Scripps Institution of Oceanography

OFFICE: 22 Old Scripps Bldg., Scripps Institution of Oceanography
http://www-siograddept.ucsd.edu/

Professors

Courses

The graduate department of Scripps Institution of Oceanography offers instruction leading to Ph.D. degrees in oceanography, marine biology, and earth sciences. Although students are not admitted specifically for an M.S. degree, it is possible to obtain an M.S. on the way to completing the Ph.D. program. A graduate student’s work normally will be concentrated in one of the curricular programs within the department: applied ocean science, biological oceanography, climate sciences, geosciences, geophysics, marine biology, marine chemistry and geochemistry, and physical oceanography.

No undergraduate major is offered in the department though most courses in the department are open to enrollment for qualified undergraduate students with the consent of the instructor. The UCSD Earth Sciences Undergraduate Program offers an earth sciences major leading to a B.S. or a combined B.S./M.S. degree. The interdisciplinary nature of research in marine and earth sciences is emphasized; students are encouraged to take courses from various UCSD departments, and to consider interdisciplinary research projects.

The Curricular Programs

Applied Ocean Science is a multidisciplinary program focused on the application of advanced technology to ocean exploration and observation. AOS students perform research in marine acoustics, optics, electromagnetics, geophysics, ecology, sediment transport, coastal processes, physical oceanography, and air-sea interaction. The emphasis is on the resolution of key scientific issues through novel technological development. The science focus of the Scripps AOS program is complemented by parallel Applied Ocean Science programs in both the Mechanical and Aerospace Engineering (MAE) and Electrical and Computer Engineering (ECE) departments. Students have access to professors, courses, and research facilities across all three departments.

Biological Oceanography is concerned with the interactions of populations of marine organisms with one another and with their physical and chemical environment. Because these interactions are frequently complex, and because the concepts and techniques used are drawn from many fields, biological oceanography is, of necessity, interdisciplinary. Therefore, studies in physical oceanography, marine chemistry, marine geology, and several biological areas are pertinent.

Research is conducted on space/time scales ranging from short-term interactions between individual organisms (mm., sec.) to interdecadal variation in widely dispersed populations. The techniques used in these investigations are diverse, and can include field observation and manipulations, experimentation in the laboratory, and mathematical modeling.

Research topics include primary and secondary productivity and nutrient regeneration, fishery biology and management, community ecology of benthic and pelagic organisms, population dynamics, habitat changes and disruptions, systematics and biogeography, population genetics and evolution, and behavior as it affects distribution. Development and testing of new tools (molecular, optical, acoustic), design of sampling programs, and statistical/mathematical analyses of data also are significant activities.

Climate Sciences concerns the study of the climate system of the earth with emphasis on the physical, dynamical, and chemical interactions of the atmosphere, ocean, land, ice, and the terrestrial and marine biospheres. The program encompasses changes on seasonal to interannual time scales and those induced by human activities, as well as paleoclimatic changes on time scales from centuries to millions of years. Examples of current research activities include: interannual climate variability; physics and dynamics of El Niño; studies of present and future changes in the chemical composition of the atmosphere in relation to global warming and ozone depletion; effects of cloud and cloud feedbacks in the climate system; paleoclimate reconstructions from ice cores, banded corals, tree-rings, and deep-sea sediments; the origin of ice ages; air-sea interactions; climate theory; terrestrial and marine ecosystem response to global change.

Geosciences emphasizes the application of general principles of geology, geochemistry, and geophysics to problems in the marine and terrestrial environments of the Earth. Graduate students routinely participate in expeditions at sea and on land and many doctoral theses evolve from these experiences.

Research areas in the geological sciences include: the origin and evolution of the ocean-atmosphere system and global climate; geology, geochemistry, and geophysics of oceanic crustal rocks and near-shore environments; tectonic and structural evolution of the oceans, plate margins, and back-arc basins; the role of fluids in the crust; chemistry of rare gases in active volcanoes; the use of natural nuclear processes for understanding physical and chemical processes in the Earth; paleomagnetic applications in geology and geophysics.

Geophysics emphasizes the application of general principles of mathematics and experimental physics to fundamental problems of the oceans, oceanic and continental lithosphere, and crust and deep interior of the Earth. Research interests of the group include: observational and theoretical studies of electric and magnetic fields in the oceans and on the land; paleomagnetism; theoretical seismology with special emphasis on the structure of the Earth from free-oscillation and body wave studies; broadband observational seismology, including ocean bottom and multichannel seismology; earthquake source mechanisms; the measurements of slow crustal deformations using satellite and observatory methods on continents and in the oceans; marine geodynamics and tectonophysics; gravity measurements; geophysical inverse theory; magnetohydrodynamics of the core of the Earth; geophysical instrumentation for oceanic and continental geophysical measurements; acoustic propagation in the oceans.

Marine Biology is the study of marine organisms. It is concerned with evolutionary, organismic, genetic, physiological, and biochemical processes in these organisms, and the relationship between them and their biotic and physical environment. Marine biology encompasses several major areas of modern biology, and is interpreted by understanding the physical and chemical dynamics of the oceans. Faculty research focuses on microbiology, photobiology, high pressure biology, deep-sea biology, developmental biology, genetics, biomechanisms, comparative biochemistry and physiology, behavior, ecology, biogeography, and evolution of marine prokaryotes and eukaryotes. Processes ranging from the fertilization of sea urchin eggs to the role of bacteria in marine food web dynamics are under study in over twenty independent research laboratories.

Marine Chemistry and Geochemistry concerns chemical and geochemical processes operating in a broad range of study areas: the oceans, the solid earth, the atmosphere, marine organisms, polar ice sheets, lakes, meteorites, and the solar system.

Areas of advanced study and research include the physical and inorganic chemistry of seawater; ocean circulation and mixing based on chemical and isotopic tracers; marine organic and natural products chemistry; marine bioinorganic chemistry; geochemical interactions of sediments with seawater and interstitial waters; geochemistries of volcanic and geothermal phenomena; chemical exchanges between the ocean and the atmosphere; geochemical cycles of carbon, oxygen, sulfur, nitrogen, and other elements; isotopic geochemistry of the solid earth and meteorites; atmospheric trace gas chemistry; paleoatmospheric composition recorded in polar ice cores, corals and sediments; and chemistry of lakes and other freshwater systems.

Studies are typically interdisciplinary and involve integration of chemical concepts with information about the physical, biological, or geological processes that influence natural systems. Students in the marine chemistry and geochemistry curricular group are encouraged to explore these links.

Physical Oceanography is the field of study that deals with mechanisms of energy transfer through the sea and across its boundaries, and with the physical interactions of the sea with its surroundings, especially including the influence of the seas on the climate of the atmosphere. Research activities within this curricular group are both observational and theoretical and include: study of the general circulation of the oceans, including the relations of ocean currents to driving forces and constraints of the ocean basins; fluctuations of currents, and the transport of properties; the mechanisms of transport of energy, momentum, and physical substances within the sea and across its boundaries; properties of wind waves, internal waves, tsunami and planetary waves; the thermodynamic description of the sea as a system not in equilibrium; optical and acoustic properties of the sea; and the influence of surf on near-shore currents and the transport of sediments.

Requirements for Admission

Candidates for admission should have a bachelor’s or master’s degree in one of the physical, biological, or earth sciences; degrees in mathematics or engineering science are also accepted. A scholastic average of B or better in upper-division courses, or prior graduate study, is required. The student’s preparation should include:

1. mathematics through differential and integral calculus
2. physics, one year with laboratory (the course should stress the fundamentals of mechanics, electricity, magnetism, optics, and thermodynamics, and should use calculus in its exposition)
3. chemistry, one year with laboratory
4. an additional year of physics, chemistry, or mathematics
5. all applicants are required to submit scores from the general test of the Graduate Record Examinations (GRE) given by the Educational Testing Service of Princeton, New Jersey. Marine biology applicants must also submit scores of the GRE biology (or biochemistry, cell, and molecular biology) subject test.

All international applicants whose native language is not English and whose undergraduate education was conducted in a language other than English must take the TOEFL and submit their test scores to the UCSD Office of Graduate Admissions.

Specific additional requirements for admission to the various curricular programs are as follows:

Applied Ocean Science—Students are admissible with a strong background in physical science, engineering science, or mathematics. Three years of physics or applicable engineering and three years of mathematics at college level are expected.

Biological Oceanography—Two years of chemistry, including general and organic chemistry, and a year of general biology are required. Physical chemistry requiring calculus may be substituted for physics requiring calculus where a more elementary physics course was taken. Zoology or botany may be substituted for general biology. Preparation should also include a course in general geology and at least one course in each of the following categories: systematics (e.g., invertebrate zoology), population biology (e.g., ecology), functional biology (e.g., physiology). In special cases, other advanced courses in mathematics or natural sciences may be substituted. Biological oceanography applicants are encouraged, but not required, to submit scores of the biology subject test of the GRE.

Climate Sciences—Students are admissible if they satisfy the requirements of the physical oceanography, geophysics, or marine chemistry and geochemistry curricular programs. Biology and geology majors may also be admissible if the Scripps faculty feel that they have a sufficiently strong background in mathematics and physical science.

Geosciences—A major in one of the earth sciences and undergraduate physical chemistry and calculus are required. Preparation beyond the minimum requirements in mathematics, physics, and chemistry is strongly recommended.

Geophysics—A major in physics or mathematics, or equivalent training, is required.

Marine Biology—A major in one of the biological sciences (or equivalent), with basic course work in botany, microbiology, or zoology; two years of chemistry, including organic chemistry, is required. Training in one or more of the following areas is strongly recommended: cellular biology, molecular biology, comparative physiology, genetics, developmental biology, ecology, evolutionary biology, vertebrate and invertebrate zoology, microbiology, and/or botany. Biochemistry and physical chemistry will be expected of students in experimental biology, although the student may, if necessary, enroll in these courses at UCSD after admission.

Marine Chemistry and Geochemistry—A major in chemistry, geology, biochemistry, or related field, is required.

Physical Oceanography—A major in a physical science, including three years of physics and mathematics, is required.

Special consideration occasionally can be given to candidates with outstanding records who do not meet all required preadmission criteria.

Programs of Study

Programs of study vary widely among the curricular groups, but generally first-year students are expected to enroll in core courses that cover physical, geological, chemical, and biological oceanography and in other courses recommended by the student’s faculty adviser. Then, by the end of the first year, students usually select a particular area of focus and choose a major professor. As students advance beyond the first year, they begin to function effectively as research assistants or, in some cases, as teaching assistants. During their third to fifth year they are working toward writing their dissertations.

The interdisciplinary nature of research in marine and earth sciences is emphasized; students are encouraged to take courses in several programs and departments, and to select research problems of interdisciplinary character. The curricular programs of study are as follows:

Applied Ocean Science—The AOS academic program is designed to provide both a broad background and a core technical base to support the diverse interests and activities of the students. Early participation in an ongoing research project is encouraged. However, specialization and focus on a specific thesis topic is not required until the second or third year of the program. Required courses include SIO 214A Introduction to Fluid Mechanics, SIO 221A Analysis of Physical Oceanographic Data, and the two-quarter Wave Physics sequence SIO 202A–B. Two of the four SIO introductory courses (SIO 210, 240, 260, 280), must be completed during the first year, with the remaining two required prior to passing the doctoral qualifying exam at the end of the third year. In addition, the applied math sequence SIO 203 A–B or MAE 294 A–B is taken in either the first or second year of study. The AOS Seminar (SIO 208) serves as a communications bridge across the program; enrollment in this seminar is required during the student’s entire period of study. Beyond these core classes, the majority of each student’s academic program is tailored to individual interests. The AOS departmental examination, held at the end of the first year, is based on the core technical courses SIO 214A, SIO 221A, SIO 202A–B, and two of the four introductory courses (chosen by the student). The exam has both oral and written components.

Biological Oceanography—The student will be expected to be familiar with the material presented in the following courses: SIO 210, 240, 260, 270 or 270A, 275A or 277, 280, and at least one of SIO 271, 282, 284, or 294. Other course work ordinarily will be recommended by the student’s advisory committee, usually including 278 (or equivalent participatory seminar) one quarter of each year, a course in introductory parametric statistics, and at least one advanced-level course in physical, chemical, or geological oceanography. Participation in an oceanographic cruise (minimum of two weeks’ duration) and service as a teaching assistant (one quarter) are required. Individual advisers and/or doctoral committees may require foreign languages or computer programming languages of individual candidates.

Climate Sciences—The emphasis of this curricular group is on education through interdisciplinary research. All students are responsible for the fundamental material in the following “core” courses: SIO 210, 217A-B-C, 260. Students are also expected to supplement their backgrounds with five to seven additional courses, including, for most Climate Sciences students, at least one additional quarter of fluid dynamics. These additional course(s) will be chosen in consultation with the students’ advisors. It is recommended that students participate actively in at least two quarters of seminar courses designed to complement and stimulate individual research. Though the group stresses interactions across disciplines, students will specialize in a particular subdiscipline or track that will be chosen by the student following discussions with a 3-person faculty advisory committee soon after arrival. Examples of current tracks include: (1) atmospheric/ocean/climate dynamics and physics; (2) atmospheric chemistry (emphasizing climatic interactions); and (3) paleoclimate studies. Additional course requirements for these tracks will be tailored to the needs of the individual student.

Geosciences—The geosciences curriculum consists of a series of core courses and a series of research focus courses. All students whether pursuing an earth sciences or an oceanography degree are responsible for material in the core courses: Marine Geology (SIO 240), Marine Chemistry (SIO 260), and Physical Oceanography (SIO 210) during their first year of study. The research courses are selected from three themes: Geochemistry, Paleoclimate and Earth History, and Geology and Geophysics. A total of four research courses are required during the first year of study, with at least one from each theme. Additional courses offered by other curricular programs (e.g., geophysics, marine chemistry, and geochemistry) can be selected and scheduled depending on the student’s background and interests any time during the student’s career at SIO. A three-member faculty advisory committee is assigned to each student to help select the research and additional courses to be taken. Each student is also encouraged to participate in the Special Topics seminars (SIO 249) every quarter during the first two years of graduate study. Students wishing to graduate with an oceanography degree are also responsible for the material in SIO 280 (Biological Oceanography). Normally, students will take a comprehensive oral departmental examination near the end of their third quarter of residence. The qualifying examination will be given before the end of the third year.

Geophysics—There is no single course of study appropriate to the geophysics curriculum; instead, the individual interests of the student will permit, in consultation with the adviser, a choice of course work in seismology, geomagnetism, etc., although the content of certain core courses is usually taken during most of the first year. In the summer or early fall quarter following that year each student will be given written and oral departmental examinations, which are intended to cover the student’s formal training. A brief presentation of possible research interests will also be expected at this exam.

Marine Biology—Entering graduate students will be expected to gain research experience in one or more laboratories during their first year. In the spring term of their first year at SIO, students will take a departmental exam consisting of a presentation of their first-year research in the form of a paper and short talk to the curricular group, followed by a meeting with their first-year advisory committee. In this exam they also will be expected to demonstrate competence in the material covered in the following courses: SIO 210, 260, 280, 290A-B as well as any other course work recommended by the advisory committee. After their first year all students are expected to enroll and actively participate in at least one seminar course (SIO 278, 296, or equivalent) per year to provide in-depth knowledge and reading in selected areas, and to provide practice presenting scientific material. In addition to the seminar requirement discussed above, second-year students will present their research in a special Marine Biology mini-symposium, held in spring quarter; students in the third year and beyond are expected to participate in the research presentation class (SIO 291) each year. The curricular group coordinator, in consultation with the Ph.D. advisory committee, may waive specific course requirements in individual cases.

For the Marine Biodiversity and Conservation MAS program, refer to the separate Catalog listing.

Marine Chemistry and Geochemistry—In their first year at SIO, students in this curricular group are required to take SIO 210, 260, and either SIO 280 or SIO 240, as well as three additional elective courses. In their second year, students are required to take a further three elective courses. Although the exact choice of such courses will depend on the student's research interests, these required electives must be four-unit courses that are offered at the graduate level, and that have been approved by the curricular group as suitable electives. A list of approved courses is on file at the SIO Department office. If a student desires to take (as a required elective) a course that is not already on this list, he or she should consult with one of the curricular group advisers to get approval.

Physical Oceanography—The physical oceanography curriculum combines a comprehensive program of coursework with individually tailored specialization to meet student needs. Students will demonstrate proficiency in foundation courses required for all subdisciplines of physical oceanography (SIO 203A-B, 214A, 212A), as well as additional courses appropriate to their specialization or interdisciplinary interest. Presently defined “tracks” in the curriculum are (i) Observational Physical Oceanography, (ii) Theoretical Physical Oceanography, and (iii) the Atmospheric/Ocean Climate System. All tracks are similar in the entry-year Fall Quarter, diverging as students become more familiar with the field and in their interests. A faculty Curriculum Advisory Committee meets with students to tailor tracks to individual needs, or to create new tracks as appropriate. In any track, the total body of required knowledge is equivalent to 16 four-unit courses, of which about 12 are covered during the first year. As part of the overall requirement, tracks include a breadth component of 2 or more four-unit courses in other oceanographic disciplines. These might come from the SIO core courses in other disciplines (SIO 240, 260, 280) or from related graduate level courses taught at UCSD.

Language Requirements

The department has no formal language requirements. Within the department, some curricular programs may require demonstration of ability to use certain foreign languages pertinent to a student’s research. All students must be proficient in English.

Departmental and Qualifying Examinations

Doctoral candidates normally will be required to take a departmental examination not later than early in the second year of study. The examination will be oral and/or written depending on the curricular group. The student will be required to demonstrate, in a quantitative and analytical manner, comprehension of required subject material and of the pertinent interactions of physical, chemical, biological, or geological factors.

When the student has passed the departmental examination, and has completed an appropriate period of additional study, the department will recommend appointment of a doctoral committee which will supervise the student’s performance and reporting of his or her research. The doctoral committee must be formed before the student may proceed to the qualifying examination.

The doctoral committee will determine the student’s qualifications for independent research by means of a qualifying examination, which will be administered no later than the end of the third year. The nature of the qualifying examination varies between curricular groups. In biological oceanography, marine biology, geosciences, physical oceanography, applied ocean science, and climate sciences the student will be expected to describe his or her proposed thesis research and satisfy the committee, in an oral examination, as to mastery of this and related topics. In marine chemistry and geochemistry the student, in an oral examination, is required to present and defend a single research proposition in his or her specialized area. The student also is required to provide a written summary of the research proposition, with references, prior to the examination. In geophysics, the student presents an original research problem, in the form of a written proposition, to the doctoral committee. The student’s oral presentation and defense of this proposition completes the examination.

Dissertation

A requirement for the Ph.D. degree is the submission of a dissertation and a final examination in which the thesis is publicly defended. We encourage students to publish appropriate parts of their theses in the scientific literature. Individual chapters may be published as research articles prior to completion of the dissertation.

Departmental Ph.D. Time Limit Policies

Students must complete a qualifying examination by the end of three years, and must be advanced to candidacy for the Ph.D. Degree by the end of four years. Total university support may not exceed seven years and total registered time at UCSD may not exceed eight years.

Special Financial Assistance and Fellowships

In addition to teaching assistantships, and graduate student researcher positions, fellowships, traineeships, and other awards available on a campus-wide competitive basis, the department has available a certain number of fellowships and graduate student researcher positions supported from research grants and contracts, or from industrial contributions.