Scripps Institution of Oceanography
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Graduate Courses
For course descriptions not found in the UC San Diego General Catalog, 2012–13, please contact the department for more information.
BS/MS Course
228. Research Seminar (2)
A three-quarter required sequence for BS/MS earth sciences students to prepare students for thesis writing. Prerequisites: current earth sciences BS/MS student. Department stamp required.
Graduate
200A. Computational Ocean Acoustics and Signal Processing I (4)
Overview of ocean acoustics. Acoustics Wave Equation with some analytic solution techniques. Ray Methods. Introduction to Spectral and Normal Modes methods. Introduction to beamforming including matched field processing. Computer programs will be constructed on all subjects covered. Prerequisites: graduate standing or consent of instructor. Kuperman (F)
200B. Computational Ocean Acoustics and Signal Processing II (4)
Continuation of SIO 200A. Range dependent propagation models including adiabatic and coupled mode models and parabolic equations. More advanced topics in matched field processing. Prerequisites: graduate standing and SIO 200A or consent of instructor. Kuperman (W)
200C. Computational Ocean Acoustics and Signal Processing III (4)
Continuation of SIO 200B. Modeling interference such as ambient noise. Time domain methods. Matched field tomography, nonlinear optimization methods, and geophysical inversion. Prerequisites: graduate standing and SIO 200B or consent of instructor. Kuperman (S)
201. Geological Record of Climate Change (4)
Introduction to geological archives; the tools for paleoclimate reconstruction and a sampling of important issues from the geological record, including the development of “greenhouse” and “icehouse” worlds, the origin and evolution of glacial cycles, and the origin of “millennial scale” climate variability. Prerequisites: chemistry and physics required for graduate admission to SIO, SIO 101 or equivalent, or consent of instructor. Charles (S)
202A–B. Fundamentals of Wave Physics (4-4)
This two-quarter sequence is designed to introduce a broad background of students to basic principles of wave physics, including generation, propagation, dispersion, refraction, diffraction, reflection, waveguides, etc. A variety of wave motions of environmental relevance, including acoustic, ocean surface and internal (SIO 202A), optical and seismic (SIO 202B) are used to illustrate these principles. In-class experiments, data collection, and analysis exercises are incorporated. Prerequisites: calculus and partial differential equations. Kuperman, Melville, Stramski, Gerstoft (W,S)
203A. Introduction to Applied Mathematics I (4)
Review of exact methods for ordinary differential equations. Expansions about regular and irregular singular points. Introduction to asymptotic expansions. Approximate methods for nonlinear differential equations. Regular and singular perturbation theory. Additional topics depending upon the interests of the instructor. Cross-listed with MAE 294BA. Prerequisites: Math 110, Math 120A, or consent of instructor. (F)
203B. Introduction to Applied Mathematics II (4)
Asymptotic methods: method of steepest descent (if not covered in I) WKB, method of multiple scales, boundary layer theory. Elements of complex analysis. Cross-listed with MAE 294B. Prerequisites: MAE 294A or SIO 203A or consent of instructor. (W)
203C. Introduction to Applied Mathematics III (5)
Partial differential equations: characteristics, similarity solutions, Green’s functions, images, wave equation, diffusion equation, Laplace’s equation. Applications to continuum mechanics, potential fields, and transport phenomena such as diffusion, linear and nonlinear waves, Burger’s equation, shocks, and other topics. Other topics according to the interests of the instructor. Cross-listed with MAE 294C. Prerequisites: graduate standing and MAE 294B or SIO 203B or SIO 215B or consent of instructor. W. Young (S)
204. Acoustics (4)
Theory of radiation, transmission, and scattering of sound with special application to ocean acoustics. Students who have taken SIO 204B for credit may not receive credit for SIO 204. Prerequisites: graduate standing or consent of instructor. Buckingham (W)
206. Land Surface Hydrology (4)
Advanced introduction to natural processes that govern water occurrence and transport over the land surface. Principles of global hydrologic cycle and land-surface water balance, runoff and fluvial geomorphology, infiltration and subsurface water flow, evaporation and plant transpiration. Prerequisites: graduate standing or consent of instructor. Staff (S)
207A. Fundamentals of Digital Signal Processing (4)
Discussion of discrete-time signals and systems, Discrete-Time Fourier Transform (DFT) and window functions, Fast Fourier Transform (FFT), design of Finite Impulse Response (FIR) and Infinite Impulse Response (IIR) digital filters and their implementations, finite word length effects, applications to data acquisition and analysis. Prerequisites: graduate standing or consent of instructor. Hodgkiss (F)
207B. Digital Signal Processing I (4)
Discrete random signals; conventional (FFT based) spectral estimation. Coherence and transfer function estimation; model-based spectral estimation; linear prediction and AR modeling, Levinson-Durbin algorithm and lattice filters, minimum variance spectrum estimation. Cross-listed with ECE 251A. (Recommended prerequisites: ECE 153 in addition to either ECE 161 or 161A and SIO 207A or equivalent background.) Prerequisites: graduate standing. Hodgkiss, Rao (W)
207C. Digital Signal Processing II (4)
Adaptive filter theory, estimation errors for recursive least squares and gradient algorithms, convergence and tracking analysis of LMS, RLS, and Kalman filtering algorithms, comparative performance of Wiener and adaptive filters, transversal and lattice filter implementations, performance analysis for equalization, noise canceling, and linear prediction applications. Cross-listed with ECE 251B. (Recommended Prerequisites: ECE251A or ECE 251AN.) Prerequisites: graduate standing ECE 251A (for ECE 251B); SIO 207B (for SIO 207C). Hodgkiss (S)
207D. Array Processing (4)
The coherent processing of data collected from sensors distributed in space for signal enhancement and noise rejection purposes or wavefield directionality estimation. Conventional and adaptive beamforming. Matched field processing. Sparse array design and processing techniques. Applications to acoustics, geophysics, and electromagnetics. Cross-listed with ECE 251D. (Recommended Prerequisites: ECE251A or ECE 251AN.) Prerequisites: graduate standing; ECE 251C (for ECE 251D); SIO 207C (for SIO 207D). Hodgkiss (F)
208. Seminar in Applied Ocean Sciences (1)
Topics in applied ocean sciences. One-hour seminar. (S/U grades only). Staff (F,W,S)
209. Special Topics (1–4)
Within the next few years, lectures on various special subjects will be offered by members of the staff. The emphasis will be on topics that reveal the interdependence of the biological, chemical, geological, and physical processes operating in the oceans. (S/U grades permitted.) Staff (F,W,S)
210. Physical Oceanography (4)
Physical description of the sea; physical properties of seawater, methods and measurements, boundary processes, regional oceanography. Prerequisites: graduate standing or consent of instructor. Hendershott, Talley (F)
211A–B. Ocean Waves (4-4)
Propagation and dynamics of waves in the ocean including the effects of stratification, rotation, topography, wind, and nonlinearity. Prerequisites: graduate standing or consent of instructor. Hendershott, Guza, Winant (W,S)
212A. Geophysical Fluid Dynamics I (4)
The equations of motions for rotating stratified flow and their application to the atmospheric and oceanic dynamics; Ekman layer dynamics, potential vorticity dynamics, the quasigeostrophic approximation, theories of the wind-driven oceanic circulation, theories of the atmospheric Hadley circulation, geostrophic adjustment, and baroclinic instability. Prerequisites: graduate standing or consent of instructor. MacKinnon (W)
212B. Geophysical Fluid Dynamics II (5)
The equations of motion for rotating stratified flow and their application to the atmospheric and oceanic dynamics; Ekman layer dynamics, potential vorticity dynamics, the quasigeostrophic approximation, theories of the wind-driven oceanic circulation, theories of the atmospheric Hadley circulation, geostrophic adjustment, and baroclinic instability. Prerequisites: graduate standing and SIO 212A and SIO 214A or consent of instructor. Cessi (S)
213. Turbulence and Mixing (4)
Mixing mechanisms, their identification, description, and modeling. Introduction to turbulence, semi-empirical theories, importance of coherent structures, effects of stratification and rotation on turbulent structure, entrainment and mixing. Cross-listed with MAE 216. (S/U grades permitted.) Armi (S)
214A. Introduction to Fluid Mechanics (4)
A survey of classical problems in fluid mechanics and approximate techniques of analysis. Topics include conservation equations, straight laminar flows, low and high Reynolds number laminar flow, stability of laminar flows, turbulent flow. Prerequisites: graduate standing or consent of instructor. Hendershott, Winant (F)
214B. Environmental Fluid Dynamics (4)
Single-layer flows with a free surface, two-layer flows including exchange flows in harbors, estuaries, seas, and buildings. Continuously stratified flows with meteorological and oceanographic applications. Topographic effects, plumes, jets, and thermals. Planetary boundary layers. Prerequisites: graduate standing or consent of instructor. Armi (S)
215A. Applied Mathematics for Oceanographers I (4)
Intended for first-year graduate students who seek a quantitative way to describe how the ocean works: vector analysis, complex quantities, Fourier and Laplace transforms, ordinary differential equations, nonhomogeneous ordinary differential equations, initial and boundary value problems, Heat and Laplace equations. Prerequisites: graduate standing or consent of instructor. Hendershott, Winant (F)
215B. Applied Mathematics for Oceanographers II (4)
An introduction to the mathematical description of waves, beginning with a description of the linear oscillator, and followed by normal modes, the flexible string, membranes, water waves, ray theory, method of characteristics, and basic linear algebra. Prerequisites: graduate standing and SIO 215A or consent of instructor. Hendershott, Winant (W)
215C. Applied Mathematics for Oceanographers III (4)
An introduction to Perturbation theory, including regular and singular expansions, Poincare's method, two-scale method, the WKB approximation and boundary layer theory. Prerequisites: graduate standing and SIO 215B or consent of instructor. Hendershott, Winant. (S)
216. Introduction to the Physics of Complex Systems (4)
Emergent complex behavior in nonlinear, dissipative, open dynamical systems will be investigated by studying fundamental properties and their manifestation in examples drawn from the physical and biological sciences. Topics to include fractals, chaos, self-organization, artificial life, and neural networks. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Werner (W)
217A. Atmospheric and Climate Sciences I (4)
Thermodynamics and statics of dry and moist air, atmospheric composition, Earth radiation budget, vertical structure of the atmosphere, global energy balance, thermodynamic feedbacks in the climate system. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Russell (F)
217B. Atmospheric and Climate Sciences II (4)
Structure of midlatitude synoptic systems; equations of motion, scale analysis, elementary applications and wave solutions; baroclinic instability theory; atmospheric general circulation and energetics; tropical dynamics; relationships between atmospheric dynamics, clouds, precipitation, and other weather and climate phenomena. Prerequisites: graduate standing and SIO 217A or equivalent background, or consent of instructor. J. Norris (W)
217C. Atmospheric and Climate Sciences III (4)
Physical and dynamical processes that determine climate and climate change; role of aerosols; water vapor; CO2 and other greenhouse gases; cloud-radiative interactions; atmospheric general circulation; role of convection; tropical climate including El Niño. Prerequisites: graduate standing and SIO 217A and SIO 217B or equivalent background, or consent of instructor. Ramanathan (S)
217D. Atmospheric and Climate Sciences IV (4)
Atmospheric chemistry that impacts climate change, including photochemical reactions, ozone chemistry, and aerosol evolution in the troposphere and stratosphere. Atmospheric applications of catalytic cycles, heterogeneous chemistry, and microphysical processes will include the ozone hole, urban smog, and aerosol-cloud interactions. Prerequisites: undergraduate general physics, chemistry, and mathematics (including differential equations). Russell (S)
219. Special Topics in Physical Oceanography (1–4)
Example topics are case histories and methods in physical oceanography, theories of the ocean circulation, numerical methods in large-scale ocean and atmospheric models, and natural electromagnetic phenomena in the earth and the oceans. (S/U grades permitted.) Staff (F,W,S)
220. Observations of Large-Scale Ocean Circulation (4)
General circulation of the oceans; tropical, subtropical, and high-latitude current systems of the Atlantic, Indian, and Pacific Oceans and marginal seas; ocean heat flux and thermohaline circulations; observational basis of large-scale dynamics. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Roemmich (S)
221A. Analysis of Physical Oceanographic Data (A) (4)
Fundamental elements of analysis of geophysical and oceanographic time series, including sampling problems, least squares techniques, spectral analysis, interpretation of series, design of experiments. Prerequisites: consent of instructor. Pinkel (F)
221B. Analysis of Physical Oceanographic Data (B) (4)
Techniques for analysis of physical oceanographic data involving many simultaneous processes including probability densities, sampling errors, spectral analysis, empirical orthogonal functions, correlation, linear estimation, objective mapping. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Rudnick (W)
221C. Data Analysis Laboratory (4)
This course is to give students practical experience with analysis techniques. Students complete three projects. Topics include empirical orthogonal functions, objective mapping, complex demodulation, inference of geostrophic flow, minimization of CTD salinity spiking, isolation of wind-driven currents, wavelets. Prerequisites: graduate standing or consent of instructor. (S/U grades only.) Gille (F)
222. Underwater Bioacoustics (4)
Introductory course to familiarize a broad spectrum of participants to underwater sound and its relationship to underwater animals. Basic physics of sound propagation, use of sound to study underwater animals and, the sounds made by the animals themselves for echolocation and communication will be covered. Prerequisites: consent of instructor. (S/U grades permitted.) J. Hildebrand, Jaffe (W)
223A. Geophysical Data Analysis I (4)
Probability and statistics and their application to make inferences from geophysical data: point processes, distributions, maximum likelihood estimation, hypothesis testing and confidence intervals, least squares, density estimation, interpolation and smoothing. Prerequisites: graduate standing or consent of instructor. (W)
223B. Geophysical Data Analysis II (4)
Analysis of geophysical measurements, especially time series, Fourier theory digital signal processing, and spectral analysis. Prerequisites: graduate standing and SIO 223A or consent of instructor. Agnew (S)
224. Internal Constitution of the Earth (4)
An examination of current knowledge about the composition and state of the earth’s interior revealed by geophysical observations. Seismic velocity and mass density distributions; equations of state; phase changes; energy balance and temperatures; constraints on composition from extraterrestrial samples and exposed rocks; spherical and aspherical variations of properties. Prerequisites: calculus and differential equations, basic chemistry and physics, or consent of instructor. Masters, Stegman (S)
225. Physics of Earth Materials (4)
Mathematics and physics of continuous media, focusing on geophysical problems. Topics include deformation, stress, conservation laws, elasticity, attenuation, viscoelasticity, fracture mechanics, and porous media. Prerequisites: graduate standing or consent of instructor. Agnew, Fialko (F)
226. Introduction to Marine Geophysics (4)
Methods of exploration geophysics with emphasis on those useful at sea. Magnetic and gravitational potential field methods, multi-beam echo sounding reflection and refraction seismology will be covered. Recent papers from the literature will also be read and discussed. Prerequisites: differential equations; at least one geology course. (S/U grades permitted.) Dorman, Chadwell (S)
227A. Introduction to Seismology (4)
Introduction to seismometers and seismograms; stress and strain; potentials and the wave equation; geometrical ray theory and travel times in layered media; representation of seismic sources; WKBJ and synthetic seismograms; seismic hazards and other applications of seismology. Prerequisites: consent of instructor. (S/U grades permitted.) Shearer (W)
227B. Advanced Seismology I (4)
Introduction to low-frequency digital data; continuum mechanics and the equations of motion; free oscillation solutions; construction of Earth models; excitation of free-oscillations and source mechanism retrieval; array processing of long-period data; modelling aspherical structure; surface waves. Prerequisites: consent of instructor. (S/U grades permitted.) Masters (S)
227C. Advanced Seismology II (4)
High-frequency wave propagation; methods for computing synthetic seismograms including WKBJ, reflectivity and finite differences; body-wave spectra; attenuation of body waves; source physics; reflection and refraction seismology; seismic tomography. Prerequisites: consent of instructor. (S/U grades permitted.) Staff (S)
229. Gravity and Geomagnetism (4)
Introduction to potential theory, with applications to gravity and geomagnetism. Topics include the geoid, spherical harmonics, Laplace’s equation, the Dirichlet problem on a sphere, and Fourier methods. Gravity anomalies and geomagnetic field modeling and sources are discussed; also paleomagnetic observations. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) C. Constable (S)
230. Introduction to Inverse Theory (4)
Solution of linear and nonlinear inverse problems in geophysics by optimization techniques such as norm minimization and linear programming. Construction of models by regularization; inference by bounding functionals. Illustrations from gravity, geomagnetism, and seismology. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) C. Constable (W)
231. Introduction to EM Methods in Geophysics (4)
Introduction to electromagnetic methods for both global geophysics and applied/exploration methods. Covers history of EM induction, conduction in rocks, binary mixing laws, self potential, induced polarization, DC resistivity, magnetotellurics, geomagnetic depth sounding, elementary inverse methods, global conductivity structure, and marine EM methods. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) S. Constable (F)
232. Ethical and Professional Science (2)
Review and group discussion of professional behavior and survival skills in the earth and ocean sciences, including ethics, data management, plagiarism, authorships, preparing proposals, public speaking, conflict of interest, working with industry. Prerequisites: graduate standing or consent of instructor. (S/U grades only.) C. Constable, S. Constable (S)
233. Introduction to Computing at SIO (4)
Introduction to the SIO computing environment and common software tools in geophysics and other disciplines. Topics include UNIX, Matlab, Postscript, GMT, LaTex, HTML, and a scientific programming language such as C or Fortran90. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Shearer, Tauxe (F)
234. Geodynamics (4)
A general course on the dynamics and kinematics of the solid earth based on the text of Turcotte and Schubert. Topics include plate tectonics, heat flow, lithospheric cooling, flexure, viscous flow, gravity, crustal dynamics, and other related topics. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Sandwell (W)
236. Satellite Remote Sensing (4)
Satellite remote sensing provides global observations of Earth to monitor environmental changes in land, oceans, and ice. Overview physical principles of remote sensing including: orbits, electromagnetic radiation, diffraction, electro-optical, and microwave systems. Weekly labs explore remote sensing data sets. Graduate students will also be required to write a term paper and do an oral presentation. Conjoined with SIO 135. Prerequisites: graduate standing or consent of instructor. Sandwell (S)
237A. Introduction to Ocean Optics (4)
Overview of ocean optics. Concepts in radiometry. Inherent and apparent optical properties. Radiative transfer equation. Light absorption and scattering by seawater constituents. Optics of air-water interface. Light fields within and leaving the ocean. Optics of marine particles. Measurement methods and instrumentation. Prerequisites: basic physics and differential calculus, or consent of instructor. Stramski (F)
237B. Ocean Color Remote Sensing (4)
Overview of ocean color satellite missions. Concepts in radiometry. Inherent and apparent optical properties. Radiative transfer equation. Solar radiation and elements of atmospheric optics. Propagation of light across the sea surface and within the ocean. Light absorption and scattering by seawater. Water-leaving radiance and remote-sensing reflectance. Ocean color algorithms and applications. Prerequisites: basic physics and differential calculus, or consent of instructor. (S/U grades permitted.) Stramski (F)
237C. Optical-Biological Interactions in the Ocean (2)
A discussion class with emphasis on the interaction of light with marine plankton. Topics will include light absorption, fluorescence, and scattering by phytoplankton and effects of growth conditions on phytoplankton optical properties. Classic and contemporary papers dealing with these topics will be discussed. Prerequisites: basic physics and biology, or consent of instructor. (S/U grades only.) Stramski (F)
238. Sensor Networks (4)
Characteristics of chemical, biological, seismic, and other physical sensors; signal processing techniques supporting distributed detection of salient events; wireless communication and networking protocols supporting formation of robust sensor fabrics; current experience with low power, low cost sensor deployments. Conjoined with MAE 149 and ECE 156. Prerequisites: upper-division standing and approval of instructor, or graduate student in science or engineering. (S/U grades permitted.) Hodgkiss (S)
239. Special Topics in Geophysics (1–4)
Special course offerings by staff and visiting scientists. Example topics are seismic source theory, geophysical prospecting methods, dislocation theory and seismic mechanisms, tectonic interpretation of geodetic data, and dynamo theory. (S/U grades permitted.) Staff (F,W,S)
240. Marine Geology (4)
Introduction to the geomorphology, sedimentation, stratigraphy, vulcanism, structural geology, tectonics, and geological history of the oceans. Prerequisites: the physics and chemistry required for admission to the graduate curriculum in SIO, and ES 101 or equivalent, or consent of instructor. Cande, Castillo, Charles (F)
242A. Marine Biotechnology I: Tools and Methods (4)
The course will explore cutting-edge techniques as it applies to genomics, transcriptomics, proteomics, metabolomics and the bioinformatics needed to analyze such data sets. Next generation sequencing, state-of-the-art mass spectrometry and NMR techniques and bioinformatic challenges. Students may not receive credit for SIO 242A and SIO 242. Prerequisites: graduate standing or consent of instructor. Gaasterland, L. Gerwick (W)
242B. Marine Biotechnology II: Applications (4)
This course will explore the diverse biotechnological applications of marine science. Topics will include natural product drug discovery, biomaterials, nanotechnology, synthetic biology, aquaculture, and extremophiles. Students may not receive credit for SIO 242B and SIO 242. Prerequisites: graduate standing or consent of instructor. Bartlett, Jensen (S)
243. Marine Paleoecology (4)
Paleoecology of marine plankton, nekton, and benthos. Patterns and changes in marine communities and ecosystems over geological time in relation to changes in the physical, chemical, and geological environment and biotic interactions. The preservation filter and inference of ecological processes from fossils and biogeochemical proxies. Biotic interchanges, incumbency, escalation and trends, mass extinctions, and recovery. Lectures, seminar discussion, laboratory, and field trips. Prerequisites: bachelor’s degree in science or consent of instructor; open to undergraduates with completion of SIO 104 and either BIEB 130 or BIEB 140, or equivalent. Staff (S)
244. Shape and Structure of the Ocean Floor (4)
Description and explanation of the structural geomorphology of oceanic crust, and of the tectonic and volcanic processes responsible for it. Description and interpretation of deep-sea sedimentary landforms (e.g., deep-sea fans, drifts, bedforms) and of the bottom currents that shape them. Offered in alternate years. Prerequisites: any previous graduate/undergraduate earth science or geology course. Lonsdale (W)
245. Marine Sediments-Paleo Proxies (4)
On the chemical and isotopic records of marine sediments and implications for the history of seawater chemistry and paleoceanography. Will concentrate on the isotopic systems: Li, B, C, O, S, Sr, and Nd, in marine phases that reliably preserve the records, and on associated diagenetic problems. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Kastner (S)
246. Global Tectonics and Basin Formation (4)
Plate tectonics of the crust and upper mantle, examining a variety of environments from ridge crests to continental margins, including plate interiors, with an emphasis on basin formation in these tectonic settings. Prerequisites: graduate standing. Cande, Driscoll (W)
247. Rock Magnetism and Paleomagnetism (4)
Rock magnetism and acquisition of magnetic remanence in geological materials as well as laboratory procedures and data analysis (isolating remanence components and statistical approaches). The paleomagnetic literature will be used to illustrate applications in geological and geophysical problems. Prerequisites: one year each of college-level physics and geology; mathematics through calculus. (S/U grades permitted.) Tauxe (S)
248. Evolution of Earth’s Biosphere (4)
Paleoecological development of marine and terrestrial environments during Earth’s evolution. Ecological and chemical evolution of the oceans, atmosphere, biogeochemical cycles, and environments with particular emphasis on the long-term history and climate of the Earth’s surface. Substantial field component (three weekend field trips in San Diego County) complement and extend the lecture material. Additionally, at graduate level oral presentation or research paper required. Conjoined with SIO 148. Prerequisites: graduate-level standing or consent of instructor. R. Norris (S)
249. Special Topics in Marine Geology (1–4)
Special course offerings by staff and visiting scientists. (S/U grades only.) Staff (F,W,S)
251. Whole Earth Geochemistry (4)
A geochemical overview of Earth materials and chemical processes involved in the Earth’s evolution. Topics include formation and differentiation of the Earth, linkages between the solid Earth and the atmosphere/ hydrosphere, and isotope and trace element composition of igneous and metamorphic rocks. Graduate students, additionally, must submit a term paper in one aspect of work discussed during the quarter to be presented orally in class. Prerequisites: graduate standing or consent of instructor. Hilton (S)
252A. Introduction to Isotope Geochemistry (4)
Radioactive and stable isotope studies in geology and geochemistry, including geochronology, isotopes as tracers of magmatic processes, cosmic-ray produced isotopes as tracers in the crust and weathering cycle, isotopic evolution of the crust and mantle. Graduate level requires student presentation. Conjoined with SIO 144. Prerequisites: graduate-level standing or consent of instructor. Castillo, Keeling (W)
252B. Advanced Isotope Geochemistry I (4)
An advanced treatment of noble gas and stable isotope geochemistry. Offered in alternate years with SIO 252C. Prerequisites: SIO 252A/SIO 144. Castillo, Keeling (S)
252C. Advanced Isotope Geochemistry II (4)
An advanced treatment of radiogenic and cosmogenic isotope geochemistry. Offered in alternate years with SIO 252B. Prerequisites: SIO 252A/SIO 144. (S)
253. Interactions of Oceanic Plates and the California Margin (4)
How the geology of Alta and Baja California has been shaped, especially in the past 30MYR, by changing patterns of ocean plates and microplates that have subducted beneath the North American Margin, slid obliquely past it, and captured continental crust. Prerequisites: graduate standing, or consent of instructor and any other earth science class for undergraduates. Lonsdale
255. Paleobiology and History of Life (6)
An introduction to the major biological transitions in Earth history from the origins of metabolism and cells to the evolution of complex societies. The nature and limitations of the fossil record, patterns of adaptation and diversity, and the tempo and mode of biological evolution. Laboratories and substantial field component complement and extend lecture material. Program and/or material fee may apply. Graduate students, additionally, will give oral presentation or research paper. Conjoined with SIO 104. Prerequisites: graduate-level standing or consent of instructor. R. Norris (S)
255A. Topics in Paleobiology and History of Life (3)
Lecture topics on the major transitions in the evolutionary history of life including origin of metabolisms, microbes, major eukaryote radiations, ecosystems and societies. Prerequisites: graduate standing or consent of instructor. R. Norris (S)
257. Seminar in Petrology (4)
Discussion of current research in petrology and mineralogy. (S/U grades permitted.) (W)
259. Atmospheric Geochemistry (4)
Topics in this introductory course include: structure and composition of the atmosphere; chemistry and isotopes of natural and man-made carbon-, nitrogen-, and sulfur-bearing trace gases; ozone and hydroxyl radical; halogenated gases; air-sea exchange; aerosols; climatic effects. (S/U grades permitted.) (S)
260. Marine Chemistry (4)
Chemical description of the sea; the distribution of chemical species in the world oceans, and their relationships to physical, biological, and geological processes. Aluwihare, Barbeau, Dickson, Martz (W)
261. Energetics and Kinetics in Marine Systems (4)
This course teaches the physical chemical principles that control chemistry in marine systems. After a basic introduction to thermodynamics and its application to an understanding of the marine environment, the emphasis will be on the study of a variety of kinetic processes. Prerequisites: graduate standing or consent of instructor. Dickson (S)
262. Seminar in Marine Natural Products (1)
Students will give seminars on current research topics in marine natural products chemistry. Prerequisites: graduate standing or consent of instructor. (S/U grades only.) Fenical, W. Gerwick, Moore (F,W,S)
263. Aqueous Chemistry (4)
This course emphasizes the chemical principles that control basic aqueous chemistry in marine systems. The focus will be to show that the geochemistry of the various elements in sea water and biological systems can be understood as a consequence of basic general chemical concepts such as electron structure, chemical bonding, and group and periodic properties. Prerequisites: undergraduate chemistry equivalent to UC San Diego Chemistry 6 sequence. Dickson (F)
264. Special Topics in Marine Natural Products Chemistry (3)
This course provides the foundation for advanced study in the field of marine natural products chemistry. Topics vary from the history of natural products to the organic chemistry of terpenes, alkaloids, acetogenins, and other natural product classes. Varying by topic quarterly, this class is given each quarter and may be repeated. Prerequisites: one year general organic chemistry. (S/U grades only). Fenical, W. Gerwick, Moore (F,W,S)
267. Biogeochemistry (4)
Examines quantitatively the impact of the biota on the chemistry of the atmosphere and ocean. Emphasis given to isotopes as tracers of biogeochemical processes. Attention given to paleoclimatic and paleoatmospheric data from ice cores to reveal mechanisms. Prerequisites: graduate standing or consent of instructor. Severinghaus, R. Keeling (S)
268. Seminar in Geochemistry and Marine Chemistry (1)
Student seminars on topics related to geochemistry and the chemistry of the marine environment. (S/U grades only.) Dickson (S)
269. Special Topics in Marine Chemistry (1–4)
Special course offerings by staff and visiting scientists. (S/U grades permitted.) Staff (F,W,S)
270. Pelagic Ecology (4)
An analysis of the concepts and theories used to explain the biological events observed in the water column. Alternate years. Prerequisites: SIO 210, 280, or consent of instructor. Checkley, Ohman (S)
270A. Fisheries Oceanography (4)
Aspects of marine ecology relevant to the reproduction, survival, and distribution of commercially important marine species. Alternate years only. Prerequisites: graduate standing or consent of instructor. Checkley (S)
271. Marine Zooplankton (5)
Lectures and laboratories treating the morphological, behavioral, and life history variations of the principal phyla of planktonic invertebrates and heterotrophic protists. Constraints of life at low Reynolds numbers; principles of allometry; growth processes of heterotrophic organisms. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted.) Ohman (S)
272. Biogeography (3)
A lecture course concerning the origin, development, and perpetuation of distributional patterns with emphasis on benthic marine organisms. (W)
273. Professional Ethics in Science (2–4)
A seminar on the historical and contemporary ethics and ethos of scientific research, based on published documents. Given in alternate years. Prerequisites: graduate standing and consent of instructor. Department stamp required. Dayton (W)
274. Natural History Below the Tides (4)
Exposure to local underwater habitats by scuba with basic material to comply with AAUS certification. Lectures and shore dives in local coastal habitats (protected bay and outer coast sites). Aids students in diving research by providing experience with SIO scientists. Prerequisites: department stamp required. Students must qualify to take the SIO dive course. This includes a physical exam as well as swimming and diving proficiency. Dayton, Leichter (F)
275A. Benthic Ecology (4)
Evolution and maintenance of benthic communities from the terrestrial margins to the deep sea. Special emphasis will be placed on physical and biological scaling and processes determining patterns of distribution and abundance; interrelationships between community structure and population phenomena, including trophic relationships, reproductive and recruitment patterns, succession, and life history biology. Offered in alternate years with SIO 275B. Prerequisites: consent of instructor; open to undergraduates. (S/U grades permitted.) Leichter, Levin (W)
275B. Natural History of Coastal Habitats (6)
Two three-hour lecture/laboratories per week, three week-long field trips to coastal habitats in the Southwest and northern Mexico. Several day field trips to local habitats. Offered in alternate years with SIO 275A. Prerequisites: consent of instructor. (S/U grades permitted.) Dayton, R. Norris (S)
276. Quantitative Theory of Populations and Communities (4)
An introduction to the quantitative tools and conceptual issues underlying the study of the dynamics and structure of ecological systems. Prerequisites: calculus (three quarters) or consent of instructor. (S/U grades permitted.) Sugihara (F)
276L. Quantitative Ecology Project Lab (4)
A laboratory complement to SIO 276, to apply quantitative tools to conceptual issues underlying the study of the dynamics and structure of ecological systems. Prerequisites: graduate standing, SIO 276 and consent of instructor. Department stamp. Sugihara (W)
277. Deep-Sea Biology (4)
The ecology, zoogeography, taxonomy, and evolution of deep-sea organisms, with emphasis on the benthos. Course includes one day cruise to the San Diego Trough to examine deep sea organisms (700–1200 meters) (two-hour steam from Point Loma). Offered alternate years. Prerequisites: graduate standing or consent of instructor. Levin (W)
278. Seminar in Ocean Biosciences (2)
Presentations of reports, review of literature, and discussion of current research in the marine biological and oceanographic sciences. (S/U grades permitted.) Staff (F,W,S)
279. Special Topics in Biological Oceanography (1–4)
(S/U grades permitted.) Staff (F,W,S)
280. Biological Oceanography (4)
The biology and ecology of marine plankton, nekton, and benthos. Emphasis will be on processes regulating species, community, and ecosystem patterns and changes, including productivity, trophic relationships and species interactions with the physical, chemical, and geological environment. One or more field trips. Prerequisites: bachelor’s degree in science or consent of instructor. Franks or Checkley, Levin (F)
281. Marine Physiology (4)
Biochemical and physiological mechanisms of adaptation of organisms to the marine environment. Special emphasis is on biological responses to temperature, salinity, carbon dioxide, pH and bicarbonate levels. Prerequisites: graduate standing or consent of instructor. Tresguerres
282. Phytoplankton Diversity (4)
Molecular, biochemical, ecological, and evolutionary perspectives on the diversity of eukaryotic and prokaryotic phytoplankton. Prerequisites: consent of instructor. Palenik (W)
283. Phycology: Marine Plant Biology (5)
Lecture and laboratory course emphasizing the biology, ecology and taxonomy of marine plants and seaweeds. Laboratory work mainly involves examination, slide preparation and dissection of fresh material collected locally. An oral presentation on a current research topic is required. Program or course fee may apply. Graduate students, additionally, are required to write a research paper. Offered in alternate years. Prerequisites: graduate standing or consent of instructor. J. Smith (W)
284. Marine Invertebrates (6)
Course emphasizing the diversity, evolution and function morphology of marine invertebrates. Laboratory work involves examination of live and prepared specimens. An oral presentation on a current research topic is required. Graduate level additionally requires a research paper with extensive literature review and critical analyses. Program or course fee may apply. Conjoined with SIO 184. Prerequisites: graduate standing or consent of instructor. Rouse (W)
285. Physical-Biological Interactions (4)
Physical and biological processes affecting growth and patchiness of plankton. Concepts and equations from physical oceanography will be presented and explored in a biological context. Ideas will be treated both theoretically and with examples from the literature. Prerequisites: introductory calculus and SIO 210, or consent of instructor. Franks (S)
286. Marine Science, Economics and Policy (4)
This course investigates global issues in marine conservation and potential policy solutions. The approach is interdisciplinary, fast-paced, and discussion oriented. Students will become acquainted with sufficient background in marine biology, ecology, marine and conservation economics, international law, and policy as preparation for participation in discussion on real-world issues in marine conservation. Topics and instructors change each quarter. Prerequisites: graduate standing or consent of instructor. (S/U grades permitted) Staff (F,W)
287A. Marine Microbial Ecology (4)
Recent developments in the study of marine bacteria. Emphasis will be on biochemical and physiological adaptations of marine bacteria to the ocean environment. Bacterial metabolism, growth, and death will also be discussed in the context of trophic interactions and flows of material and energy in marine ecosystems. Molecular biology techniques used in the study of bacterial ecology will also be discussed. Prerequisites: consent of instructor. (S/U grades permitted.) Azam (W)
287B. Microbial Physiology (4)
Prokaryotic microbial physiology will be discussed primarily from a biochemical standpoint with emphasis on mechanism. Topics will vary from year to year but will include the following themes: Central Metabolism. Bioenergetics, Biosynthesis, Regulation, Differentiation. Prokaryotic Structure-Function Relationships. Conjoined with BIMM 130. Prerequisites: BIBC 100 or BIBC 102 or equivalent. Saier (S).
288. Marine Microbiology Laboratory (4)
Advanced techniques and theory in environmental microbiology. Students will perform experiments concerning (a) enrichment of diverse microbes (b) microbial enumeration and identification (c) metabolic and physiochemical adaptations, and (d) biotechnology, along with an independent project. Prerequisites: consent of instructors. Brahamsha, Palenik (S)
289. Pollution, Environment, and Health (4)
The goal is to understand the scope of the pollution problem facing the planet. Students will learn the properties of chemicals in the environment and survey the biological mechanisms that determine their accumulation and toxicity. Graduate students will also be required to write a research paper. Prerequisites: graduate standing or consent of instructor. Hamdoun
290. Marine Biology (4)
An introduction to the field of marine biology, especially to the diversity of marine organisms at all taxonomic levels and their adaptations to the marine environment. Prerequisites: graduate standing. N. Holland (W)
291. Biology Graduate Research Presentations (2)
Graduate students in the biological sciences present research in a seminar or poster format. Class participants provide oral and written feedback on presentations. Required of second through fourth year students in the marine biology curricular group. Open to all SIO graduate students. (S/U grades only.) Latz (S)
292. Communicating Science to Informal Audiences (4)
Students develop fundamental science communication and instructional skills through the understanding and application of learning theory, interpretative techniques, and pedagogical practices, which occurs in the context of communicating ocean science concepts to a diverse audience at Birch Aquarium at Scripps. Graduate science students will develop fundamental communication, and instructional skills through the understanding and application of learning theory, interpretive techniques, and pedagogical practices, including the development of an education/outreach plan to support a competitive research proposal. Conjoined with SIO 180. Prerequisites: graduate standing or consent of instructor. (F)
293. Applications of Phylogenetics (6)
Overview of the computer-based methods for constructing phylogenetic trees using morphological and molecular data. Lectures and labs cover evolutionary and ecological transformations, biodiversity measurements, biogeography, systematics and taxonomy. An independent project and presentation are required. Prerequisites: graduate standing or consent of instructor. Rouse (W)
294. Biology of Fishes (5)
The comparative evolution, morphology, physiology, and ecology of fishes. Special emphasis on local and deep-sea and pelagic forms in laboratory. Prerequisites: graduate standing or consent of instructor. Hastings (S)
295S. Introduction to Marine Biodiversity and Conservation—Seminar (8)
Lectures on ecological, economic, social, and legal issues related to marine biodiversity and case studies on socioeconomic and legal issues. Students are expected to attend field trips at sea and to various sites around San Diego County as a part of the corequisite course. Students who have taken SIO 295 may not receive credit for SIO 295S. Corequisite: SIO 295LS. Prerequisites: MAS students only; consent of instructor. (Su)
295LS. Introduction to Marine Biodiversity and Conservation—Lab (8)
Laboratory work on major biological taxa, field trips on biodiversity in situ, computer labs for informatic tools. Students are expected to attend field trips at sea and to various sites around San Diego County as a part of the course. Students who have taken SIO 295L may not receive credit for SIO 295LS. Corequisite: SIO 295S. Prerequisites: MAS students only; consent of instructor. (Su)
296. Special Topics in Marine Biology (1–5)
Example topics are reproduction in marine animals, adaptation to marine environments, larval biology, marine fisheries, macromolecular evolution, physical chemical topics in physiology, philosophy of science. (S/U grades permitted.) Staff (F,W,S)
297. Marine Biology Seminar (1)
Lectures given by visiting scientists and resident staff and students. (S/U grades only.) Staff (F,W,S)
298. Special Studies in Marine Sciences (1–4)
Reading and laboratory study of special topics under the direction of a faculty member. Exact subject matter to be arranged in individual cases. Prerequisites: graduate standing. (S/U grades permitted.) Staff (F,W,S)
299. Research (1–12)
(S/U grades only.) Staff (F,W,S)
500. Teaching Apprenticeship (1–4)
This practicum for graduate students provides experience in teaching undergraduate oceanography courses. Prerequisites: department approval. (S/U grades only.) Staff (F,W,S)