.)

Recommended Texts

Wills, Christopher, and Jeffrey Bada. The Spark of Life. Cambridge, MA: Perseus, 2000.

Kump, Lee R., James F. Kasting, and Robert G. Crane. The Earth System. Upper Saddle River, N. J.: Prentice Hall, 1999.

Calendar

LEC #	TOPICS
1	Overview of Course; Time Scales; The Big Bang; Origin and Compositions of the Solar System, Earth and Moon; Creation and Distribution of the Chemical Elements
2	Earth Segregation; Formation and Composition of Early Atmosphere; Characteristics of the 'Habitable Zone'
3	Geologic Evidence for Antiquity of Life
4	Theories about the Origin of Life
5	Anaerobic Metabolism, Energy Yields, Deep Biosphere
6	Oxygenic Photosynthesis; The Rise of Atmospheric O₂
7	Life's Three Domains; Evolution of Algae; Fossil and Biogeochemical Evidence for Their Presence and Evolution through Geological Time
8	Biogeochemical Carbon Cycle
9	Proterozoic Ocean Chemistry (Guest Lecturer: Dr. Yanan Shen, Harvard University)
10	The Cambrian Explosion and the Evolution and Radiation of Metazoans (Guest Lecturer: Professor Andrew Knoll, Harvard University)
11	Long-Term Climate Cycles #1: Faint Young Sun Paradox; CO₂-Climate Connection; Proterozoic Glaciations
12	Long-Term Climate Cycles #2: Permian Glaciations, The Rise of Vascular Plants; Mesozoic Warmth, Cenozoic Cooling; Evolution of Vascular Plants and Ruminants
	Mid-term Exam
13	Mass Extinctions #1 PC-C Boundary, P-T Boundary
14	Mass Extinctions and Re-radiation #2; K-T Boundary, LPTM. Volcanism, Carbon Cycle Perturbation or Impact?
15	Biogeochemical Tracers #1: Fractionated Isotopes
16	Biogeochemical Tracers #2: Lipid Biomarkers
17	Biogeochemical Tracers #3: Sedimentary Records of Life and Environment
18	The Fate of Buried Organic Carbon; Petroleum and Natural Gas Occurrence and Distribution
19	Biogeomorphology: Plants and The Landscape (Guest Lecturer: David Mohrig)
20	Long-term Climate Cycles
21	Methane Hydrates; Formation, Distribution, Potential Role in C-Cylce and Subsurface Ecosystems Dependent upon Them
	Student Presentations
	Student Presentations
22	Pleistocene Glaciations, Holocene Climate; Abrupt Climate Change; Anthropogenic Forcing of Climate
	Exam Review

Readings

References

Topics for each class session are listed below. The readings listed in the table refer to the following:

Stanley, Steven M. Earth System History. New York: W. H. Freeman & Co., 1999. (On reserve in Lindgren Library.)

Kump, Lee R., James F. Kasting, and Robert G. Crane. The Earth System. Upper Saddle River, N. J.: Prentice Hall, 1999.

LEC #	TOPIC	READINGS
1	Overview of Course; Time Scales; The Big Bang; Origin and Compositions of the Solar System, Earth and Moon; Creation and Distribution of the Chemical Elements
2	Earth Segregation; Formation and Composition of Early Atmosphere; Characteristics of the 'Habitable Zone'
3	Geologic Evidence for Antiquity of Life	Stanley, pp. 320-323
4	Theories about the Origin of Life	Stanley, pp. 306-311
5	Anaerobic Metabolism, Energy Yields, Deep Biosphere
6	Oxygenic Photosynthesis; The Rise of Atmospheric O₂	Stanley, pp. 257-269 and 323-325
7	Life's Three Domains; Evolution of Algae; Fossil and Biogeochemical Evidence for Their Presence and Evolution through Geological Time	Stanley, Chap. 3
8	Biogeochemical Carbon Cycle	Kump et. al., Chap. 7
9	Proterozoic Ocean Chemistry (Guest Lecturer: Dr. Yanan Shen, Harvard University)
10	The Cambrian Explosion and the Evolution and Radiation of Metazoans (Guest Lecturer: Professor Andrew Knoll, Harvard University)
11	Long-Term Climate Cycles #1: Faint Young Sun Paradox; CO₂-Climate Connection; Proterozoic Glaciations	Stanley, pp. 269-282 and 325-329
12	Long-Term Climate Cycles #2: Permian Glaciations, The rise of Vascular Plants; Mesozoic Warmth, Cenozoic Cooling; Evolution of Vascular Plants and Ruminants
13	Mass Extinctions #1; PC-C Boundary, P-T Boundary	Stanley, Chap. 7 and pp. 341-360, 369-386
14	Mass Extinctions and Re-radiation #2; K-T Boundary, LPTM. Volcanism, Carbon Cycle Perturbation or Impact?	Stanley, Chap. 7 and pp. 341-360, 369-386
15	Biogeochemical Tracers #1: Fractionated Isotopes
16	Biogeochemical Tracers #2: Lipid Biomarkers
17	Biogeochemical Tracers #3: Sedimentary Records of Life and Environment
18	The Fate of Buried Organic Carbon; Petroleum and Natural Gas Occurrence and Distribution
19	Biogeomorphology: Plants and The Landscape (Guest Lecturer: David Mohrig)
20	Long-term Climate Cycles
21	Methane Hydrates; Formation, Distribution, Potential Role in C-Cylce and Subsurface Ecosystems Dependent upon Them
22	Pleistocene Glaciations, Holocene Climate; Abrupt Climate Change; Anthropogenic Forcing of Climate	Kump et al., Chap. 11 Stanley, pp. 526-536 Stanley, Chap. 20

Assigned Readings

Catling D. C., K. J. Zahnle, and C. P. McKay. "Biogenic Methane, Hydrogen Escape, and the Irreversible Oxidation of Early Earth." Science 293 (2001): 839-843.

Kasting, J. F. "Earth's Early Atmosphere." Science 259 (1993): 920-926.

Holland, H. D. "Evidence for Life on Earth More than 3850 Million Years ago." Science 275 (1997): 38-39.

Owen, T., R. D. Cess, and V. Ramanathan. "Enhanced CO₂ Greenhouse to Compensate for Reduced Solar Luminosity on Early Earth." Nature 277 (1979): 640-642.

Walker, J. C. G., P. B. Hays, and J. F. Kasting. "A Negative Feedback Mechanism for the Long-term Stabilization of Earth's Surface Temperature." J. Geophys. Res. 86 (C10) (1981): 9776-9782.

Recommended Readings

Ahrens, T. J. "The Origin of the Earth." Phys. Today (August, 1994): 38-45.

Holland, H. D. "When did the Earth's Atmosphere become Oxic? A Reply." Geochem. News 100 (July, 1999): 20-22.

Holland, H. D., B. Lazar, and M. McCaffrey. "Evolution of the Atmosphere and Oceans." Nature 320 (1986): 27-33.

Jenkins, G. S., H. G. Marshall, and W. R. Kuhn. "Precambrian Climate: The Effects of Land Area and Earth's Rotation Rate." J. Geophys. Res. 98(D5) (1993): 8785-8791.

Karhu, J., and S. Epstein. "The Implication of the Oxygen Isotope Records in Coexisting Cherts and Phosphates." Geochim. Cosmochim. Acta 50 (1986): 1745-1756.

Kasting, J. F., D. H. Eggler, and S. P. Raeburn. "Mantle Redox Evolution and the Oxidation State of the Archean Atmosphere." J. Geol. 101 (1993): 245-257.

Kump, L. R., and H. D. Holland. "Iron in Precambrian Rocks: Implications for the Global Oxygen Budget of the Ancient Earth." Geochim. Cosmochim. Acta 56 (1992): 3217-3223.

Origin of Life

Schopf, J. W., A. B. Kudryavtsev, D. G. Agresti, T. J. Widowiak, and A. D. Czaja. "Laser-Raman Imagery of Earth's Earliest Fossils." Nature 416 (2002): 73-76.
(Defends biogenicity of 3.5 Ga fossils from Apex chert, W. Australia.)

Brasier, M. D., O. R. Green, A. P. Jephcoat, A. K. Kleppe, M. J. Van Kranendonk, J. F. Lindsay, A. Steele, and N. V. Grassineau, "Questioning the Evidence for Earth's Oldest Fossils." Nature 416 (2002): 76-81.
(Geochemical and morphologic evidence against biogenicity of Apex microfossils.)

Dalton, R. "Squaring up over Ancient Life." Nature 417 (2002): 782-784.
(Dramatized (tabloid!) report of Brasier-Schopf battle over biogenicity of Apex "fossils".)

Gee, H. "That's Life?" Nature 416 (2002): 28.
(Further commentary on debate over Apex fossils.)

van Zuilen, M. A., A. Lepland, and G. Arrhenius. "Reassessing the Evidence for the Earliest Traces of Life." Nature 418 (2002): 627-630.
(Molecular and isotopic evidence for cyanobacteria and oxygenic photosynthesis 2.7 Ga)

Cody, G. D., N. Z. Boctor, T. R. Filley, R. M. Hazen, J. H. Scott, A. Sharma, H. S. Yoder Jr. "Primordial Carbonylated Iron-sulfur Compounds and the Synthesis of Pyruvate." Science 289 (2000): 1337-1340.

Shen, Y., and D. E. Canfield. Isotopic Evidence for Microbial Sulphate Reduction in the Early Archaean Era." Nature 410 (2001): 77-81.

Wächtershäuser, G. "Life as We Don't Know It." Science 289 (2000): 1307-1308. (van Zuilen, Lepland et al. 2002)

Webliography:

Projects

Some Ideas for Paper Topics

Here is a list of some broad themes that you might consider writing a paper on. Of course you will need to narrow the focus quite a bit for your paper and presentation. We present this list to you merely as a place to start when trying to choose a topic. You are also welcome to choose a topic of your own as long as it falls under the very broad envelope of Geobiology!

Geologic Evidence for the Origin of Life
Theories for the Origin of Life
Evidence for Panspermia
Probability of Life Existing Elsewhere in the Universe
Is a Rocky Planet Essential for Habitation?
Cosmic Influences on Planetary Habitability
Recent Challenges to the 'Snowball Earth Hypothesis'
The History of Atmospheric Oxygen
The Redox History of the Ocean
Stromatolites: Ancient and Contemporary
Defining the 'Habitable Zone'
Vascular Plant Influence on Geology, Carbon Cycle and Climate
Geological Evidence for the Radiation of Algae
Water on Mars
The Importance of Oxygenic Photosynthesis as a Biogeochemical Process
The Importance of Methanogenesis as a Biogeochemical Process
The Importance of Sulfate Reduction as a Biogeochemical Process
Isotopic Biosignatures
Molecular Biosignatures
Cambrian Radiation of Animals