Core Biological Oceanography Courses

Biological Oceanography students are expected to complete the following courses in their first year. In addition, all first-year graduate students must complete a research project (minimum of 2 credits as Ocean 600). Acceptable alternatives to Ocean 600 include Ocean 534, summer courses offered by Biological Oceanography faculty at the Friday Harbor Laboratories, Ocean 575, and some laboratory courses offered by other departments and schools on campus (with prior approval from the adviser).

 

OCEAN 530 Biological Oceanography: Bacteria (3) W Bacteria, Archaea and viruses in the marine environment with emphasis on their diversity, activity and physiology. Topics include methods for measuring biomass and activity, the fate of organic carbon in the ocean, the link between the carbon cycle and other biogeochemical cycles, biofilms and hydrothermal vents. John Baross or Jody Deming or Marvin Lilley.

 

OCEAN 531 Biological Oceanography: Phytoplankton (3) W - Phytoplankton in the marine environment, with emphasis on ecology and physiology. Biology, morphology and life cycles; spatial and temporal distributions in coastal and oceanic environments; primary production; nutrient uptake; role in global cycles. Ginger Armbrust.

 

OCEAN 532 Biological Oceanography: Zooplankton (3) Sp - Distribution and abundance of pelagic animals in space and time; analysis of their interactions. Topics include small-scale distributions and behavior, population dynamics and energetics, trophic structure and dynamics, pelagic community structure, models of populations and food webs, secondary production, and biogeography. Bruce Frost or Evelyn Lessard.

 

OCEAN 533 Biological Oceanography: Benthos (3) Sp - Analysis of marine benthos, emphasizing differences from pelagic and terrestrial biota at the individual, population, community and ecosystem levels. Ecologically important physics, chemistry and geology of the benthic boundary layer. Environments include the deep sea, continental shelves, estuaries and the intertidal, focusing on soft substrata. Taxa covered comprise microphytobenthos, heterotrophic bacteria, protists and metazoan invertebrates. Jody Deming.

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Advanced Course Work

Biological Oceanography students beyond their first year of study are required to present one seminar each year in OCEAN 539A (the Biological Oceanography lunch seminar). Master's level students are required to take a minimum of 3 credits of advanced oceanography courses or seminars on specialty topics; doctoral students are required to take at least 3 more oceanography credits. Advanced courses are offered in alternating years and explore subdisciplines of biological oceanography in greater depth than the core courses. Advanced seminars serve the important role of treating current specialized and often interdisciplinary topics; the emphasis is on student presentations. Advanced summer courses are offered at the Friday Harbor Laboratories in some years.

OCEAN 534 Methods and Measurements in Biological Oceanography (2) - Application of laboratory and/or field methods for measurement of biological oceanographic rates and processes to an individual or class project. Faculty.

 

OCEAN 539A Current Theory and Research (1) AWSp - Biological Oceanography lunch seminar. Student presentations on her/his own research or related topic. Each student meets with the instructor prior to and after her/his presentation. Faculty.

 

OCEAN 539B-F Biological oceanography seminar (1-9) - Advanced Biological Oceanography seminars on specialized and often interdisciplinary topics, with an emphasis on student presentations. Faculty.

 

OCEAN 570 Marine Microbial Interactions (1-3) - Structure, function, and dynamics of natural mixed-species populations of marine bacteria and their interactions with higher organisms; synecological and molecular methods including applications to biotechnology and bioremediation; species assemblages in specialized environments, mutualisms, sites and patterns of genetic exchange; biogeochemical interactions.  OCEAN 530 or permission of instructor. John Baross, Jody Deming, Marvin Lilley.

 

OCEAN 571 Marine Phytoplankton Processes (1-3) - Emphasis on biological processes that regulate phytoplankton abundance in the ocean. Molecular/ genetic basis of phytoplankton responses to environmental changes such as variable light intensities, nutrient status. Patterns and mechanisms of marine primary production, including photosynthesis, bio-optics and remote sensing, nutrient utilization and modeling.  OCEAN 531 or permission of instructor. Ginger Armbrust.

 

OCEAN 572 Zooplankton Ecology (1-3) - Current research problems, with emphasis on heterotrophic protists and animals in alternate years. Topics include: life history patterns; distributions and sampling; diversity of form and function; feeding mechanisms and functional responses; bioenergetics; nutrient regeneration; food web interactions and dynamics. OCEAN 532 or permission of instructor. Bruce Frost, Evelyn Lessard.

 

OCEAN 573 Benthic Biological Processes (1-3) - Biological processes characteristic of benthic environments; taxa or trophic groups of particular interest; areas and methods of rapid current progress; open research questions. OCEAN 533 or permission of instructor.  Jody Deming, Marvin Lilley.

 

OCEAN 574 Principles and Applications of Molecular Methods (3) A - Techniques of molecular analysis with emphasis on DNA methods, including PCR, DNA sequencing, RFLP, RAPD and VNTR analysis and cloning. Applications of these techniques to fisheries, aquaculture, oceanography, population and evolutionary studies, and other areas of science. Ginger Armbrust, Paul Bentzen.

 

OCEAN 575 Molecular Techniques (4) Sp - Laboratory on DNA methods. Experiments analyzing genetic variation at the intra- and interspecific level, including one experiment of student's own design. Techniques include DNA extraction and quantitation, PCR, DNA sequencing, RFLP analysis and cloning. Paul Bentzen, Ginger Armbrust.

 

OCEAN 578 Advanced Topics in Biological Oceanography (9) - A special topics course offered during Summer Quarter at the Friday Harbor Laboratories. Faculty.

 

OCEAN 600 Independent Study (1-9)

 

OCEAN 700 Master's Thesis (1-9)

 

OCEAN 800 Doctoral Dissertation (1-9)

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The School Out-Of-Option Requirements

A minimum of 12 credits of numerically graded, 500-level courses, 6 credits of which must be taken as 3-credit courses in two options outside a student's option. The remaining 6 out-of-option credits may be in courses in oceanography (outside a student's option) or in a related science selected at the discretion of the student and supervisory committee. These courses must be completed within the first two years of study. A grade of less than 3.0 in any course will necessitate repeating the course or taking another course in that area as recommended by the student's committee.

Chemical Oceanography Courses

Chemical Oceanography students are expected to complete the following course:

 

OCEAN 520 MARINE CHEMISTRY (3) Autumn - Processes controlling the chemical composition of seawater. Chemical distributions in the ocean, marine physical chemistry, chemical equilibrium and concepts of mass balance. Mechanisms and models used to explain distributions of stable and radioactive isotopes, gases, trace metals, and biochemicals in the world's oceans. Dr. Steven Emerson.

 

Students are required to take three of the following seven courses for a Master's degree; six of the seven must be completed for a Ph.D.

 

OCEAN 521 AQUATIC CHEMISTRY (3) Spring - Application of physical chemistry and thermodynamics to processes that control chemical composition of natural waters. Equilibrium approach. Acid/base chemistry, the carbonate system, dissolution and precipitation, metal ions in solution, oxidation-reduction chemistry, silicate mineral reactions. Prerequisite: 520 or permission of instructor. Dr. James Murray.

 

OCEAN 522 MARINE ORGANIC GEOCHEMISTRY (3) - Sources, reactions, and fates of organic molecules in the marine environment. This course comprehensively covers the major molecular and isotopic constituents of natural organic materials in contemporary aquatic environments and processes which affect their distributions. (Offered alternate years). Dr. Rick Keil.

 

OCEAN 580 AQUATIC KINETICS (3) Spring - The rates of chemical reactions in water and their applications to aquatic environments. The theory of reaction rates and reaction rate catalysis using examples of CO2 hydration; iron, manganese and sulfur oxidation; organic matter degradation; solid calcite and opal dissolution; mineral weathering; and stable isotope fractionation. (Offered alternate years). Dr. Steven Emerson.

 

OCEAN 582 RIVER BASIN BIOGEOCHEMISTRY (3) - How rivers and river basins function in the transport of materials to the oceans and the importance of rivers in the biogeochemical cycles of elements, including origin of water and water routing with drainage basins, sources of dissolved and particulate materials in transport, within river modification of materials in transport, ecological theory, and reactions and transformations occurring in estuarine mixing zones. (Offered alternate years). Dr. Allan Devol, Dr. Jeffrey Richey.

 

OCEAN 583 ISOTOPE BIOGEOCHEMISTRY (3) - A The use of stable isotopes to study biogeochemical cycles in the oceans and atmosphere; specifically carbon, nitrogen, and sulfur cycles. Isotopic effects during photosynthesis, respiration, organic matter degradation, CaCO3 dissolution, methanogenesis, nitrification/denitrification, and sulfate reduction. (Offered alternate years). Dr. Paul Quay.

 

OCEAN 584 OCEAN Tracers and MIXING (3) Sp - Distribution of natural and bomb-produced radioactive tracers in the ocean. Application of models used to derive information concerning time scales of (1) gas transfer at the water atmosphere interface; (2) whole ocean, thermocline, and deep-ocean water circulation; and (3) particulate settling in the marine environment. Knowledge of elementary differential equations suggested. (Offered alternate years). Dr. Mark Warner.

OCEAN 588 THE GLOBAL CARBON CYBLE AND CLIMATE (3) W - Oceanic and terrestrial biogeochemical processes controlling atmospheric CO2 and other greenhouse gases. Records of past changes in the earth's carbon cycle form geological, oceanographic and terrestrial archives. Anthropogenic perturbations to cycles. Develop simple box models, discuss results of complex models. Dr. Steve Emerson and Lyatt Jaegle.

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Seminars

There is a weekly seminar in Chemical Oceanography. Students are required to attend and encouraged to present the results of their research after their first two years. In addition, courses on special topics of interest are offered as OCEAN 529, Seminar in Chemical Oceanography.

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The School Out-of-Option Requirements

A minimum of 12 credits of numerically graded, 500-level courses, 6 credits of which must be taken as 3-credit courses in two options outside a student's option. The remaining 6 out-of-option credits may be in courses in oceanography (outside a student's option) or in a related science selected at the discretion of the student and supervisory committee. These courses must be completed within the first two years of study. A grade of less than 3.0 in any course will necessitate repeating the course or taking another course in that area as recommended by the student's committee.

 

Chemical Oceanography students are also encouraged to have a mathematical background through partial differential equations (equivalent to Applied Math 351/353 or 401/402) and a strong background in physical, inorganic or organic chemistry.

Physical Oceanography Courses

Physical Oceanography graduate students are expected to complete the following courses:
OCEAN 500 Current Problems in Oceanography (1) Autumn - An introduction to Physical Oceanography faculty and facilities. For First Year Physical Oceanography Students.

 

OCEAN 510 PHYSICS OF OCEAN CIRCULATION (3) Autumn - Structure of ocean basins; physical properties of seawater and the equation of state; heat, salt, and fresh water budgets; Coriolis effect and geostrophic balance; major current systems and water masses; mixing and stirring in the ocean; modern experimental methods in physical oceanography.

 

OCEAN 511 PHYSICAL FLUID DYNAMICS (3) Autumn - The fundamentals of fluid mechanics, as a basis for understanding problems in geophysical fluid dynamics. Topics include: Cartesian tensors, derivation of the Navier-Stokes equation, Bernoulli's equation and potential flow, dimensional analyses, introduction to mathematical approximation techniques, flows with rotation, effects of density stratification.

 

OCEAN 512 GEOPHYSICAL FLUID DYNAMICS I (3) Winter - Small and medium-scale dynamics of rotating stratified fields, including a compact treatment of introductory fluid mechanics. Observed properties of oceanic and atmospheric circulation. Equations of motion on a rotating Earth. Free particle on a rotating sphere. Ideas of buoyancy and pressure. Scale analysis for geostrophic, hydro-static flows. Vorticity principles. Thermal wind balance, velocity spirals. Geostrophic adjustment under gravity. Equations for gravity and inertial waves. Wave propagation theory: stationary phase, group velocity, refraction and scattering. Wave guides (the equator, coasts, and thermocline) and wave breaking. Action and energy principles. Molecular diffusion and mixing.

 

OCEAN 513 GEOPHYSICAL FLUID DYNAMICS II (3) Spring - Theories, models of large-scale dynamics of oceans, atmospheres. Potential vorticity, Q principles; Rossby waves, ray tracing, Green's function, setup of general circulation; atmospheric "channels" versus ocean "basins"; wave-mean flow interaction, mountain drag, internal momentum flux; "Lagrangian" motion of particles, tracers; cascades, eddy flux of heat, moisture, Q. Prerequisite: OCEAN 512.

 

OCEAN 514 WAVES (3) Winter - Wave kinematics: phase and group velocity, dispersion; governing equations. Waves in a homogeneous ocean: the Laplace Tidal Equations, including long gravity waves, Sverdrup-Poincare waves, coastal Kelvin waves, topographic Rossby waves, and planetary Rossby waves. Waves in a density-stratified ocean: equivalent depth and the vertical and horizontal structure equations; internal inertia-gravity waves including WKBJ scaling for variations in stratification, consistency and amplitude-energy relations, reflection properties, and Garrett-Munk synthesis; wind forcing; and equatorial waves. Waves in a spatially-varying ocean: turning points, ray tracing in a current, wave action flux conservation, and wave-mean flow interaction.

 

OCEAN 515 OCEAN CIRCULATION: OBSERVATIONS (3) Spring - A summary of the state of modern, large- and mesoscale physical oceanographic observations. The emphasis will be on the interpretation of observations in terms of contemporary theories of ocean circulation. Topics to be covered include:

1. The spectrum of temporal variability in the ocean, from periods of minutes to years; spectral characteristics of relevant variables and the kinematic relations linking them.

2. Eddies and eddy fluxes; the importance of eddies to momentum, heat, and property fluxes in the global ocean circulation.

3. Thermocline ventilation as a mechanism for transporting properties from the ocean surface into the deep sea; advection-diffusion scenarios operative in the ocean.

4. Determining the ocean circulation - what is the optimum mix of observational resources necessary for determining the global circulation with acceptable error?

Prerequisite: OCEAN 510 or permission of instructor.

 

OCEAN 517 METHODS & MEASUREMENTS IN PHYSICAL OCEANOGRAPHY (2) Autumn (Alternate years) - The principal instruments and experimental methods of modern Physical Oceanography. Devices and systems to measure pressure, temperature, electrical conductivity, sea state and velocity will be discussed in the classroom, and complete systems will be examined/operated in the laboratory

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Applied Mathematics Courses

Physical Oceanography students are expected to take a sequence of three courses in Applied Mathmatics.

AMATH 568 Methods of Applied Mathematics II (5) Winter

AMATH 581 Mathematical Problem Solving Using Computers (5) Autumn

ATM S 552 Objective Analysis (3) Winter

 

Other courses, depending on the background and interests of the student, can be substituted. Examples:

For AMATH 568, AMATH 402 (taught at a lower level).

For AMATH 581, AMATH 569 (taught more analytically) or

For ATM 552, AMATH 403

 

There are a variety of courses that would give students exposure to data analysis techniques. These include:

AMATH 506 Applied Probability Statistics (4)

AMATH 584 Applied Linear Algebra and Introductory Numerical Analysis (5)

E E 505 Probability and Random Processes (4)

E E 520 Spectral Analysis of Time Series (4)

OCE 569 Time series analysis (3)

OCE 569 Combining Models and Data in Climate and Ocean Circulation Studies

 

For students with a poor math background, a course that can be taken the summer before starting graduate school is AMATH 351 Introduction to Differential Equations and Applications (3)

 

An introductory course on probability and statistics would also be beneficial for many of our students and the one recommended is Q SCI 482 Statistical Inference in Applied Research (5)

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Seminars for Advanced Students

OCEAN 569 seminars are offered each quarter and are intended to give students a wide perspective on many specialized facets of the practice of physical oceanography. Most are offered in alternate years, or even more sporadically, so it is recommended that all students beyond their first year regularly sample these offerings in order to gain as much breadth as possible in physical oceanography. Recent and scheduled seminars include:

 

GFD Laboratory Models, Dr. Rhines	Coastal Processes, Dr. Hickey
Internal Wave Interactions, Dr. Kunze	Abyssal Circulation of the Ocean, Dr. Riser
Tropical Oceanography, Dr. Eriksen	Ocean Mixing Processes, Dr. Gregg
Remote Sensing/Satellite Oceanography, Dr. Martin	Circulation of Puget Sound, Dr. Gregg
Geophysical Fluid Dynamics III, Dr. Thompson	Polar Oceanography, Dr. D'Asaro
Numerical Modeling, Dr. Kawase	Ocean Tracers, Dr. Warner
Time-Series Analysis, Dr. Eriksen	Upper Ocean Processes, Dr. Kunze
Estuarine Circulation & Mixing, Drs. Gregg & MacCready	Lagrangian Methods in Oceanography, Dr. Riser

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The School Out-of-Option Requirements

A minimum of 12 credits of numerically graded, 500-level courses, 6 credits of which must be taken as 3-credit courses in two options outside a student's option. The remaining 6 out-of-option credits may be in courses in oceanography (outside a student's option) or in a related science selected at the discretion of the student and supervisory committee. These courses must be completed within the first two years of study. A grade of less than 3.0 in any course will necessitate repeating the course or taking another course in that area as recommended by the student's committee.

Marine Geology & Geophysics Courses

OCEAN 540 Marine Geological Processes (3) Winter - Principles of thermodynamics, heat and mass transfer, fluid mechanics, continuum mechanics and time-series analysis applied to marine geological and geophysical data. Applications to thermal balance of the oceanic lithosphere; Pleistocene sedimentation and global climate change; sediment transport in high energy environments. (McDuff, Heath)

 

OCEAN 541 Marine Sedimentary Processes (3) Spring - Erosion, trans­portation and deposition of sediment in estuarine, beach, conti­nental shelf and slope, and deep sea environments. Development of equations characterizing boundary shear flows, initiation of grain motion, bedload and suspended load transport. Evaluation of primary bed forms, processes of sediment accumulation, and measurement techniques. Prerequisite: permission of instructor.

 

OCEAN 544 Geochemical Evolution of Oceanic Lithosphere (3) Autumn - Chemical principles of magmatic evolution and hydrothermal interaction as they apply to the formation and evolution of the oceanic lithosphere. Comparisons of theoretical models with field studies conducted using submersibles and deep ocean drilling.

 

OCEAN 545, 546 Physics of the Oceanic Lithosphere I, II (3,3) Winter - The physical processes responsible for the formation and evolution of the oceanic lithosphere. Thermodynamic mechanisms of mantle creep; fluid dynamics of mantle flow; decompressional melting; formation of oceanic crust; and cooling of the oceanic lithosphere. Prerequisite: GPHYS 501.

 

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Seminars

OCEAN 549A, the weekly seminar in Marine Geology & Geophysics is required and, after their first year, students are encouraged to present the results of their research. In addition, seminars on specialized facets of the field are offered to give students a wide perspective.

 

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The School Out-of-Option Requirements

A minimum of 12 credits of numerically graded, 500-level courses, 6 credits of which must be taken as 3-credit courses in two options outside a student's option. The remaining 6 out-of-option credits may be in courses in oceanography (outside a student's option) or in a related science selected at the discretion of the student and supervisory committee. These courses must be completed within the first two years of study. A grade of less than 3.0 in any course will necessitate repeating the course or taking another course in that area as recommended by the student's committee.

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Lithosphere and Mantle Dynamics

GPHYS 501 GEOPHYSICAL CONTINUUM MECHANICS (3) Autumn - Analysis of stress, finite and strain. Measurement and interpretation of strain in geological materials. Elasticity applied to determine stress in the earth's lithosphere. Creep of solids and flow of geological materials.

GPHYS 502 SEISMOLOGY (3) Winter - Theoretical and observational seismology. Elastic plane wave propagation through stratified media. Surface waves, eigenvibrations, ray theory. Structure of the earth's mantle and core. Seismicity distributions, earthquake focal mechanisms and relationship to tectonics.

GPHYS 503 GEOPHYSICS: THE EARTH (3) Spring - Study of gravity, magnetism, heat flow, seismology. Earth's outer structure, studied through unifying concepts of plate tectonic theory. Quanitative approaches to problems, using techniques of classical physics.

GPHYS 504 GEOPHYSICS: FLUIDS (3) Autumn - Geophysical fluid dynamics. Fluids in geophysics with emphasis on the oceans. Development of the equations of motion with examples drawn from oceanography and solid earth geophysics.

CHEM 456 PHYSICAL CHEMISTRY (3) Autumn/Winter/Summer - Chemical thermodynamics. Laws of thermodynamics presented with applications to phase equilibria, chemical equilibria, and solutions.

 

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Applied Mathematics Courses

Students are required to complete an Applied Mathematics sequence, such as AMATH 401, 402, and 403.

 

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Advanced Course Work

Students are encouraged to take advance non-seminar 500-level courses, at least one in Geophysics and one in Geology. In addition, students are strongly encouraged to take the following advanced courses:

UNIVERSITY OF WASHINGTON SCHOOL OF OCEANOGRAPHY

 

OCEAN 550 GEOCHEMISTRY AND GEOPHYSICS OF MELT GENERATION (3) Autumn - Mantle flow beneath mid-ocean ridges and hotspots, major element systematics, constraints from trace elements and isotopes on melting and mantle reservoirs, melt extraction, and crustal thickness and axial topography. Prerequisites: OCEAN 544 or permission. Offered alternate years.

OCEAN 551 MARINE SEISMOLOGY (3) - The practical application of seismic techniques to the study of the ocean basins; analysis of refraction data, multichannel reflection profiling, surface wave studies, and earthquake analysis. Prerequisites: GPHYS 502 or permission of instructor. Offered alternate years.

OCEAN 552 SEMINAR IN GEOPHYSICAL AND GEOLOGICAL DATA ANALYSIS (1) Spring - Practical geophysical data analysis, map projections, gridding, multibeam bathymetry processing, gravity and magnetic anomalies, downward continuation, magnetic inversion, seismic refraction and reflection, and microearthquake locations. Prerequisite: permission.

OCEAN 559 ADVANCED SEMINAR ON MID-OCEAN RIDGE PROCESSES (1-9) - Lectures, discussions, and practical work on selected topics of current interest in mid-ocean ridge research. Prerequisite: permission.

 

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Marine Sediment Dynamics

Students are expected to complete the following courses:

OCEAN 540 MARINE GEOLOGICAL PROCESSES (5) Winiter - Principles of thermodynamics, heat and mass transfer, fluid mechanics, continuum mechanics and time-series analysis applied to marine geological and geophysical data. Applications to thermal balance of the oceanic lithosphere; Pleistocene sedimentation and global climate change; sediment transport in high energy environments.

OCEAN 511 PHYSICAL FLUID DYNAMICS (3) Autumn (and other) - Fundamentals of fluid dynamics: Cartesian tensors, derivation of the Navier-Stokes equation, Bernoulli's equation and potential flow, dimensional analyses, introduction to mathematical approximation techniques, flows with rotation, effects of density stratification. OCEAN 452 PRINCIPLES OF SEDIMENT TRANSPORT BY TURBULENT FLOW (3) SP Theoretical and experimental tech-niques for studying erosion, transportation, and deposition of sediment. Initial motion of sediments, bed-load motion, suspension of sediment by turbulent flows, erosion and deposition of sediments.

Students are encouraged to consider these recommended courses:

GEOL 565 INTERPRETATION OF SEDIMENTARY STRUCTURES (2-4) - Physical and environmental analysis of sedimentary structures, including biogenic sedimentary structures, and clastic sediments and rocks.

OCEAN 514 WAVES (3) Winter - Application of marine hydrodynamic principles to wave motion in the ocean.

ME 543 FLUID TURBULENCE (3) - Methods of characterizing fluid turbulence; spatial, temporal velocity correlations; energy spectra; probability concepts; isotropic, nonisotropic turbulence; hot-wire measurement techniques; phenomenological turbulence models; higher-order closure models; and local equilibrium concepts.

OCEAN 569 TIME SERIES ANALYSIS (3) - Oceanographic time-series analysis: Fourier transforms and series, sampling, convolution, filtering, estimation of spectra and coherences and their associated confidence intervals, admittance function, empirical orthogonal functions, and frequency-wavenumber estimation.