Courses

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: basic physics and familiarity with differential equations and some linear algebra. 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. Prerequisite: SIO 200A. 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. Prerequisite: SIO 200B. 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. Prerequisite: chemistry and physics required for graduate admission to SIO, SIO 101 or equivalent, or consent of instructor. Charles (S)

202 A-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. Buckingham, Kuperman, Stramski, Melville, Hildebrand, Dorman (W,S)

203A. Introduction to Applied Mathematics I (4) (Cross-listed with MAE 294A.) 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. Prerequisites: Math. 110, Math. 120A, or consent of instructor.

203B. Introduction to Applied Mathematics II (4) (Cross-listed with MAE 294B.) Asymptotic methods: method of steepest descent (if not covered in I) WKB, method of multiple scales, boundary layer theory. Elements of complex analysis. Prerequisite: MAE 294A or SIO 203A or consent of instructor.

203C. Introduction to Applied Mathematics III (4) (Cross-listed with MAE 294C.) 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 and shocks. Other topics according to the interests of the instructor. Prerequisite: MAE 294B or SIO 203B or consent of instructor.

204B. Advanced Acoustics II (4) Theory of radiation, transmission and scattering of sound with special application to ocean acoustics. Prerequisites: concurrent registration in ECE 145BL recommended; SIO 204A 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. Prerequisite: graduate standing or consent of instructor. Staff (S)

207A. Introduction to Digital Signal Processing (4) Review of discrete-time systems and signals, discrete-time Fourier transform and its properties, the fast Fourier transform, design of finite impulse response (FIR) and infinite impulse response (IIR) filters, implementation of digital filters. Cross-listed with ECE 161A. Prerequisites: ECE 101 and ECE 109 with grades of C- or better. Hodgkiss, Rao (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 251AN. Prerequisites: ECE 153, 161 or 161A, or consent of instructor. 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 Weiner and adaptive filters, transversal and lattice filter implementations, performance analysis for equalization, noise canceling, and linear prediction applications. Cross-listed with ECE 251BN. Prerequisite: ECE 251AN. Hodgkiss, Rao (S)

207D. Array Processing (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 251DN. Prerequisites: ECE 251AN, 161 or 161A, or consent of instructor. Hodgkiss, Rao (W)

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: the mathematics and physics required for admission to the graduate curriculum in the Scripps Institution of Oceanography (see text), 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: for SIO 211B, SIO 211A and SIO 214A, or consent of instructor. Guza, Hendershott, Melville, Salmon, (W,S)

212A-B. Geophysical Fluid Dynamics (4-4) 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. Prerequisite: SIO 214A or consent of instructor. Cessi, Young (W,S)

213. Ocean 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 214B. (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. Prerequisite: partial differential equations. 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. Cross-listed with MAE 224. Prerequisite: introductory graduate-level course in fluid mechanics. Armi (S)

215. Introduction to Atmospheric Radiative Transfer (4) Introduces elementary concepts in electromagnetism and quantum mechanics to explain scattering, absorption and emission by gases, aerosols, and clouds. Elegant analytical solutions to the transfer equation will be employed in conjunction with satellite and laboratory measurements to consider phenomena such as the CO2 greenhouse effect, albedo effect of clouds, color of the skies, and atmospheric radiative cooling. Prerequisites: undergraduate courses in physics and differential calculus. Ramanathan (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: basic solid and fluid mechanics, mathematics through PDEs, and computer programming skills. (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: undergraduate general physics and mathematics through differential equations. (S/U grades permitted.) (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, CO2 clouds, precipitation, and other weather and climate phenomena. Prerequisite: SIO 217A. 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 Ni o. Prerequisites: SIO 217A and 217B or equivalent background. Ramanathan (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. Prerequisite: SIO 210. (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. Prerequisite: 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. Prerequisite: SIO 221A 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. Prerequisite: SIO 221A-B or equivalent. (S/U grades only.) Rudnick, 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. Prerequisite: consent of instructor. (S/U grades permitted Jaffe (W)

223. Geophysical Data Analysis (4) Design of geophysical experiments and analysis of geophysical measurements, interpretation of geophysical time series; sampling, least squares, spectrum analysis. Staff (W)

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 (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. Prerequisite: consent of instructor. Agnew, Fialko (W)

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, Hildebrand (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. Prerequisite: consent of instructor. (S/U grades permitted.) Shearer (F)

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. Prerequisite: consent of instructor. (S/U grades permitted.) Staff (W)

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. Prerequisite: 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: advanced calculus, differential equations, complex variables, and familiarity with Maxwell s equations, or consent of instructor. (S/U grades permitted.) C. Constable, Parker (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. Prerequisite: consent of instructor. (S/U grades permitted.) Parker (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. Prerequisite: graduate standing or consent of instructor. (S/U grades permitted.) S. Constable (F)

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. Prerequisite: consent of instructor. (S/U grades permitted.) Shearer (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, global gravity, crustal structure, and other related topics. Prerequisite: familiarity with partial differential equations and Fourier transforms. (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. Graduate students will additionally do term paper. Conjoined with SIO 135. Weekly labs explore remote sensing data sets. Prerequisite: graduate-level standing or consent of instructor. (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 (4) 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. Prerequisite: upper-division standing and approval of instructor, or graduate student in science or engineering. (S/U grades permitted.) Hodgkiss, Rao (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. Staff (F)

241. Fluids in Active Tectonic Systems (2) Introduction to the role that fluids play in the physical development of active tectonic systems. Discussions will focus on the nature of the processes controlling fluid flow through the Earth s crust and the dynamic interaction of fluid migration and faulting. Prerequisite: ES 101 or equivalent. (S/U grades permitted.) Brown (S)

242. Marine Biotechnology (4) The class will contain lectures discussing current topics and new technologies in the marine sciences (biology, chemistry). Faculty that are part of the marine biotechnology training grant will lecture on their own research and techniques that are being used. The students will select and present a paper that is an application of topics discussed. The areas of genomics, proteomics, expression analysts, mutagenesis, microbial diversity, etc., will be presented. Staff (F)

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. Jackson, 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. Prerequisite: any previous graduate/undergraduate earth science or geology course. Lonsdale (W)

245. Sedimentary Geochemistry for Chemical Paleoceanography (2) Chemical paleoceanography will be the focus, emphasis, on seawater and/or sediment chemical and isotopic records; discussions will concentrate on some of the following istopic systems: Li, B, C, O, S, Sr, and Nd, and on select chemical tracers such as Cd and Ir; on the marine phases that most reliably record seawater chemical and isotope compositions; and on diagenetic problems, how to identify and deal with them. Prerequisite: SIO 260 and consent of instructor. (Offered in alternate years.) (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. Prerequisite: 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.Additionally, at graduate level oral presentation or research paper required. Conjoined with SIO 148. Prerequisite: graduate-level standing or consent of instructor (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)

250. Earth History (4) Geologic history of the Earth including evolution of the oceans, atmosphere, and life s diversity. Major developments and current controversies in Earth history and biological evolution covered in a combination of lecture, student-led discussion of key papers, and weekend field trips. Prerequisite: SIO 101 (or equivalent) or consent of instructor. R. Norris (F)

251. Petrology and Geochemistry of the Solid Earth (4) A geochemical and petrogenetic overview of the Earth and planets. Topics include formation and differentiation of the Earth into core, mantle, crust, and atmosphere/hydrosphere, generation of magma, and isotope and trace element geochemistry 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. Conjoined with SIO 155. Prerequisite: graduate-level standing or consent of instructor. (W)

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. Prerequisite: graduate-level standing or consent of instructor. (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. Bada, Hilton, Wahlen (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. Lal (S)

254. Macroevolution (4) Tempo and mode of evolution with emphasis on the marine fossil record. Large-scale patterns and trends in diversity, speciation, and extinction. Innovation, disparity, and adaptive radiation. Evolutionary turnover and the role of the environment in macroevolution. Additionally, oral presentation or research paper required. Conjoined with SIO 154. Prerequisite: graduate-level standing or consent of instructor. (S)

255. Paleobiology and History of Life (5) 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. Graduate students, additionally, will give oral presentation or research paper. Conjoined with SIO 104. Prerequisite: graduate-level standing or consent of instructor. (S)

256A. Introduction to Field Geology (4) Principles of stratigraphy and structural geology applicable to field geologic studies. Discussion and laboratory exercises. Prerequisites: consent of instructor. Brown (W)

256L. Structural Geology (4) Principles of stratigraphy and structural geology applicable to field geologic studies. Discussion and laboratory exercises. Two to three field trips required. Graduate students, additionally, will complete an in-depth literature-based focused study consisting of a written report and a forty-five-minute seminar on topics related to structural geology. Conjoined with SIO 162. Prerequisite: graduate-level standing or consent of instructor. (W)

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.) Wahlen, Weiss (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, R. Keeling (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: undergraduate chemistry equivalent to UCSD Chemistry 6 sequence, SIO 260. Dickson (S)

262. Seminar in Marine Natural Products (1) Students will give seminars on current research topics in marine natural products chemistry. Prerequisite: consent of instructors. (S/U grades only.) Fenical (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. Prerequisite: undergraduate chemistry equivalent to UCSD 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. Prerequisite: one year general organic chemistry. (S/U grades only). Fenical (F,W,S)

265. Chemical Ecology of Marine Organisms (4) An outline of the organic chemicals from marine organisms with special reference to their function in the marine environment. The differences between terrestrial and marine natural products will be stressed. Prerequisite: basic organic chemistry. Fenical (W)

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. Prerequisite: undergraduate inorganic chemistry and calculus and SIO 210 and SIO 260 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: SIO 210 and 280, or consent of instructor. (S/U grades only.) Checkley (S)

271. Marine Zooplankton (4) 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. Prerequisite: SIO 280 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)

273A. Professional Ethics in Science (2) A seminar on the historical and contemporary ethics and ethos of scientific research, based on published documents. Given in alternate years. Dayton (W)

273B. Science and Marine Environmental Policy (2) Lectures by the instructor, visiting lecturers, and class discussions focusing on how scientists can help policy makers transform scientific understanding into policy. Topics will emphasize conservation, fisheries management, and pollution issues. Given in alternate years. Dayton (W)

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. Prerequisite: consent of instructor; open to undergraduates. (S/U grades permitted.) Levin, Dayton, Sala (W)

275B. Natural History of Coastal Habitats (4) Two three-hour laboratories per week, three four-six day field trips to sites from Mexico to Monterey Bay. Several one-day field trips to local habitats including lagoons, sand and rock intertidal habitats, areas of marine fossils, and areas with migrating birds. Format of course variable depending on student interests. Alternate years with 275A. Prerequisites: open to undergraduates with consent of instructor and completion of BIEB 130, Introductory Marine Ecology. (S/U grades permitted.) Dayton (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. Prerequisite: calculus (three quarters) or consent of instructor. (S/U grades permitted.) Sugihara (F)

277. Deep-Sea Biology (4) The ecology, zoogeography, taxonomy, and evolution of deep-sea organisms, with emphasis on the benthos. Offered alternate years. Prerequisite: consent of instructor. (S/U grades only.) Levin, K. Smith j (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. Prerequisite: bachelor s degree in science or consent of instructor. Franks or Checkley, Levin (F)

281. Environmental Physiology and Biochemistry of Marine Organisms (4) Biochemical mechanisms of adaptation of organisms to the marine environment. Special emphasis is on the effects of pressure, temperature, salinity, oxygen, and light on the physiology and biochemistry. Conjoined with BIBC 130. Prerequisites: adequate training in biochemistry and biology and consent of instructor. Felbeck (F)

282. Phytoplankton Diversity (4) Molecular, biochemical, ecological, and evolutionary perspectives on the diversity of eukaryotic and prokaryotic phytoplankton. Prerequisite: consent of instructor. Palenik (W)

284. Invertebrate Zoology (5) Invertebrate zoology covering all of the major and minor phyla: phylogeny, anatomy, physiology and natural history. Lecture and laboratory demonstrations. Prerequisite: consent of instructors; no audits. Holland (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. Prerequisite: graduate standing or consent of instructor. (S/U grades permitted) Knowlton, Sala and 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. Prerequisite: 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. Prerequisite: consent of instructors. Bartlett, Brahamsha (S)

289. Introduction to Quantitative Marine Ecology and Evolution (4) An introduction to basic questions and problems in quantitative ecology with emphasis on marine organisms: spatial and temporal patterns, population dynamics and the behavior of higher order systems, multispecies populations and communities, and population genetics and life histories. Prerequisites: some undergraduate mathematics and ecology will be assumed; or consent of instructor. Burton, Jackson, Sala, Sugihara

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. Prerequisite: graduate standing. Palenik and Staff (W)

291. Biology Graduate Research Presentations (1) Graduate students in the biological sciences present their research in a seminar or poster format. Class participants and instructors provide written feedback on the presentations. Required of third-year and beyond marine biology curricular group students during spring quarter. Open to all SIO graduate students. (S/U grades only.) Latz (S)

292. Scientific Communication (2) Forms of scientific communication, practical exercise in scientific writing and short oral communication and in criticism and editing; preparation of illustrations, preparation of proposals; scientific societies and the history of scientific communication. Examples from any field of science, most commonly biology, marine biology, ecology, and neuroscience. Prerequisite: graduate status in science. (S/U grades only.) Yayanos, Staff (S)

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. Prerequisite: graduate standing or consent of instructor. Hastings (S)

295. 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. Corequisite: SIO 295L for IGERT and MAS students only. Prerequisite: permission of instructor. Knowlton, Jackson (Su)

295L. Introduction to Marine Biodiversity and Conservation Lab (7) Laboratory work on major biological taxa, field trips on biodiversity in situ, computer labs for informatic tools. Corequisite: SIO 295 for IGERT and MAS students only. Prerequisite: permission of instructor. Knowlton, Jackson (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. Prerequisite: graduate standing. (S/U grades permitted.) Staff (F,W,S)

299. Research (1-12) (S/U grades permitted.) Staff (F,W,S)