Biology (BIOLOGY)

Professors Barber, Benfey, Brandon, Christensen, Clark, Crowder, Dong, Forward, Goldstein, Jackson, Kiehart, Kirby, McClay, Mitchell-Olds, Morris, F. Nijhout, Nowicki, Rausher, Reynolds, Rosenberg, Shaw, Siedow, Smith, Staddon, Sun, Terborgh, Uyenoyama, Vilgalys, Willard, Wray, and Yoder; Associate Professors Alberts, Bejsovec, Cunningham, Drea, Johnsen, Lutzoni, Manos, McShea, Noor, Pei, Pryer, Rittschof, Roth, Willis, and Wilson; Assistant Professors Baugh, Bernhardt, Chen, Haase, Koelle, Leal, Magwene, D. Sherwood, Wright; Professors Emeriti Boynton, Fluke, Gillham, Gregg, Klopfer, Knoerr, Nicklas, Searles, Stone, Strain, Tucker, Wainwright, Ward, White, and Wilbur; Research Professors Cook-Deegan, Livingstone and Vogel; Assistant Research Professor N. Sherwood; Senior Research Scientist Culberson; Adjunct Professors Antonovics, Eubanks, Funk, Hartshorn, Kohorn and Lacey; Adjunct Associate Professor M. Nijhout; Adjunct Assistant Professors Gastreich, Guindon, Isikhuemhen, Lindquist, Riginos, and Zahawi; Associate Professors of the Practice Armaleo, Broverman, Mercer, Motten

The Department of Biology offers a variety of training opportunities leading to the PhD degree. Students in the department may specialize in a wide variety of areas including anatomy; behavior; physiology; cellular and molecular biology; community, ecosystem, physiological, and population ecology; evolution; functional morphology; developmental, ecological, molecular, organelle, and population genetics; genomics; and systematics.

There is a high level of interaction among the various areas of biology and other programs. Faculty members participate in the University Programs in Developmental Biology, Ecology, Genetics and Genomics, Cellular and Molecular Biology, Computational Biology and Bioinformatics, Strucural Biology and Biophysics, and Neurobiology; tropical research is facilitated through the University's membership in the Organization for Tropical Studies. There are also strong relationships with the departments of Biological Anthropology and Anatomy (primatology, phylogenetic systematics, macroevolution), Mathematics (theoretical biology), and Psychology (behavior); the School of Engineering (biomechanics); the Medical Center (molecular biology and genomics); and the Nicholas School of the Environment and Earth Sciences (ecology).

Students entering the program generally have a broad background in biological sciences supplemented with basic courses in chemistry, mathematics, and physics. Biochemistry and physical chemistry are strongly recommended for students interested in molecular areas, and advanced courses in mathematics are recommended for students in population genetics and ecology. While deficiencies may be corrected by taking appropriate courses during the first year of graduate study, it is advised that students search widely in both the Bulletin of Duke University; Undergraduate Instruction and the Bulletin of Duke University; Graduate School for information about the intellectual resources of the University. Special attention should be given to announcements of the programs and departments listed above, as well as to those of Cultural Anthropology, History, Immunology, Molecular Genetics and Microbiology, Pharmacology, Philosophy, and Sociology, and of the School of Engineering and the Nicholas School of the Environment and Earth Sciences.

203. Marine Ecology. Ecology from a policy and management perspective. Recitations and discussions target a policy- and management-oriented graduate audience. Lecture topics include factors that influence the distribution, abundance and diversity of marine organisms, characteristics of marine habitats, adaptation to environment, species interactions, biogeography, larval recruitment, and communities found in rocky shore, tidal flats, beached, mangrove, coral reefs and subtidal areas. Recitations and discussions cover ecological principles form a policy and management perspective. Not open to students who have taken BIO 129L and not open to undergraduates. (Given at Beaufort fall and summer). Prerequisite: Introductory Biology. Instructors: Crowder or Kirby-Smith (Beaufort).. 4 units. C-L: Environment 219

203L. Marine Ecology. Ecology from a basic science perspective. Laboratories target a science-oriented graduate audience. Lecture topics include factors that influence the distribution, abundance, and diversity of marine organisms, characteristics of marine habitats, adaptation to environment, species interactions, biogeography, larval recruitment, and communities found in rocky shores, tidal flats, beaches, mangrove, coral reefs, and subtidal areas. Laboratories and field trips cover ecological principles from a basic science perspective. Not open to students who have taken BIO 129L and not open to undergraduates. (Given at Beaufort.) Prerequisite: Introductory Biology. Instructors: Crowder or Kirby-Smith. 4 units. C-L: Environment 219L

204LS. Field Ecology. Ecosystem, community, and physiological ecology of temperate plants and animals through hands-on experimentation. How biological processes are affected by biotic interactions. Theory and methods reviewed through discussions; hypothesis formulation, experimental design, data acquisition and processing, and data analysis learned through field investigation. Includes several field trips, including two weekends. Prerequisites: Biology 25L, Mathematics 31. Biology 110L, 116, or other course in ecology, or consent of instructor. Instructor: Reid or Wright. 4 units. C-L: Environment 204LS

205LS. Experiments in Developmental and Molecular Genetics. Experimental approaches in development and genetics using animal and plant models. Laboratory training in molecular genetics, immunochemistry, microscopy, protein chemistry, and genetic screening. Experiments include immunochemical localization, in situ hybridization, polymerase chain reaction, genetic screening, embryo micromanipulation, microscopic imaging, and mutant analysis. Prerequisite: Biology 118; recommended, prior or concurrent registration in Biology 119. Instructor: Staff. 4 units.

207AL. Experimental Tropical Marine Ecology. Distribution and density of marine and semi-terrestrial tropical invertebrate populations; behavioral and mechanical adaptations to physical stress, competition, and predation using rapid empirical approaches and hypothesis testing. Offered only at Beaufort, with preparation for fieldwork before and analysis and presentation of projects after required one week intensive field experience on the coast of Panama. Consent of instructor required. Instructor: Rittschof. 2 units. C-L: Marine Sciences

207BL. Marine Ecology of the Pacific Coast of California. Ecology of the rocky intertidal, kelp forest, and mud flat habitats. Introduction to marine mammals, fish and other large West Coast vertebrates. Offered only at Beaufort, with preparation for fieldwork before and analysis and presentation of projects after required one week intensive field experience on the coast of Northern California. Prerequisite: Concurrent registration in Biology 129L and consent of instructor. Instructor: Crowder. 2 units. C-L: Marine Sciences

207CL. Ocean Ecosystems. Interaction of physical, chemical and biological processes, emphasizing processes that determine species composition and quality of plants and animals. Field work with marine organisms, especially plankton, sampling habitats from the continental shelf to the subtropical gyre. Offered only at Beaufort, with preparation for fieldwork before and analysis and presentation of projects after required one week intensive field experience at sea on an oceanographic vessel. Consent of instructor required. Instructor: Barber. 2 units.

207EL. Harmony in Brittany: French Use of Marine Environments. Intensive field experience on the coast of Brittany, including French maritime cultural heritage, regional and national coastal reserves (Le Parc naturel régional d'Armorique; Presqu'île de Crozon), shellfish aquaculture (La Tremblade), seaweed harvest (Lanildut), and tidal energy (La Rance). Offered only in Beaufort, with preparation for fieldwork before and analysis and presentation of projects after required one week intensive field experience on the coast of France over Fall Break. Prerequisites: Biology 25L and consent of instructor. Instructor: Van Dover. 2 units. C-L: Marine Sciences

208LS. Human Embryology. The development of the mammalian embryo. Emphasis on human embryology, the origin of major human teratologies, birth defects, ethical and social issues of reproductive biology, aspects of comparative vertebrate development. The evolution of developmental patterns, and the molecular mechanisms of development. Laboratory sessions examining various vertebrate, including human embryos. Prerequisites: Biology 108L or 205L or Biological Anthropology and Anatomy 133L or equivalent. Permission of instructor required. Instructor: Smith and Wall. 4 units. C-L: Biological Anthropology and Anatomy 208LS

211L. Microbial Ecology and Evolution. Survey of new advances in the field of environmental and evolutionary microbiology, based on current literature, discussion, and laboratory exercises. Topics to include bacterial phylogeny, molecular ecology, emerging infectious diseases, bacterial symbiosis, experimental evolution, evolution of drug resistance, and microbial genomics. Prerequisite: Biology 25L, 103L, 118, or consent of instructor. Instructor: Vilgalys. 4 units.

216. Sojourn in Singapore: Urban Tropical Ecology. The mix of human ecology, tropical diversity, disturbed habitats and invasive species in Singapore. How Singapore maintains and enhances the quality of life of its citizens while radically modifying its environment. Research on politics, management or biology. Travel to Singapore required. Taught in Beaufort. Consent of instructor required. Instructor: Orbach and Rittschof. 3 units. C-L: Marine Sciences

217. Ecology and Global Change. Feedbacks between ecological processes and global environmental change; physiological and ecosystem ecology using a variety of sources, including the primary scientific literature. Topics include global warming, biodiversity, land-use change, ozone depletion, and the application of ecological research to policy. Prerequisite: Biology 25L or equivalent; recommended: Biology 110L or 116 or equivalent. Instructor: Jackson. 3 units.

224L. Herpetology. Biology of recent amphibians and non-avian reptiles, evolutionary history, morphology, life history, physiology, behavior, and ecology. Local field trips. Prerequisites: Biology 25L or equivalent. Instructor: Leal. 4 units.

237L. Systematic Biology. Laboratory version of Biology 237. Theory and practice of identification, species discovery, phylogeny reconstruction, classification, and nomenclature. Prerequisite: Biology 25L or equivalent. Instructors: Lutzoni and Swofford. 4 units.

252. Marine Conservation Biology. Ecological effects of fishing, the major threat to marine biodiversity, examined through selected case studies. Conservation strategies and ways that science and policy can be integrated to solve real-world problems. Field trip to Hawaii required. (Taught at Beaufort.) Instructor: Read. 3 units.

254. Vertebrate and Invertebrate Endocrinology. Comparative study of the major pathways of hormonal regulation from the organismal to the molecular level in vertebrate and invertebrate models. Applications of endocrinology in pharmaceuticals, cosmetics, and environmental issues. Prerequisites: Biology 25L and Chemistry 152L. A biochemistry course recommended. (Given at Beaufort.) Instructor: Rittschof. 3 units. C-L: Marine Sciences

256S. Speciation. Experimental and phylogenetic approaches to the origin of plant and animal species. Emphasis on current literature and modern approaches to evolutionary patterns and processes. Prerequisites: basic courses in systematics and genetics. Instructor: Noor or Willis. 3 units.

258S. The Making of the Modern Evolutionary Synthesis. An examination of the intellectual and historical development of the modern evolutionary synthesis. Topics will include: the state of evolutionary theory and the debate between the "Mendelians" and "Darwinians" in the early part of the 20th century, the development of modern population genetics and its synthesis with ecology, systematics and paleontology. Contributions of Fisher, Wright, Dobzhansky, Mayr, and Simpson will be highlighted with focus on original literature. What was and was not part of the synthesis, and why, and the current state of evolutionary theory will also be discussed. Enrollment limited to graduate students. Instructors: K. Smith and J. Willis. 3 units.

259S. The Life and Work of Darwin. Readings by and about Darwin and his contemporaries, especially Wallace. Darwin's "Autobiography" and Janet Browne's biography as context for readings of some of his major works and works of his contemporaries. Consent of instructor required. Instructors: Alberts and McShea. 3 units.

260. Cancer Genetics. Overview of the genetic changes associated with cancer and the molecular events that transform normal cellular processes into tumor-promoting conditions. Topics include: tumor viruses, oncogenes, growth factors, signal transduction pathways, tumor suppressors, cell cycle control, apoptosis, stem cells, and metastasis. Prerequisites: Biology 118 and Biology 117 or 119. Instructor: Bejsovec. 3 units.

267L. Biodiversity Science and Application. Processes responsible for natural biodiversity from populations to the globe. Topics include species interactions (e.g., competition, predation, parasitism), natural and human disturbance, climate change, and implications for management and conservation. Lab section involving observation and data from large-scale manipulations, such as experimental hurricanes, fire, and herbivore exclosures. Instructor: Clark or Wright. 3 units. C-L: Environment 257L

268L. Models for Environmental Data. Formulation of environmental models and applications to data. Topics include physiology, population growth, species interactions, disturbance, and ecosystem dynamics. Model development, analysis, and interpretation. Discussions focus on classical and current primary literature. Lab focuses on analysis of data using R, making use of likelihood models, bootstrapping, and Bayesian approaches. Instructor: Clark. 3 units. C-L: Environment 231L

271. Genomics. Introduction to the field of genomics. Genomic techniques including genome sequencing, microarray analysis, proteomics, and bioinformatics; applications of genomics to understanding biological problems including biological networks, human origins, evolution; applications to medicine and agriculture. Lecture and discussion. Prerequisites: Biology 118 or consent of instructor. Instructor: Benfey or Staff. 3 units.

272. Biogeochemistry. Processes controlling the circulation of carbon and biochemical elements in natural ecosystems and at the global level, with emphasis on soil and surficial processes. Topics include human impact on and social consequences of greenhouse gases, ozone, and heavy metals in the environment. Prerequisite: Chemistry 12L or 22L or equivalent. Instructor: Bernhardt. 3 units. C-L: Earth and Ocean Sciences 272

274. Genomic Perspectives on Human Evolution. Human evolutionary history as studied from the perspective of the genome. Nature of contemporary genomic data and how they are interpreted in the context of the fossil record, comparative anatomy, psychology, and cultural studies. Examination of both the origin of modern humans as a distinct species and subsequent migration across the world. Emphasis on language, behavior, and disease susceptibility as traits of particular evolutionary interest. Prerequisite: Biology 118 or equivalent course. Instructor: Wray. 3 units. C-L: Biological Anthropology and Anatomy 274

275S. Sensory Signal Transduction. Recent progress in sensory signal transduction mediated by calcium channels and receptors. Topics include history and techniques in the study of ion channels, such as electrophysiology, calcium imaging, and cell and molecular biology; cell surface perception for external signals, including light receptors, olfactory receptors, taste receptors, hot and cold receptors, and mechanical receptors; heart and brain pacemakers; sensory channel receptor-related human diseases; and plan sensory signaling network. Instructor: Pei. 3 units.

278S. Genetic Basis of Behavior. The relationship between genotype and behavioral phenotype. Readings from the primary literature, including papers on humans, lab mice, and wild animal populations. Exploration of two philosophical topics: the question of causality in the natural world and the question of determinism in biology. Short research paper required. Instructor: Alberts. 3 units.

279S. Developmental Biology Colloquium. Lectures, seminars, and discussion of current topics in developmental biology. Prerequisites: Biology 118 and/or 119 or equivalent. Consent of instructor required. Instructor: McClay. 3 units.

280S. Genetic Engineering and Biotechnology. Applications of recombinant DNA in medicine and in agriculture. Topics include diagnosis of genetic diseases, gene therapy, drugs for AIDS and cancer, DNA fingerprinting, cloning of mammals, phytoremediation, crop improvement, and pharmaceutical protein production in transgenic plants and animals. Social and environmental impacts of biotechnology. Prerequisites: Biology 118 and 119 or consent of instructor. Instructor: Sun. 3 units.

284. Molecular Population Genetics. Genetic mechanisms of evolutionary change at the DNA sequence level. Models of nucleotide and amino acid substitution; linkage disequilibrium and joint evolution of multiple loci; analysis of evolutionary processes, including neutrality, adaptive selection, and hitchhiking; hypothesis testing in molecular evolution; estimation of evolutionary parameters; case histories of molecular evolution. For graduate students and undergraduates with interests in genetics, evolution, or mathematics. Instructor: Uyenoyama. 3 units.

287S. Macroevolution. Evolutionary patterns and processes at and above the species level; species concepts, speciation, diversification, extinction, ontogeny and phylogeny, rates of evolution, and alternative explanations for adaptation and evolutionary trends. Prerequisite: Biology 25L, 26L, or other course in plant or animal diversity; recommended, Biology 116 or equivalent. Instructor: Roth. 3 units. C-L: Biological Anthropology and Anatomy 287S

289S. Advanced Topics in Genome Science Research. Exploration of current experimental and computational approaches in genomics and genetics and their applications to contemporary research questions. Formulation and design of interdisciplinary research plans with discussion of implications for biology, medicine and society. Utilizing primary scientific literature, students write critical reviews and research proposals. Prerequisite: Biology 195S (Genomes, Biology, Medicine), 118, 119 or 271, or consent of instructor. Recommended co- or prerequisite: independent study in genomics or computational biology. Instructor: Willard. 3 units.

292. Population Ecology. Explores key questions in population ecology from a theoretical perspective. Topics include demography and dynamics of structured populations, stochastic population dynamics, and life history characteristics. Prerequisites: Biology 110L or 116 and consent of instructor. Instructors: Morris and Wilson. 3 units.

293. Simulating Ecological and Evolutionary Systems. Computer programming using C within a UNIX environment applied to ecological and evolutionary problems. The relationship between simulation and analytic modeling. Knowledge of programming or work within the UNIX computer environment not expected. Consent of instructor required. Instructor: Wilson. 3 units.

297. Research Independent Study. Continuation of Biology 191. Individual research and reading of the primary literature in a field of special interest, under the supervision of a faculty member, the major product of which is a substantive paper or written report containing significant analysis and interpretation of a previously approved topic. Open to juniors and seniors only with consent of supervising instructor. May be repeated. Instructor: Staff. 3 units. C-L: Marine Sciences

300. Tropical Biology: An Ecological Approach. Highly intensive, field-oriented course conducted in Costa Rica under auspices of the Organization for Tropical Studies. For additional information refer to the chapter ''Special and Cooperative Programs.'' 6 to 8 units. Instructor: Staff. Variable credit.

303. Principles of Environmental Modeling. Design, implementation, and interpretation of mathematical and computer models in environmental science and management. Combination of lectures, discussion sessions, and computer lab exercises. Goals of course are to develop skills: (1) to conceptualize environmental problems and (2) to design, program, implement and interpret mathematical and computer models to help solve environmental problems. Instructor: Reynolds. 3 units. C-L: Environment 303

304. Modeling Plant and Ecosystem Response to Global Change. Examination of current models used to evaluate potential effects of global change, e.g., land use, atmospheric composition, biological diversity and climate, on terrestrial ecosystems. Ecosystem responses considered in terms of changes in function and vegetation composition/structure. Design, analysis and interpretation of models of plant and ecosystem biogeochemical cycles. Concepts of hierarchy and scaling emphasized in context of regional and global predictions using Dynamic Global Vegetation Models. Combination of lectures, student-moderated discussions and seminars and computer lab exercises. Prerequisites: Ecology (BIO 110) or equivalent. Recommended: Physiological Plant Ecology (BIO 265). Instructor: Reynolds. One Course. 3 units.

315S. Population Genetics Seminar. Discussion of recent developments in population genetics. Topics include population dynamics, forces affecting gene frequency change, molecular evolution, philosophy of evolutionary biology. Student presentations are integral to the course. Instructor: Staff. 1 unit.

325S. Developmental, Cellular, and Molecular Biology Seminar. Weekly presentations in developmental, cellular, and molecular biology topics by students, faculty, and invited speakers. Consent of instructor required. Instructor: Staff. 1 unit.

326S. Developmental, Cellular, and Molecular Biology Seminar. Weekly presentations in developmental, cellular, and molecular biology topics by students, faculty, and invited speakers. Consent of instructor required. Instructor: Staff. 1 unit.

343L. Bryophyte Biology and Ecology. Identification, classification, evolution, and ecology of byrophytes (mosses, liverworts, and hornworts). An ecological survey of bryophytes in their natural habitats focusing on the skills required to identify bryophytes and use them as indicators of environmental features. Natural plan communities of the southeastern United States. Uses of bryophytes for ecological assessment. Prerequisites: Course in introductory biology and organismal diversity, or equivalent. Instructor: Shaw. 4 units.

370. Principles and Practice of Microscopy. Concepts involved in a wide variety of microscopy, demonstrations of various imaging systems and discussions of specialist techniques. The course is intended for people who will do a significant amount of biological imaging in their graduate research. Areas covered: Transmitted light, fluorescence, widefield imaging, scanning confocal, TIRF, live-cell imaging, multiphoton excitation, image processing and analysis. Consent of instructor required. Instructor: Johnson. 1 unit.

390. Seminar in Teaching Biology. Syllabus design, best practices, and instructional methods in biology for graduate students in Duke University's Preparing Future Faculty Program in Biology. Seminar discussions and projects guided by Duke faculty in conjunction with faculty from Elon, Guilford, and Meredith Colleges. Topics may include ''Biological Literacy''; ''Using Information Technology''; and ''Different Learning Styles, Different Contexts.'' Consent of instructor required. Instructor: Lemons. 1 unit.

2008-09 Bulletin of the Duke University Graduate School

2008-09 Bulletin of the
Duke University Graduate School