Geobiology Courses

Ge 11 b. Introduction to Earth and Planetary Sciences: Earth and the Biosphere. 9 units (3-3-3); second term. Prerequisites: Ch 1 a. Systematic introduction to the origin and evolution of life and its impact on the oceans, atmosphere, and climate of Earth. Topics covered include ancient Earth surface environments and the rise of atmospheric oxygen. Microbial and molecular evolution, photosynthesis, genes as fossils. Banded iron stones, microbial mats, stromatolites, and global glaciation. Biological fractionation of stable isotopes. Numerical calibration of the geological timescale, the Cambrian explosion, mass extinctions, and human evolution. The course usually includes one major field trip and laboratory studies of rocks, fossils, and geological processes. Although Ge 11 abcd is designed as a sequence, any one term may be taken as a standalone course. Biologists are particularly welcome.
Instructors: Fischer, Kirschvink

ESE 103. Earth's Biogeochemical Cycles. 9 units (3-0-6); second term. Global cycles of carbon, nitrogen and sulfur. Photosynthesis, respiration and net primary production. Soil formation, erosion, and carbon storage. Ecosystem processes, metrics, and function. Nutrient supply and limitation. Microbial processes underlying weathering, decomposition, and carbon remineralization. Stable isotope tracers in the carbon and hydrologic cycles. The human footprint on the Earth.
Instructor: Frankenberg

Ge 104. Introduction to Geobiology. 9 units (3-0-6); second term. Prerequisites: instructor's permission. Lectures about the interaction and coevolution of life and Earth surface environments. We will cover essential concepts and major outstanding questions in the field of geobiology, and introduce common approaches to solving these problems. Topics will include biological fractionation of stable isotopes; history and operation of the carbon and sulfur cycles; evolution of oxygenic photosynthesis; biomineralization; mass extinctions; analyzing biodiversity data; constructing simple mathematical models constrained by isotope mass balance; working with public databases of genetic information; phlyogenetic techniques; microbial and molecular evolution.
Instructors: Fischer, Kirschvink

Bi/Ge/ESE 105. Evolution. 12 units (3-4-5); second term. Prerequisites: Completion of Core Curriculum Courses. Maximum enrollment: 15, by application only. The theory of evolution is arguably biology's greatest idea and serves as the overarching framework for thinking about the diversity and relationships between organisms. This course will present a broad picture of evolution starting with discussions of the insights of the great naturalists, the study of the genetic basis of variation, and an introduction to the key driving forces of evolution. Following these foundations, we will then focus on a number of case studies including the following: evolution of oxygenic photosynthesis, origin of eukaryotes, multicellularity, influence of symbiosis, the emergence of life from the water (i.e. fins to limbs), the return of life to the water (i.e. limbs to fins), diversity following major extinction events, the discovery of Archaea, insights into evolution that have emerged from sequence analysis, and finally human evolution and the impact of humans on evolution (including examples such as antibiotic resistance). A specific focus for considering these issues will be the island biogeography of the Galapagos. Given in alternate years; not offered 2020-21.
Instructors: Phillips, Orphan

Ge 112. Sedimentology and Stratigraphy. 12 units (3-5-4); third term. Prerequisites: Ge 11 ab. Systematic analysis of transport and deposition in sedimentary environments and the resulting composition, texture, and structure of both clastic and chemical sedimentary rocks. The nature and genesis of sequence architecture of sedimentary basins and cyclic aspects of sedimentary accumulation will be introduced. Covers the formal and practical principles of definition of stratigraphic units, correlation, and the construction of a geologic timescale. Field trip and laboratory exercises. Given in alternate years; not offered 2020-21.
Instructor: Grotzinger

Ge 116. Analytical Techniques Laboratory. 9 units (1-4-4); second term. Prerequisites: Ge 114 a or instructor's permission. Methods of quantitative laboratory analysis of rocks, minerals, and fluids in geological and planetary sciences. Consists of five intensive two-week modules covering scanning electron microscopy (imaging, energy-dispersive X-ray spectroscopy, electron backscatter diffraction); the electron microprobe (wavelength-dispersive X-ray spectroscopy); X-ray powder diffraction; optical, infrared, and Raman spectroscopy; and plasma source mass spectrometry for elemental and radiogenic isotope analysis. Satisfies the Institute core requirement for an additional introductory laboratory course.
Instructors: Asimow, Jackson, Rossman

Ge 121 abc. Advanced Field Geology. 12 units (0-9-3); first, second, third terms. Prerequisites: Ge 120 or equivalent, or instructor's permission. Field mapping and supporting laboratory studies in topical problems related to the geology of the southwestern United States. Course provides a breadth of experience in igneous, metamorphic, or sedimentary rocks or geomorphology. Multiple terms of 121 may be taken more than once for credit if taught by different instructors.
Instructors: Avouac (a), Kirschvink (b), Stock (c)

Ge 124 a. Paleomagnetism and Magnetostratigraphy. 6 units (0-0-6); third term. Application of paleomagnetism to the solution of problems in stratigraphic correlation and to the construction of a high-precision geological timescale. A field trip to the southwest United States or Mexico to study the physical stratigraphy and magnetic zonation, followed by lab analysis. Given in alternate years; offered 2020-21.
Instructor: Kirschvink

Ge 124 b. Paleomagnetism and Magnetostratigraphy. 9 units (3-3-3); third term. Prerequisites: Ge 11 ab. The principles of rock magnetism and physical stratigraphy; emphasis on the detailed application of paleomagnetic techniques to the determination of the history of the geomagnetic field. Given in alternate years; offered 2020-21.
Instructor: Kirschvink

Ge/ESE 140 c. Stable Isotope Biogeochemistry. 9 units (3-0-6); third term. Prerequisites: Ge 140a or equivalent. An introduction to the use of stable isotopes in biogeochemistry, intended to give interested students the necessary background to understand applications in a variety of fields, from modern carbon cycling to microbial ecology to records of Ancient Earth. Topics include the principles of isotope distribution in reaction networks; isotope effects in enzyme-mediated reactions, and in metabolism and biosynthesis; characteristic fractionations accompanying carbon, nitrogen, and sulfur cycling; and applications of stable isotopes in the biogeosciences. Not offered 2020-21.
Instructor: Sessions

Ge/ESE 143. Organic Geochemistry. 9 units (3-2-4); third term. Prerequisites: Ch 41 a or equivalent. Main topics include the analysis, properties, sources, and cycling of natural organic materials in the environment, from their production in living organisms to burial and decomposition in sediments and preservation in the rock record. Specific topics include analytical methods for organic geochemistry, lipid structure and biochemistry, composition of organic matter, factors controlling organic preservation, organic climate and CO2 proxies, diagenesis and catagenesis, and biomarkers for ancient life. A laboratory component (three evening labs) teaches the extraction and analysis of modern and ancient organic biomarkers by GC/MS. Class includes a mandatory one-day (weekend) field trip to observe the Monterey Formation. Offered 2020-21.
Instructor: Sessions

Ge/ESE 149. Marine Geochemistry. 9 units (3-0-6); second term. Prerequisites: ESE 102. Introduction to chemical oceanography and sediment geochemistry. We will address the question "Why is the ocean salty?" by examining the processes that determine the major, minor, and trace element distributions of seawater and ocean sediments. Topics include river and estuarine chemistry, air/sea exchange, nutrient uptake by the biota, radioactive tracers, redox processes in the water column and sediments, carbonate chemistry, and ventilation. Given in alternate years; not offered 2020-21.
Instructor: Adkins

Ge/ESE 155. Paleoceanography. 9 units (3-0-6); second term. Prerequisites: ESE 102. Evaluation of the data and models that make up our current understanding of past climates. Emphasis will be placed on a historical introduction to the study of the past ten thousand to a few hundred thousand years, with some consideration of longer timescales. Evidence from marine and terrestrial sediments, ice cores, corals, and speleothems will be used to address the mechanisms behind natural climate variability. Models of this variability will be evaluated in light of the data. Topics will include sea level and ice volume, surface temperature evolution, atmospheric composition, deep ocean circulation, tropical climate, ENSO variability, and terrestrial/ocean linkages. Given in alternate years; offered 2020-21.
Instructor: Adkins

ESE/Bi 168. Microbial Metabolic Diversity. 9 units (3-0-6); second term. Prerequisites: ESE 142, ESE/Bi 166. A course on the metabolic diversity of microorganisms. Basic thermodynamic principles governing energy conservation will be discussed, with emphasis placed on photosynthesis and respiration. Students will be exposed to genetic, genomic, and biochemical techniques that can be used to elucidate the mechanisms of cellular electron transfer underlying these metabolisms. Given in alternate years; offered 2020-21.
Instructor: Newman

Ge/ESE/Bi 178. Microbial Ecology. 9 units (3-2-4); second term. Prerequisites: Either ESE/Bi 166 or ESE/Bi 168. Structural, phylogenetic, and metabolic diversity of microorganisms in nature. The course explores microbial interactions, relationships between diversity and physiology in modern and ancient environments, and influence of microbial community structure on biogeochemical cycles. Introduction to ecological principles and molecular approaches used in microbial ecology and geobiological investigations. Offered in alternate years; offered 2020-21.
Instructor: Orphan

Ge/Bi 244. Paleobiology Seminar. 6 units (3-0-3); third term. Critical reviews and discussion of classic investigations and current research in paleoecology, evolution, and biogeochemistry.
Instructor: Kirschvink

Ge/Bi/ESE 246. Molecular Geobiology Seminar. 6 units (2-0-4); first term. Critical reviews and discussion of classic papers and current research in microbiology and geomicrobiology. As the topics will vary from year to year, it may be taken multiple times.
Instructor: Orphan