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2014 - 2015 Graduate Catalog [ARCHIVED CATALOG]
SMS: Course Descriptions
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School of Marine Science
MSCI 501A - Fundamentals of Marine Science, Physical Oceanography
Fall (2) Brubaker
This course provides an introduction to the various types and scales of motion in the ocean, the global heat budget, major water masses, and processes controlling distributions of temperature and salinity. Discussions on phenomena associated with water motion will include global circulation, wind-driven circulation in ocean basins, tides, coastal upwelling, storm surge, waves, turbulence, and circulation in estuaries. Underlying dynamics governing water motion will be presented, elucidating the role of the rotation of the earth. The El Nino/La Nina oscillation will be examined as a key example of large-scale ocean-atmosphere interactions.
MSCI 501B - Fundamentals of Marine Science, Chemical Oceanography
Fall (2) Beck
This course presents an overview of the chemistry of estuaries and the ocean including chemical processes that occur in marine sediments and at the air/sea interface. Discussion topics will include the chemical properties of seawater, chemical equilibrium and kinetics, the seawater carbonate system and ocean acidification, the global and oceanic carbon and nitrogen cycles, ion speciation, trace metals, and nutrients, sediment diagenesis, and fundamentals of radioisotope and stable isotope biogeochemistry. Interdisciplinary applications are emphasized.
MSCI 501C - Fundamentals of Marine Geology
Fall (2) Hein
This course provides an introduction to the major topics of marine geology without expecting the student to have a background in geology. The course addresses the age and internal structure of the earth, the processes of plate tectonics including the formation of oceanic crust, seamounts, hydrothermal vents, the characteristics and classification of sediments and the distribution of sediments in the deep sea. Also addressed are the interrelationships among and importance of paleoceanography, climate change, and sea-level change, and the processes and characteristics of various marine, estuarine, and coastal sedimentary environments. The course includes discussion of various types of field equipment and logistics and of some economic and societal implications.
MSCI 501D - Fundamentals of Marine Science, Biological Oceanography
Fall (2) Steinberg
This course examines the biology and ecology of marine organisms and how they interact with their environment. Topics include the organisms and their behavior, distribution, and underlying physiology; effects of biology on elemental and nutrient cycles and visa versa; and ecosystem structure and ecological interactions. An interdisciplinary approach will be taken, as biology both depends on and influences ocean chemistry, physics, geology, and climate. The course will emphasize open ocean, pelagic systems, but will include many examples from coastal and estuarine systems, as well as shallow and deep-sea benthic ecosystems.
MSCI 501E - Fundamentals of Environmental Chemistry, Toxicology and Pathobiology
Fall (2) Van Veld, Vogelbein
This course emphasizes ongoing and emerging environmental concerns in the Chesapeake Bay and world ocean. Lectures will address basic concepts and mechanisms of contaminant chemistry and toxicology, infectious and noninfectious diseases in aquatic organisms. Case histories will be used to illustrate sources, fate and effects of anthropogenic chemical contaminants, and the important role of environmental change on disease in marine and estuarine ecosystems.
MSCI 501F - Fundamentals of Marine Fisheries Science
Spring (2) Fabrizio, Graves
This lecture course is intended for SMS students outside of the Department of Fisheries Science and will introduce the principles and techniques of fishery science. Lecture topics will include the theory and impacts of fishing, description and status of international, North American and regional fisheries, fisheries oceanography, recruitment processes, single-species and ecosystem-based approaches to stock assessment, and fisheries management, and the goals and problems of sustaining an open-access common pool resource.
MSCI 503 - Interdisciplinary Research in Estuarine and Coastal Systems
Spring (2) Brush
This is an interdisciplinary, field-based laboratory course applying concepts from MSCI 501 to a semester-long study of the estuarine and coastal environments of the lower Chesapeake Bay and Virginia’s Eastern Shore. The course is designed to expose students to today’s typical interdisciplinary research process from project conception through presentation of results. Students will organize into crossdisciplinary groups around a particular study site and research topic, and develop and implement a scientifically sound, hypothesis-driven research plan through a series of group cruises and instrument deployments. Particular emphasis will be placed on spatial and temporal patterns of biotic and abiotic processes and their interactions, along with sample design, collection, analysis, and interpretation of data. Students will also be exposed to utilizing historical and ongoing databases as well as synthesizing data from each group member to create an interdisciplinary story. The course culminates with oral presentations and a group poster.
MSCI 504 - Fundamentals of Statistical Methods and Data Analysis
Spring (4) Newman
In this course, students are introduced to the fundamental statistical methods commonly used for analysis of biological and ecological data. Topics include describing data, probability distributions, statistical inference, hypothesis testing, elementary experimental design, analysis of variance, and regression and correlation. The introductory aspects of categorical data analysis and multivariate techniques will also be covered. Course content will be integrated with a weekly laboratory session using the statistical computing language R.
MSCI 506 - Scientific Communication Skills
Spring (2) Hilton, Steinberg
The important elements of oral and written presentation skills for communicating scientific research will be reviewed in this course. The course addresses topics such as the critical evaluation of literature, development of scientific questions and rationale for research, and formulation of conceptual models for developing high-quality scientific research projects. Oral and written presentation skills are emphasized through written exercises and class presentations, with peer review.
MSCI 507 - Responsible Conduct of Research
Fall (1) Schaffner
Students will discuss responsible research and scholarly practices and develop an ability to recognize ethical choices for informed decisions based on key principles of research integrity. Class attendance and completion of VIMS CITI RCR modules are required. Grading is pass/fail.
MSCI 515A - Biological Sciences Seminar
Spring (1) Staff Graded Pass/Fail
The departmental seminar course offers a multidisciplinary review of significant areas of marine science. Guest speakers will present a variety of views, and course participants will organize and present talks related to the seminar theme.
Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
MSCI 515B - AHS Dept Seminar
Fall and Spring (1) Staff Graded Pass/Fail
The departmental seminar course offers a multidisciplinary review of significant areas of marine science. Guest speakers will present a variety of views, and course participants will organize and present talks related to the seminar theme. Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
MSCI 515C - Fisheries Science Seminar
Spring (1) Staff Graded Pass/Fail
The departmental seminar course offers a multidisciplinary review of significant areas of marine science. Guest speakers will present a variety of views, and course participants will organize and present talks related to the seminar theme. Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
MSCI 515D - Physical Sciences Seminar
Fall and Spring (1) Staff Graded Pass/Fail
The departmental seminar course offers a multidisciplinary review of significant areas of marine science. Guest speakers will present a variety of views, and course participants will organize and present talks related to the seminar theme. Students may repeat seminar registration as required by their respective departments; however, only two (2) credits will be applicable to an SMS degree.
MSCI 520 - Principles of Coastal and Ocean Dynamics
Spring (3) Brubaker, Friedrichs, Maa, Wang
Following a review of the governing equations, the lectures and discussions of this course will survey key dynamics of circulation and waves in ocean, shelf and in estuarine environments. Topics to be covered include fundamentals of wind and density-driven flow, and aspects of fronts, mixing and secondary circulation. Time-dependent motion such as surface gravity waves, internal waves, and coastally trapped waves and tides also will be discussed.
MSCI 522 - Principles of Geological Oceanography
Fall, even years (3) Staff
A brief review of the tectonic history of the oceans will be presented in this course, followed by detailed study of the ocean margins, including sea-level history and near shore geological processes in the coastal zone and continental shelf regions. The geological effects of bottom currents on ocean sediments will be examined along with ocean basin sediment history and approaches to pale oceanography.
MSCI 524 - Principles of Chemical Oceanography
Spring (3) Beck, Canuel Prerequisite(s): Instructor’s consent
This course covers in a comprehensive and integrated manner the important factors controlling the chemical composition of seawater. Basic principles of chemical thermodynamics will be applied to the seawater medium and will serve to introduce contemporary, global-scale chemical processes such as the role of the oceans in global climate change. Selected topics include distributions of the bio limiting elements; chemistry of marine sediments; trace metal chemistry; marine organic chemistry; and ocean-atmosphere interactions.
MSCI 526 - Principles of Marine Ecology
Spring, odd years (3) Staff
The course covers the fundamental processes underlying structure and functioning of marine ecosystems, both pelagic and benthic, and application of those principles to understanding responses of marine ecosystems to anthropogenic and natural global change. Lectures, readings and discussion will emphasize physical processes supporting primary production, planktonic and benthic dynamics, distribution and functional importance of marine biodiversity, biotic interactions structuring communities, and food web structure. The course concludes with a survey of the major marine ecosystem types. A central part of the course involves design, writing, reviewing, and panel discussion of student research proposals.
MSCI 527 - Coastal Botany
Fall (3) Perry
A botanical and ecological survey of vascular plant communities of the mid-Atlantic coastal plain is presented in this course. Discussion topics include the common and important terrestrial, emergent and aquatic vascular plant species of the coastal plain tidal marshes, swamps, beaches, dunes, maritime forests and submerged aquatic communities of the mid-Atlantic coastal regions as well as their strategies for survival in these coastal habitats. The course consists of field trips as well as both laboratory and lectures sessions.
MSCI 528 - Marine Fisheries Science
Spring (3) Fabrizio, Graves
This course focuses on the principles and techniques of marine fisheries science, including the theory of fishing, age and growth, definition of stocks, catch statistics, description of world fisheries, and goals and problems in managing a common property resource. Students will participate in lectures, laboratory exercises, and field trips.
MSCI 529 - Fish Physiology
Spring, odd years (3) Brill
This course is intended for students interested in incorporating physiological principles and techniques into projects addressing questions in ecology, fishery biology and environmental assessment. It will emphasize basic concepts to make physiological jargon and the published literature understandable.
MSCI 530 - Microbial Processes in a Changing Coastal Environment
Fall (2) Anderson, Reece
The course will address current topics and societal concerns in coastal and estuarine systems including microbial responses to eutrophication, harmful algal blooms, nutrient enrichment, and roles of bivalve-dominated systems, marshes, seagrasses, groundwater, and photic sediments on microbial nutrient cycling. Cross-listed with BIOL 404 and MSCI 404
MSCI 548 - Technical and Continuing Education in Marine Science
Fall, Spring and Summer (1-3) Staff Prerequisite(s): Instructor’s consent
This course provides graduate-level instruction to public school teachers and other professionals who require postgraduate certification or special training. Courses are offered on an occasional basis as demand warrants. Instructors or faculty team members identify a client group and formulate a course description that serves individual professional needs. An example of a course offered recently is experimental design in the marine science laboratory, a lecture and laboratory course for science teachers that addressed standards of learning in Virginia. Courses may include lecture and laboratory components, field trips and demonstrations.
MSCI 550 - Rivers: Processes and Problems
Spring, odd years (3) Canuel, Hein
Rivers form the main link between land and the ocean, discharging more than 35 thousand km3 of water and more than 20 billion tons of suspended and dissolved solids annually to the global ocean. Three central themes are stressed: 1) How do rivers work: the hydrologic cycle and water budget, basin character, physical and chemical erosion; 2) Temporal and spatial variations, ranging from seasonal to millennial, with particular emphasis on catastrophic events; 3) Human interactions: land degradation, river management, future impact of climatic change and anthropogenic activities. Includes a one-week field trip.
MSCI 553 - Introduction to Benthic Boundary Layers and Sediment Transport
Fall, even years (3) Friedrichs, Harris
This course addresses the physical and geological aspects of coastal and estuarine benthic boundary layers, their dynamic forcing and the associated suspension and transport of sediments. Principles of waves, tides and currents are introduced with emphasis on shall-water processes. Boundary layer structure and shear stress on the seabed, wave boundary layers and turbulence are considered in relation to the coastal environment. Forces on sediment particles, initiation of sediment movement and principles of sediment transport are treated at an intermediate level.
MSCI 554 - Principles of Numerical Computing
Spring (3) Harris, Wang
This course provides students in the marine sciences with the tools needed to pursue study and research using numerical methods. It will enable them to write programs to solve fairly complex problems, to explore and understand the current literature in which numerical methods are used. Topics include principles of floating-point computation, interpolation, linear and non-linear systems of equations, numerical integration, ordinary and partial differential equations, and optimization. Emphasis is placed on finite difference solutions to conservation of mass and momentum equations. The course consists of three lecture hours per week, assigned problems using MATLAB, and a term project in a topic chosen by the student.
MSCI 559 - Parasitology
Spring, odd years (3) Shields
Recommended:Invertebrate Zoology or comparable course. This course covers the biology and ecology of protozoan, helminth and crustacean parasites. Focus is on parasites of medical and veterinary importance. Emphasis is placed on life cycles, pathology, control methods and ecological impacts of parasitic infections. Three lecture and three laboratory hours. Cross-listed with (Bio 404 and BIOL 504 )
MSCI 560 - Fundamentals of Ecotoxicology
Spring (3) Newman Prerequisite(s): Basic Ecology
This course is an introduction to ecotoxicology, the science of contaminants in the biosphere and their effects on constituents of the biosphere, including humans. The course provides a general survey of environmental toxicology and risk assessment from an ecological vantage. Cross-listed with BIOL 404
MSCI 562 - Water Pollution
Fall (2-3) Hale
This course will introduce students to processes impacting aquatic environments. Emphasis will be on pollution by man-made chemicals and metals. Additional topics include consequences of excessive nutrients, habitat modification and introduction of exotic or elimination of native species. Students have the option to register for 2 credit hours (lecture only) or 3 credit hours (lecture with an in-class student presentation).
MSCI 563 - Environmental Chemistry
Spring (3) Unger
The fundamental physical, chemical and biological processes controlling the fate of major classes of aquatic contaminants are covered in this course. Topics such as photolysis, biodegradation, sorption and redox chemistry are examined to elucidate the mechanisms controlling chemical degradation and transport. Case studies are used to show how these basic research principals can be integrated and applied to solve real word environmental problems.
MSCI 564 - Aquatic Toxicology
Spring (3) Van Veld
This course will present factors influencing the fate and behavior of major environ-mental toxicants in aquatic organisms and mechanisms involved in their uptake, distribution, biotransformation and clearance. Topics of discussion will include the effects of toxicants on aquatic organisms ranging from effects at the biochemical and cellular level, to effects on individuals, populations and communities. Current methods of laboratory and field toxicity testing will be addressed.
MSCI 565 - Principles of Pathobiology
Spring (3) Vogelbein, Carnegie, Wargo
This course focuses on the molecular and cellular mechanisms of pathogenesis in important emerging diseases in the medical, veterinary, and aquacultural fields. Students will learn how current molecular and cellular techniques are being applied to the resolution of a variety of infectious and non-infectious diseases. Mammalian models provide a foundation for application to the diseases of fish and shellfish.
MSCI 566 - Diseases of Marine Organisms
Fall, odd years (4) Wargo, Shields
This course includes identification, life histories, pathology, and control of important infectious disease agents of fish and shellfish including viruses, bacteria, protists, helminths and arthropods. Also covered will be general principles of disease in the marine and estuarine environment. Three lecture and three laboratory hours.
MSCI 567 - Comparative Immunology
Fall, odd years (3) Kaatari Note: Some familiarity with biochemistry and genetics recommended.
This lecture course focuses on the immunology of teleost and elasmobranch fish. Topics include the biochemistry of antibody function, the molecular and cellular basis of the immune response, the role of innate and adaptive immunity in disease resistance, aquacultural vaccine design, development, and application, immunopathology, immunodeficiencies, and immunotoxicology.
MSCI 575 - Aquatic Microbial Ecology
Fall, odd years (3) Anderson, Song Note: Organic chemistry or biochemistry recommended.
This course provides an introduction to the role that microorganisms play in the biogeochemical cycling and production of dissolved and particulate inorganic and organic matter in freshwater and marine ecosystems. The approach will be ecological, relating environmental physiochemical properties to regulation of microbial processes, distributions, and biodiversity. Topics will include state of the art methods for detecting distributions, biomass, and activities of microorganisms in the natural environment, the energetics regulating microbial processes, microbial biochemical pathways, biodegradation, microbial interactions, and the role that microorganisms play in the food webs of various ecosystems. Although emphasis will be placed on marine systems, processes in lacustrine, riverine, and groundwater ecosystems will also be discussed. Readings will draw heavily on the primary literature.
MSCI 576 - Evolutionary Ecology
Fall, even years (3) Duffy
This course presents a conceptual and empirical exploration of interactions between environment and evolution of organismal structure, function, and behavior in deep time through contemporary ecological time scales. Topics include natural selection and adaptation, sexual selection and mate choice, evolution of life histories, speciation, coevolution, human evolutionary ecology, and evolutionary responses to human-induced environmental change. Reading, discussions and writing projects draw from the primary literature, concentrating on examples involving marine organisms.
MSCI 579 - Wetlands Ecology
Fall (4) Chambers, Perry Prerequisite(s): Instructor’s consent
Structural and functional attributes of tidal and non-tidal wetlands are examined in this course, with emphasis on analysis of wetland systems at the landscape and community level. The course provides and introduction and practical experience in common research techniques, including wetland classification, vegetation mapping, functional assessment models, and field sampling techniques. Individual research projects and/or a paper will be expected. The course includes lectures and field trips. Cross-listed with (BIOL 427, BIOL 627 )
MSCI 580 - Asian Environmental Issues of the 21st Century
Spring (3) Perry, Smith
This purpose of this course is to provide students with a working knowledge of past, current, and future environmental issues in East Asia in relation to societal, economic, and regulatory structures. Emphasis will be placed on large-scale environmental issues that impact ecological, social, and economic processes. Students will be expected to assimilate the course material into hypothetical development of future East Asian and global environmental policies. Grading will be based on a presentation, written mid-term prospectus, and final term paper on an individual environmental topic. Cross-listed with ENSP 440-02.
MSCI 583 - Molecular Genetic Data Analysis, Bioinformatics
Spring, even years (3) Reece, McDowell
This is a lecture and largely computer-based laboratory course covering the principles and practice of analyzing and interpreting population genetic, phylogenetic and genetic mapping datasets. Molecular data sets including sequences and genotypic profiles will be generated on agarose gels or the automated sequencers/ gel scanners. Data will be exported and processed for analysis by the appropriate suite of computer software programs. Software to be utilized include DNA sequence analysis, genotyping, population genetic, sequence alignment, phylogenetic, and mapping programs. Phylogenetic programs will include those based on genetic distance, maximum parsimony, maximum likelihood and Bayesian analyses. Population genetics programs include those such as GenePop to perform standard population genetic statistical analyses, Arlequin for doing AMOVAs, and STRUCTURE for doing assignment testing.
MSCI 599 - Thesis
Fall, Spring and Summer (1-9) Major or Co-Major Advisor(s)
This is the avenue for original research in biological, chemical, geological and physical oceanography, environmental science, marine fisheries science and marine resource management. The master’s project is chosen in consultation with the student’s major professor and the Associate Dean of Academic Studies.
MSCI 610 - Effects of Global Change on Modern Marine Systems
Fall (2-3) Canuel, Smith
The course will explore the recent literature highlighting effects of climate and global change on various aspects of marine systems including (but not limited to) biogeochemical cycling, ecosystem structure and function, alterations in ocean chemistry, and physical processes such as polar and glacial ice melting, ocean circulation and sea level rise. The course is designed as a 2-credit course. Students will be evaluated primarily on the basis of the quality and organization of the class discussion they lead (including a short introductory background presentation), as well as participation in all other class discussions. In addition, a short (5 pages) critical writing assignment assessing the effectiveness of one or more recently published papers on impacts of global change in marine systems will be required. A 3-credit option may be made available to students who wish to undertake more detailed independent study of a particular topic in the form of additional readings and a research term paper.
MSCI 611 - Estuarine Hydrodynamics I
Spring, even years (3) Wang Prerequisite(s): MSCI 520
This course examines classification of estuaries, time scales of motions, tidal dynamics in estuaries, non-tidal circulation, mechanism of arrested salt wedge, gravitational circulation, diffusion induced circulation and turbulence in stably stratified flows.
MSCI 612 - Estuarine Hydrodynamics II
Fall, even years (3) Wang Prerequisite(s): MSCI 611
The content of the course includes zero-, one- and two-dimensional descriptions of estuaries, salt intrusion, and pollutant flushing sediment transport through estuaries, field experience in estuaries and model laws for estuarine models.
MSCI 615 - Hydrodynamic Modeling of Estuarine and Coastal Waters
Spring (3) Wang Prerequisite(s): MSCI 520 or Instructor’s consent
This course will survey numerical methods for the solution of partial differential equations describing the estuarine and coastal water motion and transport. Topics include stability, accuracy, consistency and convergence analysis of numerical scheme, formulation of primitive and scalar transport equations, and the pre- and post-processing for numerical computational models. The course will involve classroom lectures, seminar readings, and application of models for operational environmental prediction.
MSCI 617 - Estuarine Water Quality Models
Fall, odd years (3) Staff Prerequisite(s): MSCI 611
This course examines the principles of mass balance, physical transport processes, diffusion and dispersion in estuarine environments. Water quality processes, representation of biochemical transformations, dissolved oxygen modeling and survey of available models are other topics of discussion.
MSCI 624 - Ocean Waves: Theory, Measurement and Analysis
Fall, even years (3) Maa Prerequisite(s): Instructor’s consent
In this course, students are introduced to linear water wave theory and its applications. Course topics include mechanisms of wave generation (wind waves and tides), the governing equations, wave properties, wave transformation, special cases for tidal wave propagation (e.g., Kelvin waves), wave bottom boundary layer, nonlinear properties (i.e., radiation stress). Practical applications of numerical models for wind wave generation, wave transformation, the spectrum analysis for wave measurements, and harmonic analysis for tides will be introduced and demonstrated.
MSCI 625 - Multivariate Analysis and Time Series
Spring, odd years (3) Forrest
This course will address the topics of regression and modeling, analysis of residuals; multivariate regression, eigenvector methods, principal component analysis and factor analysis. Fourier and stochastic models applied to geophysical and other time series data sets will be included.
MSCI 626 - Advanced Quantitative Methods for Marine Scientists
Spring (3) Staff
Topics in this course include an introduction to matrices, multiple regression, sensitivity analysis, non-linear function-fitting techniques. Additional areas of focus include empirical eigen function methods with applications, complex notation as applied to the description of sinusoidal variations, and fourier transforms spectra and filtering.
MSCI 627 - Marine Organic Geochemistry
Spring, even years (3) Canuel Prerequisite(s): Organic Chemistry
This course focuses on the characterization of organic carbon, nitrogen, phosphorus and sulfur in the marine environment. Modern methods of organic analysis that enhance our understanding of how organic materials cycle through the oceans will be discussed. Topics include the role of organic matter in the C, N, S and P cycles; chemical composition of marine organic matter; biogeochemistry; diagenetic transformations of organic materials; organic matter decomposition and preservation; and petroleum geochemistry.
MSCI 627L - Marine Organic Geochemistry Lab
Spring, even years (1) Canuel Prerequisite(s): Organic Chemistry
In this 1-credit lab module students will conduct an independent lab project that complements the lecture portion of MSCI 627 - Marine Organic Geochemistry .
MSCI 630 - Advanced Aquatic Chemistry
Spring, even years (3) Beck
This course explores the basic principles of natural water chemistry, with particular focus on marine systems. Topics include chemical kinetics and thermodynamics, ions in aqueous solution, acids and bases, carbonate chemistry, oxidation and reduction reactions, sorption and mineral precipitation/dissolution, and photochemical processes, with reference to biogeochemical cycling in marine waters.
MSCI 638 - Fish Histology and Histo-pathology
Spring, even years (4) Vogelbein
The course is a detailed examination of the normal microscopic structure and function of tissues and organs in fishes and the morphological and functional changes that occur in tissues during disease. Infectious and non-infectious diseases, including pathological changes elicited by chemical toxicants and environmental factors will be evaluated. Lab will consist of in-depth training in routine methods of paraffin histology and histochemistry. (Three lecture and three laboratory hours. Restricted to 6 students.)
MSCI 640 - Quantitative Ecotoxicology
Spring (4) Newman
This course covers essential ecotoxicology principles and quantitative methods for the analysis of ecotoxicological data. Laboratory exercises will include method applications with PC-based software. Emphasis will be placed on the scientific and statistical soundness of techniques.
MSCI 641 - Identifying, Quantifying and Communicating Environmental Risk
Fall (3) Newman
Methods for identifying harmful agents, quantifying any associated risk, and communicating that risk will be covered in this course, with an emphasis on practical, quantitative techniques. The basic NRC framework and methods for environmental risk assessment are presented for comparative, retrospective, and predictive assessments. The course explores logical and quantitative methods for identifying hazards in the presence of high uncertainty, working in teams to effectively assess risk, and communicating risk to stakeholders. Bayesian inference and estimation will be emphasized with additional theory and quantitative methods drawn from cognitive psychology, epidemiology, innovation diffusion theory and group decision theory.
MSCI 642 - Practical Environmental Statistics
Spring, even years (3) Newman Prerequisite(s): Instructor’s consent
This course explores practical statistics for sampling, measuring, and making sound inferences from environmental data. The course is intentionally a broad survey of methods applicable to physical, chemical and biological studies, drawing examples from each of these areas. It will blend lectures, student-directed exploration of concepts, and computer-based examples. Exercises will be done with the SAS statistical software package and other more specialized shareware. Eight general themes will be addressed: quantitative measurement, basic measurement quality control/outlier detection, variance structure, applications of regression analysis, sample size estimation, establishing field sampling or laboratory experiment designs, quantifying belief, and Monte Carlo/Bootstrap methods.
MSCI 648 - An Introduction to Mathematical Biology
Fall (3) Staff
In this course, students are given an introduction to developing, simulating, and analyzing models to answer biological questions. Mathematical topics may include matrix models, non-linear difference and differential equations, and stochastic models. Biological topics may include ecology, epidemiology, evolution, molecular biology, and physiology. Cross-listed with MATH 345.
MSCI 649 - Modeling Biological and Ecological Systems
Spring, even years (3) Brush, Latour
This course provides an introduction to quantitative modeling in marine science, with an emphasis on the process of constructing mechanistic models of biological, ecological, and biogeochemical processes. General topics include determination of modeling objectives and assumptions, model formulation and parameter estimation, determination of model accuracy through calibration, validation, and sensitivity analysis, and use of models to address scientific questions through simulation analysis. Types of models covered include compartmental ecosystem models, age/size-structured population models, and food web network analysis, with consideration of deterministic, stochastic, and spatially explicit approaches. Lectures are supplemented with readings from the primary literature and students receive hands-on experience building and using models through in-class lab exercises.
MSCI 650 - Estuarine Ecology
Fall, odd years (3) Brush, Schaffner Prerequisite(s): MSCI 503 .
This survey course will expose students to the key aspects of estuarine ecosystems. Topics covered will include both the abiotic settings of estuaries, including geological, physical, and chemical characteristics, and the biotic components and their interactions, including nutrient dynamics, biogeochemistry, microbial processes, primary production, ecosystem metabolism, secondary production, and food web dynamics. The course will end with overviews of current and emerging issues in estuarine science, including eutrophication and climate change. Bi-weekly class meetings will consist of interactive discussions led by the instructors based on readings from key estuarine ecology texts and the primary literature, supplemented with student-led discussions of primary literature and “virtual field trips” to a variety of well-studied estuaries. Students will work on a semester-long project to develop course materials into an estuary-focused wiki on the William & Mary wiki site. Each student will lead the development of materials for a select number of topics, and be responsible for contributing materials and editing content for all topics. Students will also lead field trips to local systems to illustrate class topics and synthesize existing datasets to conduct a comparative analysis of estuarine ecosystems.
MSCI 652 - Marine Plankton Ecology
Fall, odd years (3) Smith, Steinberg, Tang Prerequisite(s): MSCI 524 or MSCI 526 or consent of the instructors
This course will cover contemporary topics in cellular, population, community and ecosystem level dynamics of plankton systems, including nutrients and organic matter, viruses, bacteria, phytoplankton, protists and zooplankton. Course format will be primarily discussions, student presentations, literature evaluation, and writing exercises.
MSCI 653 - Marine Benthos
As required (3) Schaffner Prerequisite(s): Permission of instructor
Ecology of marine and estuarine benthos is the focus of this course. Emphasis is placed on determining how ecological processes affect function and structure of benthic communities. Consideration is given to interactions among autotrophs, microheterotrophs and larger metazoans and interactions between these organisms and their physical-chemical environments.
MSCI 655 - Stable Isotope Biogeochemistry
Fall, even years (2) Anderson, Bronk
This course is a survey of applications that use stable isotopes of carbon, nitrogen, oxygen, and sulfur to define elemental flow through experimental and natural systems. Topics include stable isotope theory; tracer versus natural abundance techniques; quantifying processes of elemental uptake, regeneration, and respiration; and defining trophic relationships using multiple tracers.
MSCI 656 - Seagrass Ecosystems
Spring, odd years (1-2) Moore, Orth
This lecture-seminar course covers topics related to seagrass ecosystems. Emphasis will be on the structure and function of seagrass communities, submerged angiosperm physiology, primary and secondary production, and integration of seagrass communities to the marine environment. Students will be assigned projects to complete. Course credit will depend upon difficulty of the assignments and must be arranged prior to registration.
MSCI 658 - Larval Ecology
Spring, odd years (3) Mann
The course is based on a broad discussion of the following topics within the marine invertebrates: the concept of the larval form, spawning and developmental patterns, limitations on the fertilization process and embryology, the Reynolds number environment at typical larval size, feeding and nutrition in the larval size range, larval size and parental investment, larval dispersal and supply in maintaining community structure, roles of physical versus biological processes in inducing metamorphosis, early post-metamorphic survival, and larval ecology in extreme environments.
MSCI 659 - Phytoplankton Ecology
Fall, odd years (3) Smith Prerequisite(s): MSCI 501 (may be taken concurrently with Instructor’s consent.)
This course will examine the factors, which influence the growth, losses and distributions of phytoplankton in marine systems. Topics include photosynthesis, pigmentation, productivity, biochemical fractionation, grazing, and nutrient uptake and interactions. A laboratory will introduce students to modern methods used in the study of phytoplankton such as isotopic measurements, HPLC analysis of pigments, fluorometry, and image analysis. Samples from the local estuaries will be used in the laboratories to illustrate the principles discussed in class.
MSCI 660 - Zooplankton Ecology
Spring (4) Steinberg
This course will examine the ecology, natural history, basic cell or body design features, physiology, and life histories of all the major groups of zooplankton. Food webs, specialized habitats, physical-biological coupling, and behavior are also discussed. Laboratories will concentrate on the groups or topics that are being discussed that week in lecture. The laboratories will be devoted to studying freshly collected (live local net tows), laboratory cultured, and occasionally museum specimens of the various taxa, and to introducing students to methods of study of zooplankton ecology (microscopy, biomass measurement, grazing experiments). There will also be field trips.
MSCI 664 - Marine Conservation Biology
Fall, even years (3) Lipcius
This course focuses on the application of multidisciplinary scientific principles to the protection, enhancement and restoration of marine biodiversity (genetic, species, community and ecosystem). Ecological emphasis will be on the conservation of biodiversity threatened by habitat degradation and loss, overexploitation, invasive species, and global change. Social, legal, economic and political influences will be discussed. Also included will be practical application through case studies and training in population viability analysis. (Lecture and laboratory)
MSCI 666 - Ichthyology
Fall (4) Hilton
Fishes form a large, diverse group of vertebrates that are culturally, economically, and scientifically important, and they offer much for the study of evolutionary biology. This course provides an intensive overview of all aspects of the evolution of fishes, with an emphasis on their morphology and systematic relationships; other topics include the biogeography, functional anatomy, and physiology of fishes. The lectures cover the diversity and evolutionary history of fossil and living fishes, and discuss the evidence for different hypotheses of their phylogenetic relationships. The mandatory lab section emphasizes dissection-based anatomical study and the global diversity of fishes, and includes some field sampling.
MSCI 667 - Experimental and Quantitative Ecology
Fall, odd years (3) Lipcius
The course addresses the design, conduct, analysis and interpretation of field and laboratory experiments in ecology. The lectures, discussion and supervised field and laboratory projects are designed to illustrate the diversity of experimental and quantitative approaches in use by ecologists. Topics include the scientific method, experimental design, the use and abuse of statistical techniques, modeling and manuscript preparation, with emphasis on topical ecological issues such as those dealing with predatory-prey interactions, recruitment phenomena, environmental science (e.g., dose-response assays) and metapopulation dynamics. (Lecture and laboratory)
MSCI 668 - Malacology
Spring, even years (3) Mann
The course begins with a discussion of the ancestral mollusc form and the fossil record, proceeds through examination of the structure and function of the molluscan shell. It concludes with reviews of molluscan taxonomy, reproductive biology, physiology, ecology, and feeding mechanisms.
MSCI 669 - Linear and Generalized Linear Models in Ecology
Fall (3) Fabrizio Prerequisite(s): MSCI 528 or consent of instructor, and ability to program in SAS or R
This course emphasizes the design and analysis of field data (e.g., retrospective studies, experimental manipulations in the field), rather than design and analysis of controlled laboratory experiments. Students will gain a working knowledge of linear and generalized linear models useful in the analysis of ecological data. Both theoretical development and application of statistical methods will be presented.
MSCI 670 - Stock Assessment Methods
Spring (3) Hoenig
This course will survey methods for assessing the status of exploited populations given various combinations of data types. Emphasis will be placed on deriving statistical methods using maximum likelihood and other analytical techniques, and on computing estimates for a variety of datasets. Population models will be used to integrate information on stock status in order to determine appropriate management measures. Additional topics include analysis of uncertainty in the assessment of results and implications of uncertainty for management, analysis of research surveys, commercial catch, fishing effort, and tagging data.
MSCI 671 - Fisheries Population Dynamics
Fall (3) Latour
This course provides an introduction to the fundamental processes governing fish population dynamics, with an emphasis on the theory and practical application of models used to characterize the factors influencing population abundance. Topics include the theory of mortality, growth, stock-recruitment (compensation, depensation), surplus production, VPA, statistical catch-at-age, tagging, and the introductory aspects of multispecies and fisheries ecosystem models. Lectures are supplemented with readings from the primary literature and students receive hands-on experience with nonlinear parameter estimation through computer laboratory sessions using the statistical software package R.
MSCI 672 - Ecology of Fishes
Fall (3) Staff
This course will provide students with an understanding of fish ecology as related to vertebrate evolution and diversity, systematics, feeding and reproductive biology, early life history ecology, and fish community structure and biotic interactions.
MSCI 673 - Marine Molecular Genetics
Spring, odd years (3) Graves, Reece, McDowell Prerequisite(s): Undergraduate Genetics or permission of instructor
Students will study the evolutionary processes responsible for the intra- and interspecific genetic relationships of marine organisms, with an emphasis on the application of current molecular methodologies. 3 hrs. Lecture.
MSCI 674 - Marine Molecular Genetics Laboratory
Spring, odd years (2) McDowell, Reece Prerequisite(s): Undergraduate Genetics or permission of instructor
Students will elucidate intra- and interspecific genetic relationships by employing a variety of molecular techniques for the analysis of proteins and nucleic acids (5 hrs. of laboratory).
MSCI 684 - Coastal and Marine Policy Implementation: The Art & Science of Governance
Spring (3) Hartley
This course will examine real world examples of implementation of local, state, federal, and regional coastal and marine policies through case studies, guest speakers, and literature from public administration, policy, and political science.
MSCI 685 - Practical Application of Marine Resource Management Techniques
As required (1-3) Hershner, Staff
In this course, students participate in real world management activities under the guidance of involved faculty members and in association and consultation with members of various levels of government. Topics may include issue identification and resolution, committee involvement at local, regional, state, interstate, and federal levels of government, development of management plans, drafting position papers, developing draft legislation and exposure to policy making mechanisms. Requirements will vary depending on the issue(s) addressed. Students will be evaluated on participation, written work (memoranda, position papers, etc.) and knowledge gained as evidenced by interaction with staff and by other means. Credit, which must be arranged in advance of registration, will depend upon difficulty of the assignment. The course may be repeated provided the instructor determines there is no duplication of material.
MSCI 687 - Environmental Policy
Fall (3) Hicks
This course will explore policy making for environmental problems and will focus on issues that are local, national, and international. The course will primarily focus on national environmental policy, and the procedures by which policy is implemented at both local and regional levels. Issues explored will include water pollution policy and land-use in the Chesapeake Bay, U.S. Marine Mammal Policy, and U.S. water and air quality regulations. For each of these issues, U.S. laws and regulations as well as federal agencies’ approaches for quantitatively assessing the benefits and costs of environmental policy will be examined. Cross-listed with PUBP 622
MSCI 689 - Public Policy for Science & Professions
Fall (3) Gilmour, Rossiter
This course examines a component of the larger process of law and rule making, for students to understand the identification and definition of a policy problem, the generation of options or choices for addressing the problem, the selection of a particular policy option through political institutions (e.g., the executive or legislative), the development of a plan for implementation, and the implementation and evaluation of the outputs and outcomes of policy. The course is specifically designed for an interdisciplinary class of graduate students from the Schools of Business, Education, Law, and Marine Science, and non-master’s in Public Policy from the School of Arts and Sciences. Students will come to understand public policy as an academic discipline and as a systematic method of thinking about the design, development and assessment of public sector policies and programs. By the end of the course students will develop the skills required to define and analyze policy issues and problems, articulate relevant decision-making criteria for policy analysis, evaluate alternative policy solutions, assess their political and economic implications. The course is taught in an engaging seminar format using provocative materials with practical application.
MSCI 693 - Environmental Law
As required (3) Law School Staff Prerequisite(s): Consent of instructor
Students will study the nature and causes of environmental pollution and of the main legal techniques for its control. The course will consider the common law, the environmental impact assessment process (e.g., the National Environmental Policy Act), and the basic regulatory framework for air, water and solid and hazardous waste control (the Federal Clean Air Act, Clean Water Act and Resource Conservation and Recovery Act), with attention given under each statute to the basic regulatory framework and the main policy issues presented by it. Other topics will include the role of the federal courts in reviewing agency action, new developments in federal administrative law (including current efforts at administrative law reform), natural resource management and allocation issues involved in the division of scarce resources (e.g., air and water) among competing users, toxic and hazardous substance regulation, and enforcement of environmental laws. Cross-listed with LAW 424 .
MSCI 694 - Land Use Control
As required (3) Law School Staff, Butler Prerequisite(s): Consent of instructor
This course presents an analysis of the legal principles governing the use and management of land and the fundamental values underlying those principles. While focusing primarily on government regulation of land use, the course also will examine common law rules, which affect the way that land is used. Topics that might be considered include judicial control of land use, zoning and the rights of landowners, zoning and the rights of neighbors, land use planning, public regulation of land development, aesthetic regulation, and the preservation of natural and historic resources. Cross-listed with LAW 425 .
MSCI 695 - Administrative Law
As required (3) Law School Staff Prerequisite(s): Consent of instructor
This course is a study of practice in the administrative process, examining the procedures for administrative adjudication and rule making; legislative and judicial control of administrative action; and public access to governmental processes and information. Cross-listed with LAW 453 .
MSCI 697 - Problems in Marine Science
Fall, Spring and Summer (1-4) Staff
This is the avenue through which supervised projects may be selected to suit the needs of the graduate student, including those wishing to perform an internship as part of the Curricular Practical Training Program. Projects are chosen in consultation with the student’s major professor and the instructor. Acceptable research outlines and project reports are required, and the amount of credit depends upon difficulty of course. Examples of projects offered in recent years include management issues in shellfish sanitation; groundwater nutrient processes; bacterioplankton methods and techniques; pesticide analysis in environmental samples; marine molecular population genetics; and law and policy relating to the introduction of non-indigenous plants. Subjects will be announced prior to registration and after approval by the Educational Policy Committee (EPC).
MSCI 698 - Special Topics in Marine Science
Fall, Spring and Summer (1-3) Staff
This is the avenue through which subjects not covered in other formal courses are offered. These courses are offered on an occasional basis as demand warrants. Examples of courses offered in recent years include: continental margin sedimentation; biomineralization in marine organisms; molecular markers and evolution; oligochaete biology; quantitative methods of image analysis; and organism-sediment interactions in coastal systems. Subjects will be announced prior to registration and after approval by the EPC.
MSCI 699 - Dissertation
Fall, Spring and Summer (1-9) Major or Co-Major Advisor(s)
This is the avenue for original research in biological, chemical, geological and physical oceanography, environmental science, marine fisheries science and marine resource management. The doctoral project is chosen in consultation with the student’s major professor and the Associate Dean of Academic Studies.
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