Biological Sciences

Chair: Edward M. Berger

Professors E. M. Berger, C. L. Folt, M. L. Guerinot, G. M. Langford, C. R. McClung, M. A. McPeek, D. R. Peart, R. D. Sloboda, L. A. Witters; Associate Professors M. P. Ayres, S. E. Bickel, K. L. Cottingham, M. R. Dietrich, P. J. Dolph, R. H. Gross, T. P. Jack, E. J. Lambie, G. E. Schaller, E. F. Smith, S. J. Vélez; Assistant Professors R. Calsbeek, A. J. Erives, A. S. Gladfelter, R. E. Irwin, K. J. Peterson; Instructor B. W. Taylor; Professors Emeriti J. J. Gilbert, R. T. Holmes; Adjunct Professors M. W. Fanger, A. J. Friedland, N. J. Jacobs, L. R. Lynd, R. K. Taylor, R. A. Virginia; Adjunct Associate Professors D. T. Bolger, T. U. Gerngross, J. H. Moore, G. A. O’Toole; Adjunct Assistant Professor K. H. Nislow; Research Professor G. C. Ruben; Research Associate Professors C. Y. Chen, E. B. Dubrovsky, R. S. Stemberger; Research Assistant Professor V. A. Dubrovskaya; Visiting Assistant Professor D. L. Church; Croasdale Fellows N. M. Grotz, D. N. M. Mbora.

REQUIREMENTS FOR MAJORS IN THE DEPARTMENT OF BIOLOGICAL SCIENCES

The Department offers four majors, one broadly based and three more specialized, as listed below. Each major has two prerequisite courses in biology, at least two other prerequisites from other departments, and requires eight additional courses, as described below.

a. Courses with numbers greater than 10 may count toward credit in any major (with some restrictions described below).

b. Introductory courses, numbered 14 through 19, have no prerequisites and are open to all students. Each major requires two of these courses as prerequisites; if more than two are taken the extras may be counted among the major courses, as specified below.

c. Intermediate courses, numbered in the twenties, require only one introductory course.

d. Advanced courses, numbered 30 through 78, may have additional requirements.

e. Research courses, numbered in the 80’s, require permission of the instructor and of the Department’s Undergraduate Committee before enrollment; one of these research courses may be counted among the eight major course requirements.

f. Students who take Biology 87 may count Biology 99 toward the degree but not among the eight required courses for the major.

g. Graduate courses, numbered above 100, are open to undergraduates only with permission. Students may count one graduate course among the eight major courses with the approval of the instructor and the Undergraduate Committee as described below.

h. All four of the departmental majors may be modified. The courses included should form an integrated program, and the value and purpose of the modified major must be made clear in writing before such a plan can be approved.

i. Students must pass all prerequisite courses for a major in order to graduate.

1. THE MAJOR IN BIOLOGY (BIOL)

Prerequisite: Biology 14 and 16; Mathematics 3 (or equivalent); Chemistry 5-6 (or equivalent).

Major Courses: Biology 15 (or 19) plus any seven courses chosen from Biology 20-79. One pertinent, advanced course from another department, one research course (Biology 85 or 87), or a graduate course in Biology may be substituted for an undergraduate biology course upon approval by the Undergraduate Committee.

Modified Major: Five prerequisites as listed above; any six biology courses numbered above 10 and below 80; and four suitable advanced courses from another department. A research course (Biology 85 or 87) may be substituted for one of the Biology courses with the approval of the proposed research supervisor and the Undergraduate Committee. The Department encourages undergraduates with special interests in other disciplines to develop modified major programs with, for example, Anthropology, Chemistry, Earth Sciences, Engineering Sciences, Environmental Studies, Physics, or Psychology. Information and advice about these joint programs and others can be obtained from the Department’s Undergraduate Committee.

2. THE MAJOR IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (BBCM)

Prerequisite: Biology 15(or 19) and 16; Chemistry 5-6 (or equivalent); Mathematics 3 (or equivalent); Chemistry 51-52.

Major Courses: Biology 23, 77 and 78; and five other courses chosen from among Biology 37, 61 through 76. One pertinent, advanced course from another department, one research course (Biology 85 or 87), or a graduate course in Biology may be substituted for one of the unspecified courses upon approval by the Undergraduate Committee.

Modified Major: Seven prerequisites as listed above; three Biology courses as specified; three Biology courses from among 37, 61-76; and four suitable advanced courses from another department. A research course (Biology 85 or 87) may be substituted for one of the biology courses with the approval of the proposed research advisor and the Undergraduate Committee.

3. THE MAJOR IN GENETICS, CELL, AND DEVELOPMENTAL BIOLOGY (BGEN)

Prerequisite: Biology 15(or 19) and 16; Chemistry 5-6 (or equivalent); Chemistry 51-52;

Mathematics 3 (or equivalent).

Major Courses: Biology 23 plus five courses chosen from among Biology 24, 27, 34, 39, 42 and 61 through 78; and two other courses in Biology chosen from Biology 14, 20-79. One pertinent, advanced course from another department, one research course (Biology 85 or 87) or a graduate course in biology may be substituted for an undergraduate biology course upon approval by the Undergraduate Committee.

Modified Major: Seven prerequisites as listed above; six Biology courses as specified; and four suitable advanced courses from another department. A research course (Biology 85 or 87) may be substituted for one of the biology courses with the approval of the proposed research supervisor and the Undergraduate Committee.

4. THE MAJOR IN ENVIRONMENTAL AND EVOLUTIONARY BIOLOGY (BEEB)

Prerequisite: Biology 14 and 16; Chemistry 5-6 (or equivalent); and Mathematics 3 (or equivalent).

Major Courses: At least six courses chosen from among Biology 20, 22, 24, 25, 28, 29, 33, 50-59, 62, Environmental Studies 79 or 80 or 89; and two other courses chosen from Biology 15(or 19), 20-78. One pertinent, advanced course from another department, one research course (Biology 85 or 87), or a graduate course in Biology may be substituted for an undergraduate biology course upon approval by the Undergraduate Committee.

Modified Major: Five prerequisites as listed above; six courses as specified; and four suitable advanced courses from another department. A research course (Biology 85 or 87) may be substituted for one of the biology courses with the approval of the proposed research supervisor and the Undergraduate Committee.

CULMINATING EXPERIENCES

All graduating seniors must participate in a culminating experience. The culminating experience must be taken for course credit and must be graded. Majors in the Biology Department have a number of options for fulfilling their culminating experience. Participation in the Biology Foreign Study Program (Biology 55-57) or conducting independent research (Biology 85 or 87) constitutes a culminating experience for any of the four majors. Each of the four majors also has other courses that satisfy the culminating experience requirement (listed below). The course fulfilling a student’s culminating experience should be taken during the senior year; students must petition the Undergraduate Committee to have a course taken in the junior year count as a culminating experience.

COURSES SATISFYING THE CULMINATING EXPERIENCE

FOR ANY OF THE FOUR MAJORS

• Biology 55-57 Foreign Study Program
• Biology 85 Independent Research in Biology
• Biology 87 Honors Research in Biology

FOR BIOCHEMISTRY AND MOLECULAR BIOLOGY (BBCM)

• Biology 78 Biochemistry II

FOR GENETICS, CELL AND DEVELOPMENTAL BIOLOGY (BGEN)

• Biology 61 Molecular Genetics of Prokaryotes
• Biology 62 Evolutionary Developmental Biology
• Biology 64 Microbiology
• Biology 65 Molecular Genetics of Eukaryotes
• Biology 71 Advanced Cell Biology
• Biology 74 Advanced Neurobiology
• Biology 75 Genomic Circuitry
• Biology 76 Advanced Genetics

FOR ENVIRONMENTAL AND EVOLUTIONARY BIOLOGY (BEEB)

• Biology 33 Animal Behavior
• Biology 52 Behavioral Ecology
• Biology 53 Aquatic Ecology
• Biology 54 Population Ecology
• Biology 58 Community Ecology
• Biology 59 Physiological Ecology
• Biology 62 Evolutionary Developmental Biology
• Biology 64 Microbiology

FOR BIOLOGY (BIOL)

• Any course that fulfills the culminating experience for another Biology Department major.

REQUIREMENTS FOR THE BIOLOGY MINOR

The Biology Department offers four different Minor programs, as described below. All these minors require Chemistry 5-6 (or equivalent) and Mathematics 3 (or 4) as prerequisites, in addition to the specific prerequisite requirements outlined below. Courses outside the Biology Department cannot be substituted for prerequisites or required Biology courses.

Biology (BIOL)

Prerequisites: Biology 14 and 16.

Required Courses: Biology 15 (or19) and any 3 courses from Biology 20-79*.

Biochemistry and Molecular

Biology (BBCM)

Prerequisites: Biology 15 (or 19) and 16, Chemistry 51 and 52.

Required Courses: Biology 23, 77, 78, and any one course from Biology 37, 61-76.

Genetics, Cell and Developmental Biology (BGEN)

Prerequisites: Biology 15 (or 19) and 16.

Required Courses: Biology 23, 27 and two other courses from 20, 22, 24, 34, 37, 39, 41, 42, 61-79*

Environmental and Evolutionary Biology (BEEB)

Prerequisite: Biology 14.

Required Courses: Five courses selected from 20, 22, 24, 25, 28, 29, 33, 50-59, 62, Environmental Studies 79 or 80 or 89.

SYNOPSES OF BIOLOGY DEPARTMENT

MAJORS

*Non-honors majors may replace one of the unspecified courses with a research course (Biology 85), a biology graduate course, or one pertinent, advanced course from another department (Chemistry 51 and 52 do not fulfill this condition).

**All Honors majors must take Biology 87 for credit. They may also include one biology graduate course or pertinent, advanced course from another department as one of the ‘unspecified elective’ major courses. Biology 99 is recommended as a ninth course for all Honors research students.

*** No courses may be substituted for Biology 14, 15, or 16 as prerequisites to any major.

†Or equivalent.

BIOLOGY DEPARTMENT MINORS***

§Offered only in the summer term; students exempted from summer residence must obtain approval for an appropriate substitute course offered by the Department of Biological Sciences.

††Some courses have additional prerequisites (e.g., Biology 77 requires Mathematics 3, Chemistry 5-6, 51-52).

***No courses may be substituted into minors.

ACADEMIC STANDING AND ADVISING

Satisfactory completion of any major option, including the modified major, requires obtaining a grade point average of at least 2.00 in all courses which are used to fulfill the major requirement (except prerequisites from other departments). No more than two transfer courses may be used for credit in any major option. Transfer credits may not be used to satisfy prerequisites.

Students should begin planning their programs as soon as possible in order to assure that prerequisites are taken in a timely fashion. Plans for all four majors should be made in consultation with a member of the Department’s Undergraduate Committee.

When selecting courses, note that most graduate departments in the biological sciences require at least two terms of mathematics, two terms of physics, and four terms of chemistry; some have additional requirements, e.g., in chemistry, mathematics, earth sciences. Some universities require a reading knowledge of at least one foreign language (most commonly German, French, or Russian) and/or programming skill in some computer language as a further requirement for the Ph.D. Students considering graduate study should seek information about specific graduate programs and schools from their departmental adviser, members of the Undergraduate Committee, and other department faculty.

CREDIT AND ADVANCED PLACEMENT

Starting with the class of 2009, the Department will give one unspecified credit for a biology course to students who receive a score of 5 on the CEEB Advanced Placement Test or a score of 6 or 7 on the Higher Level International Baccalaureate (IB) exam. This unspecified credit satisfies no prerequisite or major course requirements and allows no placement into advanced courses. Under exceptional circumstances, students (including those with IB credit) may request permission in writing, supplying suitable evidence of their preparation for placement into advanced courses, before the end of the fall term. Students who seek such credit should consult the faculty of the course in question and the chair of the departmental Undergraduate Committee. Except under exceptional circumstances, the Department gives no credit for courses taken at another college or university prior to matriculation at Dartmouth.

In order to be considered for admission into Biology 19 (Honors Introduction to Cell Biology), students must take the placement test given during Orientation.

INDEPENDENT RESEARCH AND THE BIOLOGY HONORS PROGRAM

Biology majors may undertake independent research in biology either as part of the Honors Program or separately. Participants in the Honors Program should enroll in Biology 87. The subject of the honors research project must be directly relevant to the specific major of the student. Those who conduct research outside of the Honors Program should enroll in Biology 85.

Work on an Honors thesis normally extends through three terms. Candidates for Honors must meet the minimum College requirements.. Application for the Program should be made no later than two weeks after the start of classes three terms before graduation. Plans for research should be made in the term before the project begins. Independent research conducted off campus during a leave/transfer term without the direct supervision of a faculty advisor from the Dartmouth College Department of Biological Sciences cannot be used to earn credit for Biology 85, 86, or 87.

During the first term of Honors work the candidate shall work individually, on a trial basis, with a faculty supervisor. Biology 87 (or 85) may be counted only once among the eight courses for the major, but two terms of Biology 85, 86, or 87 may be taken for course credit towards graduation.

Each Honors candidate shall submit a thesis to a committee composed of three faculty members, including the thesis supervisor, at least two weeks before the end of the last term. At least two members of this committee must be members of the Biology faculty. Each candidate’s Honors Program ends with the candidate making a public presentation of her or his work, followed by an oral examination, conducted by the thesis committee, on the thesis work and related topics.

REQUIREMENTS FOR ADVANCED DEGREES

The general requirements for advanced degrees are given in the Regulations for Graduate Study section. Each graduate student must receive credit for a set of courses chosen in consultation with the advisory committee. All graduate students are expected to participate in departmental colloquia and weekly seminars.

To receive the Ph.D. degree in Biology a candidate must satisfactorily:

1. Complete the course requirement, as described above.

2. Complete the teaching requirement as specified by the advisory committee.

3. Demonstrate mastery of conceptual and factual material in the major area of specialization in an oral examination.

4. Present and satisfactorily defend a thesis proposal before the advisory committee.

5. Satisfy the two-year residence requirement of the College.

6. Complete a doctoral dissertation.

7. Defend the dissertation before a faculty committee appointed for this purpose.

Although the graduate program is designed for students pursuing the Ph.D. degree, a master’s degree may be awarded under special circumstances. To receive an M.S. degree in Biology, a candidate 1) must satisfactorily complete course and teaching requirements, as specified by the advisory committee, 2) complete a thesis, 3) defend the thesis in an oral examination before a faculty committee, and 4) satisfy the one-year residence requirement of the College.

1. History of Modern Biology

06X: 10A

An introductory survey of the history of modern biology from Charles Darwin to the present. This course will consider major developments in biology such as Darwin’s theory of evolution, experimental embryology and the revolt against morphology, Mendelian genetics and the eugenics movement, the rise of ecology and Neo-Darwinism, and the impact of molecular biology. We will emphasize the development of biology as an experimental science and the social context for biological thought and practice.

Open to all students without prerequisite. Dist: SCI. Dietrich.

2. Human Biology

05F, 06F: 11

A course designed to help students (biologists and non-biologists) understand the biological basis of human health and disease. The course will emphasize the fundamental aspects of biochemistry, genetics, cell and molecular biology, physiology, anatomy, reproductive biology, and function of various organs as they relate to humans. Particular emphasis will be placed on specific topics in human health and disease and how these issues affect us all individually in our own health and collectively in our international society.

Open to all students without prerequisite. Dist: SCI. Witters.

4. Genes and Society

06S, 07S: 10A

This course is designed for the humanities or social sciences major. It focuses on how our current understanding of genetic mechanisms has led to new biological insights and to the development of powerful technologies with far reaching implications for our society. It is the aim of this course to provide a solid understanding of the mechanisms of molecular genetics and to discuss implications of genetic engineering and related technologies to our every day lives. Although this course will focus on the science, we will also consider the ethical, political, human, and economic impacts of these technologies. Several guest lecturers will provide personal perspectives based on their experiences. The ultimate goal of the course is to provide an understanding of the biology and technology so that students can make informed decisions on issues that continually and increasingly arise in our society. Offered in alternate years. Dist: SCI. Gross.

5. Philosophy of Biology

Not offered in the period from 05F through 07S

This course will consider philosophical issues pertinent to the biological sciences. Topics may include genetic determinism, biology and ideology, the nature of experiment in biological practice, adaptationism, the species problem, the nature of biology as a historical science, concepts of fitness and function, the units of selection debate, and phylogenetic inference.

Open to all students without prerequisite. Dist: SCI. Dietrich.

6. Dinosaurs

06W, 07W: 2A

This course is designed for the non-major. It will cover all aspects of dinosaur biology including their origin and evolution, phylogeny, behavior, physiology, and extinction. Because dinosaurs will be placed in their biological and geological contexts, other topics will include the geological record, the processes of fossilization, and vertebrate evolution in general. Particular attention will be paid to current debates including the origin of birds and mass extinction. The goal of this course is to teach the basic principles of evolutionary biology using dinosaurs as exemplars of evolutionary patterns and processes.

Open to all students without prerequisite.

Dist: SCI. Peterson.

7. First-Year Seminars in Biology

Consult special listings

9. The Biology and Politics of Starvation (Identical to Social Sciences 9)

06W: 2A

Despite the rapid advancements of science, and the best intentions of humanitarian agencies, chronic malnutrition, hunger and starvation continue to afflict more than one out of every six of the world’s people. We will examine the science and politics of malnutrition, hunger and starvation intertwining the biology of human nutrition and starvation with social, economic, environmental and political consequences of food deprivation. Student presentations will focus on the description of and lessons learned from important historical famines, the issues of world food supply and the societal responses to starvation and famine. The course will conclude with a Student World Food Congress, where we will examine and debate the reasons underlying the failure of nations to guarantee the access to food as a fundamental human right.

Open to all students without prerequisite. Dist: SOC or INT. Satisfies the Interdisciplinary requirement (Class of 2004 or earlier). Butterly, Shepherd, Witters.

14. Ecology and Evolution

05F, 06F: 10;Laboratory-Field/discussion M,Tu,W,Th, or F 1:45-5:45

This course examines fundamental concepts in the rapidly developing fields of ecology and evolution, and explores important topics, such as conservation of species diversity in the tropics and the biological testing of genetically engineered organisms, where ecology and evolution merge. Ecological mechanisms determining both global and local patterns in the distribution and abundance of plants and animals (e.g., physiological responses to environmental variables, behavior, competition, predation, and parasitism) are explored. Evolutionary processes such as speciation, selection and adaptation will also be discussed, including their applications to applied environmental issues. Laboratories focus on experimental and quantitative analyses of local ecosystems, with an emphasis on field studies.

Open to all students. Dist: SLA. Irwin, Peart.

15. Introduction to Cell Biology

06W, 06S, 07W, 07S: 9;Laboratory/discussion Tu,W, or Th 1:45-5:45, Tu,W, or Th 6:30-10:30

This course is designed to give students an introduction to the fundamental mechanisms that govern the structure and function of cells. Principles and concepts of cell and molecular biology will be illustrated with emphasis on model organisms. The laboratory section will provide students with hands-on experience in modern laboratory techniques including microscopic analysis and biochemical fractionation of eukaryotic cells.

Biology 15 and 16 can be taken in any order.

Open to all students. Dist: SLA. Sloboda, Schaller, Smith, Gladfelter.

16. Genetics

06W, 06S, 07W, 07S: 9;Laboratory/discussion

Tu,W or Th 1:45-5:45, Tu, W, or Th 6:30-10:30

A survey of modern genetics, emphasizing the transmission and expression of DNA, the hereditary material. Topics will include DNA replication, transcription, translation, recombination, mutation, complementation, Mendelian inheritance, linkage analysis and genetic mapping. Issues of genetic engineering and of the impact of genetics on society will be introduced.

Biology 15 and 16 can be taken in any order.

Open to all students. Dist: SLA. Berger, Lambie, Dolph, Jack.

19. Honors Introduction to Cell Biology

05F, 06F: 9;Laboratory Tu or Th 1:45-5:45 or 6:30-10:30

Biology 19 is a general cell biology course for students with a strong background in biology and chemistry who have an interest in majoring in Biology. This course will give students an introduction to the fundamental mechanisms that govern the structure and function of eukaryotic cells and will include discussion of the experimental basis for understanding cell function. The laboratory section will provide students with hands-on experience in modern laboratory techniques including microscopy, cell fractionation, and protein purification.

Biology 19 is open only to first-year students and enrollment is limited. Admission is by satisfactory performance on a proficiency test given during Orientation. Biology 19 is the prerequisite equivalent to Biology 15.

Prerequisite: Satisfactory performance on the biology proficiency test. Dist: SLA. Smith.

20. Life’s Innovations

07W: 10

Evolution has been an amazing problem solver, having created a huge variety of solutions to a few basic problems during the history of life. This course will introduce students to a number of these major problems and the solutions that bacteria, fungi, plants and animals have evolved. What is life? How can an organism solve many problems at one time? How should an organism make copies of itself? How do organisms acquire fuel to operate and then deal with the resulting waste by-products? How can an organism get from one place to another? How can an organism keep from becoming dinner for something else? These are some of the major problems that organisms face, and this class will explore how organisms have evolved to solve them. Offered in alternate years.

Prerequisite: Biology, 14, 15 or 16. Dist: SCI. McPeek.

22. Field Methods In Ecology

06X: 10A; Laboratory M or Tu1:45-5:45

This course is an introduction to sampling and survey methodologies for populations and communities in both aquatic and terrestrial environments. The course will be divided into week-long modules, each focusing on a particular group of organisms in the environment. A great deal of emphasis will be placed on h hypothesis generation, experimental design and statistical analysis. Participation in the laboratory/field component is both required and critical as one of the primary benefits of this course will be “on the ground�? training in field methods.

Prerequisite: Biology

14. Dist: SLA. Cottingham.

23. Molecular Biology

06X: 10A;Laboratory/discussion Tu or Th 2:00-6:00 or 7:00-11:00

This course focuses on the molecular biology underlying basic genetic principles. It is designed to build upon material found in entry level courses while providing an adequate foundation for more advanced study in molecular genetics. Topics include nuclear and chromatin structure and function, DNA replication, RNA transcription and processing, protein translation, and mechanisms controlling gene expression such as promoters and enhancers and their binding proteins. Laboratories investigate topics discussed in lecture and provide experience with some of the basic technologies of molecular biology.

Prerequisite: Biology 16. Biology 15 is also recommended. Dist: SLA. Bickel.

24. Microevolution

06W: 10A

A consideration of the genetics of natural populations and the process of organic evolution. Topics include the source and distribution of phenotypic and genotypic variation in nature; the forces which act on genetic variation (mutation, migration, selection, drift); the genetic basis of adaptation, speciation, and phyletic evolution. Offered in alternate years.

Prerequisites: Biology 14 or 16. Dist: SCI. McPeek.

25. Introductory Marine Biology and Ecology

05F, 06F: 11

A course designed both for biology majors and other students focusing on the interrelationships between marine organisms and their physical and biological environment. The course emphasizes the marine environment as an ecosystem with attention given to both benthic and openwater habitats.

Prerequisite: an introductory biology course. Dist: SCI. Chen.

27. Developmental Biology

05F, 06F: 9

An analysis of early cell and tissue development leading to organ differentiation. Fertilization, morphogenesis, and cell differentiation will be considered in terms of recent advances in developmental biology.

Prerequisite: Biology 15. Dist: SCI. Erives.

28. Macroevolution

07S: 2A

This course focuses on evolution above the level of individual species, and is designed to complement Biology 24. We will first examine the evolution of whales to learn the basic principles and methodology of macroevolutionary analysis. Then, using these tools, we will examine in detail the origin of animals, the Cambrian explosion, and their subsequent evolution from the Cambrian to the Recent. Topics covered will include body plan evolution and development, rates of morphological and molecular evolution, punctuated evolution, group selection theory, and mass extinction. Offered in alternate years.

Prerequisites: Biology 14 or 16. Dist:

SCI. Peterson.

29. Biostatistics

07W: 9;Laboratory M or Tu 1:45-5:45

The course will cover basic descriptive statistics, simple probability theory, the fundamentals of statistical inference, regression and correlation, t-tests, one-way analysis of variance, basic analyses of frequency data and non-parametric statistics, and the general philosophy of experimental design. We will explore these topics from the perspective of biological applications. Examples will be drawn from all subdisciplines of biology (e.g. biochemical kinetics, development, physiology, ecology, evolution). Offered in alternate years.

Prerequisites: One advanced course in biology. Dist: QDS. Cottingham.

33. Animal Behavior

06S: 10;Laboratory-Discussion M,Tu,W, Th or F 1:45-5:45

The causation, development, integration, evolution, and adaptive value of behavioral patterns of animals as individuals and in groups. Emphasis will be on vertebrates, but examples will also be drawn from all animal phyla. Topics include ethology, communication, orientation, and social organization. Laboratory work will emphasize field studies. Offered in alternate years.

Prerequisite: Biology 14. Dist: SLA. Mbora.

34. Neurobiology

05F, 06F: 11;Laboratory M,Tu,W,Th or F 1:45-5:45

This course emphasizes a cellular approach to the study of nervous systems. The study of the cellular basis of neuronal activity will form the foundation for studies on sensory physiology, the control of muscle movement, and neuronal integration. Selected topics of current research activities with vertebrate and invertebrate species will be discussed in order to provide a perspective on how the field of neuroscience is developing. Laboratory exercises will provide the opportunity to learn extracellular and intracellular electrophysiological recording techniques.

Prerequisite: Biology 15. Dist: SLA. Vélez.

35. Animal Physiology

06W, 07W: 11

This course emphasizes the environmental and biochemical aspects of animal physiology. The adaptive responses of different organisms, including humans, to a variety of environmental factors will be studied from the systems to the molecular level of organization. Topics to be covered include respiration, circulation, temperature regulation, osmoregulation, digestion, muscle, and integration of body functions.

Prerequisite: Biology 15. Dist: SCI. Henderson, Maue.

37. Endocrinology

06S, 07S: 10A

The regulatory functions, physiology and molecular mechanisms of the endocrine system and related metabolic pathways will be explored with an emphasis on human and mammalian biology. Course requires a student paper on selected topics, stemming from an examination of the biology and pathobiology of these systems in health and disease. These topics will be drawn, in part, from timely publications in the biomedical literature.

Prerequisite: Biology 15 and 16 or permission of the instructor. Dist: SCI. Witters.

39. Neuroimaging and Cellular Neuroscience

06W, 07W: 11

The human brain is an ever-changing, flexible structure that generates our plastic minds. How, exactly, does experience change the brain and result in learning and memory? This course will cover imaging techniques in cell biology designed to understand experience-dependent synaptic plasticity. Topics include the cytoskeleton of hippocampal neurons, membrane trafficking, axonal transport, growth cone elongation, structure and function of dendritic spines, spine plasticity and turnover, and calcium signaling in spines.

Prerequisite: Biology 15 (Biology 34 or Psychology 6 strongly recommended). Dist:SCI. Langford.

41. Plant Physiology

Not offered in the period from 05F through 07S

A study of the chemical and physical processes occurring in plants. These include photosynthesis, respiration, water relations, translocation of food, mineral absorption and utilization, metabolism of carbohydrates, lipids and proteins, and the mechanism of action of light and hormones in controlling growth and development. Offered in alternate years.

Prerequisite: An introductory biology course. Dist: SCI.

42. Plant Development

06S: 12

This course will cover a range of topics including the development of the embryo, root, trichome, leaf, flower, ovule, and seed. This literature-based course focuses on molecular genetic approaches, primarily in Arabidopsis thaliana.

Prerequisite: Biology 23 or Biology 27 or permission of the instructor. Dist:SCI. Jack.

50. Vertebrate Zoology

06W, 07W: 12

This course will examine origins, diversity, structure and function within and among the vertebrate classes (including fish, amphibians, reptiles, birds and mammals). We will consider the evolution of the vertebrate body plan and innovations associated with common organ systems (e.g., skeletal, muscular, digestive, sensory, etc.) shared by different taxa. In addition we will consider specialization of form and function to the diverse ecology of vertebrates as well as the manner in which very different taxa cope with similar habitats and environmental demands. In so doing, we will draw on evolutionary principles such as adaptation, convergent and parallel evolution and evolutionary constraints. The course will primarily consist of lecture and readings with examination of specimens and opportunities for off-campus field trips.

Prerequisites: One among Biology 14, 15, or 16. Dist. SCI. Mbora.

51. Ecosystem Ecology

07W: 9

This course will examine the of organisms in ecosystem functioning, particularly the movement of materials and energy through terrestrial, freshwater, and marine ecosystems. The course will consist of regular lectures, readings from the primary literature, homework exercises, and in-class midterm and final exams. Topics to be covered include food webs, ecosystem productivity, energy budgets, nutrient budgets and nutrient cycling, ecosystem stability, and the role of individual species in ecosystem functioning. Emphasis will be placed on evaluating the contributions of ecosystem ecology to current environmental problems. Offered in alternate years.

Prerequisite: Biology 14 and Chemistry 5-6 or permission of the instructor. Dist. SCI.

52. Behavioral Ecology

07S: 2A;Laboratory/field, to be arranged

This course will consider the evolutionary and ecological factors influencing or determining the behavior of animals in natural communities. Topics include foraging behavior, habitat selection, mating and breeding systems, territoriality, aggression and competitive behavior interactions. Seminar format, with lectures and discussions based on readings of primary literature. Laboratories will be devoted to studies of the ecology and behavior of terrestrial vertebrates in local environments. Offered in alternate years.

Prerequisite: Biology 14, 33, and permission of the instructor. Enrollment limited. Dist: SLA.

53. Aquatic Ecology

05F: 10A;Laboratory M,Tu,W or Th 1:45-5:45

A study of the interaction between biological communities and their aquatic environment. Lectures and readings provide the scientific background necessary for understanding the physical, chemical, and biological dynamics of freshwater habitats. Emphasis is placed on application of fundamental concepts to problems in conservation and management of aquatic systems and species. The laboratory and field work are designed to acquaint the student with modern methodological approaches to the study of aquatic ecosystems. Offered in alternate years.

Prerequisite: Biology 14. Dist: SLA. Taylor.

54. Population Ecology

06F: 10A;Discussion, to be arranged

This course explores the description of populations, population growth, and the determination of abundance. Examples will be drawn from a diversity of plant and animal taxa to illustrate the broad scope of population ecology, including its role as a foundation for evolutionary ecology and community ecology, and its contributions to applied problems in conservation biology, pest management, human demography, and the management of harvested populations. Throughout, this course will emphasize the development of verbal, graphical, and mathematical models to describe populations, generate predictions, test hypotheses, and formalize theory. Offered in alternate years.

Prerequisites: Biology 14 and one upper level ecology course. Dist: SCI. Ayres.

55. Ecology of Tropical Ecosystems

06W, 07W: D.F.S.P.

Introduction to ecology through intensive field studies in a variety of tropical ecosystems, including lowland rain forest, cloud forest, dry forest, montane forest, and alpine paramo. Emphasis is on identification and taxonomy of plants and animals, on developing observational skills, and on learning field and analytical methods (including hypothesis testing, statistical and software skills) for assessing the relationships among organisms and their tropical environment. The schedule is intensive, and includes extensive fieldwork, laboratories, lectures, discussions, and research projects. The course is closely integrated with Biology 57. Accommodations will be at field stations in Costa Rica.

Prerequisites (pending faculty approval): Biology 14, at least one advanced-level course in ecology, and acceptance into the program. Strong preference will be given to students who have taken at least one ecology laboratory course (e.g., Biology 22, 33, 53, and 59). Additional coursework in ecology and evolution will strengthen applications. Previous research experience is also a benefit. Selection is based on a written application and an interview with the program faculty. Dist: SLA. Peart.

56. Coral Reef Ecology

06W, 07W: D.F.S.P.

Field and laboratory investigations of marine organisms and communities in coral reef environments. Lectures will consider the biology and ecology of algae, higher plants, invertebrates, and fish, and will stress inter-specific interactions, community structure and energetics. Students will conduct individual research projects. The course is given at the Discovery Bay Marine Laboratory, Jamaica.

Prerequisites: See Biology 55. Dist: SLA. Gilbert.

57. Field Research in Tropical Ecology

06W, 07W: D.F.S.P.

Students in this course will conduct a series of research projects to test hypotheses about tropical plant and animal communities. Topics range from studies of plant-pollinator systems, chemical defenses, and coevolutionary relationships to studies of animal distribution, ecology and behavior. Emphasis will be on making observations, asking testable questions, developing experimental protocols, conducting the research, analyzing data statistically, writing of research reports, and seminar presentation. This course will be closely integrated with Biology 55. Accommodations will be at field stations in Costa Rica.

Prerequisites: See Biology 55. Dist: SLA. Ayres.

58. Advanced Community Ecology

06W: 9

This course will examine the various mechanisms structuring ecological communities of plants and animals. The course will consist of regular lectures, readings from the primary literature, and individual projects. Topics to be covered include simple two-species interactions (e.g. predation, competition, parasitism, mutualisms), simultaneous multispecies interactions, food web structure, regulation of species diversity on ecological and evolutionary time scales, community succession, and biogeography. Emphasis will be placed on the development of mathematical models and their relationship to empirical studies. Offered in alternate years.

Biology 14, and one upper level ecology course. Dist: SCI. Irwin.

59. Physiological Ecology

07S: 10A;Laboratory M,Tu,W or Th 1:45-5:45

What factors determine the distribution and abundance of organisms? What are the consequences of climate change for biological communities? This course is an exploration of environmental effects on fundamental physiological processes in plants and animals. Abiotic factors, such as temperature and water availability, interact with biotic forces, such as predation, herbivory, and competition, to constrain the ability of organisms to survive, grow, and reproduce. Physiological solutions that allow success in one environment may preclude it in another. This course seeks to build up from physiological principles to understand characteristics of populations, communities, and ecosystems. Laboratories will challenge students to generate and test their own hypotheses using contemporary theoretical frameworks and modern research apparatus. Offered in alternate years.

Prerequisite: Biology 14. Dist: SLA. Ayres.

61. Molecular Genetics of Prokaryotes and Lower Eukaryotes

06W, 07W: 2

Structure, function, organization, and control of genes in bacteriophage, bacteria, and fungi. Strategies for control of gene expression at the transcriptional and translational levels. Mechanisms for rearrangement and exchange of genetic material and the implications of such processes for the release of genetically engineered organisms into the environment.

Prerequisites: Biology 16 and 23 or permission of the instructor. Dist: SCI. Guerinot.

62. Evolutionary Developmental Biology

06S: 2A

The focus of this course is the interface between developmental biology, evolutionary biology, paleontology, and systematics. Lectures will focus on the mechanistic aspects of animal development including cis regulatory DNA and cell signaling systems, cladistics, the fossil record, and animal physiology. The evolution of animal development will be discussed in great detail paying particular attention to the origin and evolution of bilaterian body plans. Offered in alternate years.

Prerequisites: Biology 20, 21, 23, 24 or 27. Dist: SCI. Peterson.

63. Developmental Genetics

06F: 10A

Selected topics in developmental genetics, with emphasis on recent work involving model systems, e.g., Drosophila melanogaster, Arabidopsis thaliana, Caenorhabditis elegans and Mus musculus. The following areas may be considered in depth: oogenesis, spermatogenesis, fertilization, germ cell determination, embryonic and postembryonic induction, sex determination, axis specification, cell adhesion, and cell migration.

Prerequisite: Biology 27 or permission of the instructor. Dist: SCI. Lambie.

64. Microbiology

05F, 06F: 12;Laboratory W 1:45-5:45 or 6:00-10:00

A lecture, discussion, and laboratory

considering the biology of microorganisms, with emphasis on bacteria. Topics such as structure, function, genetics, and metabolism of bacterial cells will be covered. The ecological role of various species of microorganisms will also be discussed.

Prerequisite: Biology 14, 15, or 16. Dist: SLA. Guerinot, O’Toole.

65. Molecular Genetics of Eukaryotes

05F: 2

Lectures dealing with the structure, function, organization, dynamics, and regulation of genes in higher eukaryotes and their viruses. Topics ranging from transposition of genes, to regulation of transcription, to targeted gene disruption in transgenic organisms will be covered. New topics in the literature will be included as well.

Prerequisites: Biology 16 and 23 or permission of the instructor. Dist: SCI. Grotz.

66. Biology of the Immune Response

06W, 07W: 9

This course will consider immunoglobulin structure, antigen-antibody reactions, complement, hypersensitivity, immunogenetics, immunodeficiency, tumor immunology and therapy, and autoimmunity.

Prerequisite: Biology 16 or 15, or permission of the instructor. Dist: SCI. Fanger.

67. Molecular Pathogenesis of Fungi and Parasites

06W, 07W: 2A

Lectures and discussion about the biology, ecology, genetic, biochemistry and pathology of eukaryotic pathogens which are important causes of infectious diseases. Biochemical similarities between mammalian host cells and eukaryotic pathogens limit options for therapeutic strategies, challenge drug discovery efforts and heighten the impact of drug resistant organisms. The course emphasizes fungi which are major pathogens in AIDS and other immunosuppressed patients and will touch on parasites such as malaria which devastate human populations world-wide.

Prerequisites: Biology 23 and Biology 64. Biology 66 and Biology 77 are also recommended. Dist:SCI. Sundstrom.

68. Computational Molecular Biology

06W, 07W: 10A

Computers and computer programs have become essential tools in modern molecular biology. As the amount of DNA and protein sequence data continues to grow, the use and understanding of these computational tools is becoming increasingly important. Deriving biological understanding from sequence data requires sophisticated computer analyses while demanding from molecular biologists the ability to interpret intelligently the results from these analyses. Not only can these programs provide the biologist with information about his or her sequence of interest, but a solid understanding of these tools can also be used to make predictions of biological phenomena that can be tested in the lab. This course will explore computational molecular biology through both lectures and hands-on computer experimentation through homework assignments.

This course will discuss approaches to analyzing protein and DNA sequences and will foster an understanding of how to extract biologically relevant information from the numerous databases containing all this information. Topics will include basic computer architecture and operating systems, database design and searching, sequence comparisons, pattern discovery, genome comparisons, gene discovery, determining evolutionary relationships, RNA and protein structure predictions, data mining, and DNA array analysis. No computer programming experience is needed, but familiarity with using the Internet is recommended. Offered in alternate years.

Prerequisites: Biology 23 or permission of the instructor. Dist: SCI. Gross.

70. History of Genetics

05F: 2A

This course is a survey of the history of genetics for advanced students. Proceeding from Galton to the present, this course will emphasize the main intellectual trends in genetics as well as the interconnection between genetics and society. Topics for discussion will include whether Gregor Mendel was a Mendelian, the importance of Thomas Hunt Morgan’s Drosophila network, the relationship between eugenics and genetics, the effect of Atomic Energy Commission support on human genetics, and the impact of molecular biology. Offered in alternate years.

Prerequisite: Biology 16. Dist: SCI. Dietrich.

71. Advanced Topics in Cell Biology

06S, 07S: 2A

This course will cover in depth one or more specific topics in cell biology such as cell division, chromosome structure and function, signal transduction, the cytoskeleton, membrane assembly, and intracellular protein targeting. Material will be presented in a manner designed to encourage student comments and to demonstrate how modern molecular, biochemical, immunological, and genetic techniques are employed to study problems in cell biology. Reading assignments will be taken from the current research literature.

Prerequisite: Biology 15 and 23 or permission of instructor. Dist: SCI. Bickel.

73. Molecular Evolution

06S: 9

Modern molecular techniques have opened a new door on our understanding of how the diversity of life has evolved. The ability to sequence DNA and proteins has also provided a huge volume of data that is difficult to manage and make sense of. In this course we will explore how DNA and protein sequences evolve, how DNA replication influences gene evolution, how the ecology and demography of organisms shape patterns of genetic diversity, how interactions between the genomes of different organisms shape patterns of genetic diversity, how interactions between the genomes of different organisms shape the evolution of diseases, and how interactions among genes shape the entire genome. Offered in alternate years.

Prerequisites: Biology 20, Biology 23, Biology 24 or Biology 26. Dist:SCI. McPeek.

74. Advanced Neurobiology

06S: 10A

A seminar course that considers recent advances in specific areas of neurobiology. Topics to be discussed will be selected among ion channels, neurotransmitters, synaptic transmission, intracellular signaling pathways, synaptic connections, neuronal plasticity, brain biochemistry, behavioral neurobiology or developmental neurobiology. Offered in alternate years.

Prerequisite: Biology 34 and permission of the instructor. Dist: SCI. Henderson, Maue.

75. Genomic Circuitry

06S, 07S: 10

Many genomes, including the human genome, have been sequenced. Now, increasing attention has turned to a cryptic, yet fundamental component of these genomes: gene circuitry, i.e. the “wiring�? that links together activated genes in a genomic program. Specialized DNA sequences determine where and when a given gene is expressed during an organism’s life cycle. These genomic “regulatory�? sequences play a major role in basic evolutionary processes. How do regulatory sequences encode differential gene expression? How do they evolve? How do we identify and decode them? This course will investigate these questions as well as landmark papers necessary to understand present and future work in this field.

Prerequisites: Biology, 23, 24 or 27. Dist: SCI. Erives.

76. Advanced Genetics

07S: 3A

Methods and strategies for the analysis of gene structure, function and genetic interactions. The course will examine how the genetic manipulation of model organisms, including yeast, Drosophila, C. elegans, and mouse, is used to explore the mechanisms of fundamental biological processes such as cell division, development, and intercellular communication. Emphasis will be placed on the application of classical genetic methods, including mutant screens, recombination and complementation analysis, genetic mosaics, and the use of conditional mutations. Modern molecular-based approaches, including gene knockout, gene dosage and misexpression studies will also be included. Three hours of lecture and one hour of discussion per week.

Prerequisites: Biology 16 and 23. Dist: SCI. Berger.

77. Biochemistry

05F, 06F: 10;Discussion W or Th 2:00-3:00

This course studies molecular structure and function from a biochemical point of view, emphasizing the biochemistry of proteins, lipids, and carbohydrates. Topics include protein structure and function, enzymes and enzyme kinetics, lipids and membranes, and carbohydrates and cell walls. The participation of these biomolecules in metabolism is also discussed, and focuses on the metabolic pathways of glycolysis, glucogenesis, fatty acid oxidation, amino acid catabolism, the TCA cycle, and oxidative phosphorylation. The course concludes with a look at the integration of metabolism in mammals.

Prerequisites: Biology 15 and Chemistry 52 or 58 or permission of the instructor. Dist: SCI. Schaller.

78. Advanced Biochemistry

06W, 07W: 10;Discussion W or Th 2:00-3:00

This course will cover recent advances in biochemistry. The first half of the course will discuss advanced topics associated with the metabolism of carbohydrates, fatty acids, amino acids and nucleic acids, as well as how metabolic pathways are coordinately regulated. The remainder of the course will concentrate on photosynthesis, membrane transport, and signal transduction pathways. Three lectures and one discussion session per week.

Prerequisite: Biology 77. Dist: SCI. Dolph.

79. Genetics and Physiology of Behavior

06W, 07W: 2A

Examination of the genetic, physiological, cellular, and molecular bases of behavior and responses to environmental factors in eukaryotic organisms. Topics to be covered from the current and classic literature will include circadian rhythmicity, learning and memory, and other areas of current research, and will vary somewhat from year to year.

Prerequisites: Biology 23 and permission of the instructor Dist: SCI. Dunlap.

81. Clinical Biomedical Research

05F, 06S, 06F, 07S: 2A

This course teaches the fundamentals of clinical biomedical research (CBR). The CBR curriculum offers a unique combination of direct involvement in ongoing clinical research studies with a comprehensive didactic program and experience conducting and designing clinical studies. Designated as Academic Associates, the students will spend time in the DHMC Emergency Department (E.D.) playing an integral role in patient identification, enrollment, and data collection for the ongoing clinical research studies. Coupled with this “hands-on�? data collection in the E.D., the didactic program consists of weekly classes focusing on research design, data collection techniques, statistical analysis, and scientific poster preparation. At the completion of the course, each student will develop a “mock clinical research study�?.

Prerequisites: Biology 15/19 and Biology 16 and permission of the instructor. Biology 2 and Biology 72 or Mathematics 10 are also recommended. Dist:SCI. Curtis.

85. Independent Research in Biology I

All terms: Arrange

Original and independent investigation of a biological problem with associated study of primary literature sources under the supervision of a member of the staff for one academic term. Open only to Dartmouth biological sciences majors. Projects may include laboratory or field research or modeling that will further understanding of a relevant basic or applied research problem. May be taken as one course in the major by students not enrolled in the honors program. Students electing both Biology 85 and Biology 87 may count only one among the eight courses for their major. In no case may a student elect more than two courses among Biology 85, 86, and 87.

Prerequisites: at least two Biology courses, a 2.67 average in previous biology courses, and permission of the chair of the Undergraduate Committee and the supervising instructor. The application and research proposal must be submitted at least one month prior to the beginning of the term in which the course is to be elected. The staff.

86. Independent Research in Biology II

All terms: Arrange

A second term of original and independent investigation of a biological problem under the supervision of a member of the staff. Open only to Dartmouth biological sciences majors who have satisfied the requirements for Biology 85 and who wish to continue their independent research for a second term. Does not count for credit in the major.

Prerequisites: Satisfactory completion of Biology 85 (including research paper) and permission of both the chair of the Undergraduate Committee and the supervising instructor(s). The application and research proposal must be submitted at least two weeks prior to the beginning of the term in which the course is to be elected. The staff.

87. Honors Research in Biology

All terms: Arrange

Original and independent investigation of a biological problem with associated study of primary literature sources under the supervision of a member of the staff. Open only to Dartmouth Biology majors. Projects may include laboratory or field research or modeling that will further understanding of a relevant basic or applied research problem. Required of honors students as part of the major. Students taking both Biology 85 and Biology 87 may count only one term of the latter among the elective courses for their major, but can receive College credit for Biology 99. In no case may a student elect more than two courses among Biology 85 and 87.

Prerequisites: at least two Biology courses, a 3.0 average in previous biology courses, and permission of the chair of the Undergraduate Committee and the supervising instructor, obtained no later than two weeks after the start of classes three terms before graduation. The staff.

99. Senior Seminar in Biology

06S, 07S: 11

This course will focus on presentation techniques and critical evaluation of other students’ research and presentations. Students who have conducted Independent Research will present background information related to their research projects, develop seminars based on their own findings, and receive feedback. All students taking Biology 87 are encouraged to enroll in this seminar as a ninth Biology course.

Prerequisites: Senior standing and previous or current enrollment in Biology 87. Church.

GRADUATE COURSES

101. Biochemistry, Cell and Molecular Biology I (Identical to Biochemistry 101, Microbiology and Immunology 101, Genetics 101)

05F, 06F: 9

102. Biochemistry, Cell and Molecular Biology II (Identical to Biochemistry 102, Microbiology and Immunology 102, Genetics 102)

06W, 07W: 9

103. Biochemistry, Cell and Molecular Biology III (Identical to Biochemistry 103, Microbiology and Immunology 103, Genetics 103)

06S, 07S: 9

110. Scientific Integrity and Research Ethics

05F, 06F: Arrange

This course is designed to introduce scientific researchers to issues in research ethics. We will emphasize foundational principles underlying scientific integrity and their application to a range of issues including data management, animal and human subjects, collaboration, mentoring, peer review and the ethical implications of different forms of scientific research. Analysis and presentation of case studies will constitute important focal points for discussion in class meetings. Dietrich.

119. Design and Development of Scientific Proposals

Not offered in the period from 05F through 07S

This graduate seminar and practicum focuses on design and development of scientific research proposals in the Earth, Ecosystem and Ecological Sciences. Emphasis is placed on the formulation and design of testable scientific ideas and the development of these ideas into feasible projects. Each student is responsible for the development and execution of a realistic research proposal (typically following NSF proposal format). Students provide critical evaluation of each other’s ideas and written work throughout the course. Offered in alternate years.

Prerequisite: Permission of instructor. Folt.

120. Advanced Population Ecology

06F: 10A

This course explores the description of populations, population growth, and the determination of abundance. Examples are drawn from a diversity of plant and animal taxa to illustrate the broad scope of population ecology, including its role as a foundation for evolutionary ecology and community ecology, and its contributions to applied problems in conservation biology, pest management, human demography, and the management of harvested populations. Throughout, this course will emphasize the development of verbal, graphical, and mathematical models to describe populations, generate predictions, test hypotheses, and formalize theory.

Prerequisite: Permission of the instructor is required. Ayres.

122. Ecology, Evolution and the “Real World�?

Not offered in the period from 05F through 07S

We explore the actual and potential contribution of the disciplines of ecology and evolution to solving problems, to productivity and to quality of life. Are our disciplines geared to these goals or not? Should they be? Do changing conditions in the world require changes in priorities or paradigms? Students will develop answers to these questions in case studies of particular issues, or particular topics in ecology and evolution. Peart.

123. Advanced Community Ecology

06W: 9

This course examines the mechanisms structuring ecological communities of plants and animals. The course will consist of regular lectures, readings from the primary literature, and individual projects. Topics to be covered include simple two-species interactions (e.g. predation, competition, parasitism, mutualisms), simultaneous multispecies interactions, food web structure, regulation of species diversity on ecological and evolutionary time scales, community succession, and biogeography. Emphasis will be placed on the development of mathematical models and their relationship to empirical studies. Permission of the instructor is required. Irwin.

125. The Nature and Practice of Science

Not offered in the period from 05F through 07S

This course compares and contrasts the nature and practice of science across the range of contemporary biological disciplines. Topics include: What is science? What is the structure of scientific knowledge? What are the philosophical, logical, and practical aspects of hypothesis testing? What are intellectual strategies for successful research in biology? What is the role of ethics in scientific research? Format includes readings, exercises, and discussion. Ayres.

127. Phylogenetic Methods Applied to Molecular Data

Not offered in the period from 05F through 07S

In the past decade, DNA sequencing has become easy and affordable to do, and theoretical developments have made the application of DNA sequence data a necessary part of an amazing range of seemingly unrelated topics. This seminar will teach researchers to analyze DNA sequence data (and codons and protein sequence data as well) using the latest methodologies and software available, and expose them to a wide range of analysis types.

128, 129. Statistics and Experimental Design I and II

06W, 07W: Arrange

This is a two-term, graduate-level sequence in statistics and experimental design as applied to biological systems. There will be lectures and laboratories, regular homework assignments, and a major project of statistical analysis. Topics during the first term include sampling distributions and general hypothesis testing, contingency table analysis, correlation, and regression (linear, polynomial and logistic regression, and model selection techniques). Topics in the second term include analysis of variance, analysis of covariance, experimental design (e.g., factorial, blocked, latin squares, nested, and split plot designs), and a number of nonparametric techniques. Emphasis will be placed on the use of statistical computer software (SAS) in performing analyses. Alternate years.

Prerequisites: Graduate standing and at least one elementary course in statistics. Cottingham.

130. Advanced Topics in Biostatistics

Not offered in the period from 05F through 07S

This seminar course for advanced graduate students is offered intermittently whenever there is sufficient student interest in a particular statistical topic not covered in the Biology 128-129 sequence. Likely topics include multivariate statistics, time series analysis, maximum likelihood parameter estimation, and Bayesian statistics. Each course will begin with lectures and hands-on computer sessions to introduce students to the statistical approaches under consideration. Once this background material is mastered, students will read and critically evaluate important ecological papers that have used each approach in group discussions. Each student will also complete a term project that applies one or more approaches to a question relevant to her or his own research, then present the results of these projects orally and in writing.

Prerequisites: Graduate standing and Biology 128 and 129.

133. Foundations of Ecology and Evolutionary Biology

05F: Arrange

This course is a reading seminar in which graduate students will read and discuss a series of classic papers taken from the primary literature on various topics in ecology and evolutionary biology. Each week a set of 2-4 papers will be discussed covering a different major topic. The papers will be chosen to expose students to the foundations of the major ideas and theories. The course will meet one evening per week, and each week a different student will lead this discussion of the assigned papers. Irwin.

142. Plant Development

06S: 12

This course will cover a range of topics including the development of the embryo, root, trichome, leaf, flower, ovule, and seed. This literature-based course focuses on molecular genetic approaches, primarily in Arabidopsis thaliana. Jack.

161. Molecular Genetics of Prokaryotes and Lower Eukaryotes

06W, 07W: 2

Structure, function, organization, and control of genes in bacteriophage, bacteria, and fungi. Strategies for control of gene expression at the transcriptional and translational levels. Mechanisms for rearrangement and exchange of genetic material and the implications of such processes for the release of genetically engineered organisms into the environment. Guerinot.

162. Evolutionary Developmental Biology

06S: 2A

The focus of this course is the interface between developmental biology, evolutionary biology, paleontology, and systematics. Lectures will focus on the mechanistic aspects of animal development including cis regulatory DNA and cell signaling systems, cladistics, the fossil record, and animal physiology. The evolution of animal development will be discussed in great detail paying particular attention to the origin and evolution of bilaterian body plans. Offered in alternate years. Peterson.

163. Developmental Genetics

Not offered in the period from 05F through 07S

Selected topics in developmental genetics, with emphasis on recent work involving model systems, e.g., Drosophila melanogaster, Arabidopsis thaliana, Caenor habditis elegans and Mus musculus. The following areas may be considered in depth: oogenesis, spermatogenesis, fertilization, germ cel determination, embryonic and postembryonic induction, sex determination, axis specification, cell adhesion, and cell migration. Lambie.

165. Molecular Genetics of Eukaryotes

05F: 2

Lectures dealing with the structure, function, organization, dynamics, and regulation of genes in higher eukaryotes and their viruses. Topics ranging from transposition of genes, to regulation of transcription, to targeted gene disruption and gene replacement in transgenic organisms will be covered. New topics in the literature will be included as well. Grotz.

168. Computational Molecular Biology

06W, 07W: 10A

Computers and computer programs have become essential tools in modern molecular biology. As the amount of DNA and protein sequence data continues to grow, the use and understanding of these computational tools is becoming increasingly important. Deriving biological understanding from sequence data requires sophisticated computer analyses while demanding from molecular biologists the ability to interpret intelligently the results from these analyses. Not only can these programs provide the biologist with information about his or her sequence of interest, but a solid understanding of these tools can also be used to make predictions of biological phenomena that can be tested in the lab. This course will explore computational molecular biology through both lectures and hands-on computer experimentation through homework assignments.

This course will discuss approaches to analyzing protein and DNA sequences and will foster an understanding of how to extract biologically relevant information from the numerous databases containing all this information. Topics will include basic computer architecture and operating systems, database design and searching, sequence comparisons, pattern discovery, genome comparisons, gene discovery, determining evolutionary relationships, RNA and protein structure predictions, data mining, and DNA array analysis. No computer programming experience is needed, but familiarity with using the Internet is recommended. Offered in alternate years. Gross.

169. Supervised Teaching in Biology

All terms: Arrange

This course is required for all graduate students, based on the assertion that an essential element of graduate education is the experience gained in teaching other students. Such teaching experience is of particular relevance to students interested in academic careers. Students will conduct laboratory or discussion sessions in undergraduate courses under the supervision of the course faculty. The faculty and student teaching assistant work very closely to develop lab and discussion assignments. In some cases, the students are encouraged to present lectures for which they receive detailed feedback on their teaching style. In all cases students will receive instruction on effective teaching techniques through weekly preparation sessions. Topics for discussion include how to teach the material, how to run a discussion, how to evaluate student responses, and grading. Performance will be monitored throughout the term and appropriate evaluation, coupled with detailed suggestions for improvement, will be provided. This course is not open to undergraduates. The staff.

170. College Teaching in the

Life Sciences

Not offered in the period from 05F through 07S

This course is designed for graduate students and Post-docs who plan to obtain a job in which teaching is an important criterion for obtaining the job and for promotion. The course will challenge assumptions on the most appropriate ways to teach undergraduate students in the 21st century. Students will develop their abilities to design a course, identify learning objectives, and select appropriate techniques to achieve these objectives. During the course, students will become able to design a syllabus, select a text, design exams, and evaluate student work. Students will understand different learning styles and how to accommodate them, prepare appropriate class presentations and other classroom activities, and gain a general understanding of recent educational theory. Steele.

171. Advanced Cell Biology

06S, 07S: 2A

This course will cover in depth one or more specific topics in cell biology such as cell division, chromosome structure and function, signal transduction, the cytoskeleton, membrane assembly, and intracellular protein targeting. Material will be presented in a manner designed to encourage student comments and to demonstrate how modern molecular, biochemical, immunological, and genetic techniques are employed to study problems in cell biology. Reading assignments will be taken from the current research literature. Bickel.

175. Genomic Circuitry

06S, 07S: 10

Many genomes, including the human genome, have been sequenced. Now, increasing attention has turned to a cryptic, yet fundamental component of these genomes: gene circuitry, i.e. the “wiring�? that links together activated genes in a genomic program. Specialized DNA sequences determine where and when a given gene is expressed during an organism’s life cycle. These genomic “regulatory�? sequences play a major role in basic evolutionary processes. How do regulatory sequences encode differential gene expression? How do they evolve? How do we identify and decode them? This course will investigate these questions as well as landmark papers necessary to understand present and future work in this field. Erives.

176. Advanced Genetics

07S: 3A

Methods and strategies for the analysis of gene structure, function and genetic interactions. The course will examine how the genetic manipulation of model organisms, including yeast, Drosophila, C. elegans, and mouse, is used to explore the mechanisms of fundamental biological processes such as cell division, development, and intercellular communication. Emphasis will be placed on the application of classical genetic methods, including mutant screens, recombination and complementation analysis, genetic mosaics, and the use of conditional mutations. Modern molecular-based approaches, including gene knockout, gene dosage and misexpression studies will also be included. Three hours of lecture and one hour of discussion per week. Berger.

197. Graduate Research I: Level I

All terms: Arrange

An original individual experimental or theoretical investigation beyond the undergraduate level in one of the fields of biology. This course is open only to graduate students, prior to passing their qualifying examination; it may be elected for credit more than once. This course carries one course credit and should be elected by students conducting research and also electing two or more other graduate or undergraduate courses. Guerinot and the staff of the Department.

198. Graduate Research I: Level II

All terms: Arrange

An original individual experimental or theoretical investigation beyond the undergraduate level in one of the fields of biology. This course is open only to graduate students, prior to passing their qualifying examination; it may be elected for credit more than once. This course carries two course credits and should be elected by students electing only departmental colloquia in addition to research. Guerinot and the staff of the Department.

199. Graduate Research I: Level III

All terms: Arrange

An original individual experimental or theoretical investigation beyond the undergraduate level in one of the fields of biology. This course is open only to graduate students, prior to passing their qualifying examination; it may be elected for credit more than once. This course carries three course credits and should be elected by students conducting research exclusively in any one term. Guerinot and the staff of the Department.

266-270. Graduate Research Colloquium in Biological Sciences

F, W, S: Arrange

This course is required of all students during each term of residence, except summer. An essential element of scientific training is in the critical analysis and communication of experimental research in an oral format. Evaluation will be based on quality of the work described, quality of critical analysis, and on presentation style, including effective use of audiovisual materials. All students will be required to participate in at least one Journal Club/Research in Progress series. Although minor variations in format exist among the several series, all students will make oral presentations that describe work from the current literature or their own research. Normally these series meet weekly. This course is not open to undergraduates. The staff.

Biology 266, Ecology and Evolution

Biology 268, Genes and Gene Products

Biology 269, Plant Molecular Genetics

Biology 270, Computational Biology

297. Graduate Research II: Level I

All terms: Arrange

An original individual experimental or theoretical investigation beyond the undergraduate level in one of the fields of biology.

This course is open only to graduate students, subsequent to passing their qualifying examination; it may be elected for credit more than once. This course carries one course credit and should be elected by students conducting research and also electing two or more other graduate or undergraduate courses. Guerinot and the staff of the Department.

298. Graduate Research II: Level II

All terms: Arrange

An original individual experimental or theoretical investigation beyond the undergraduate level in one of the fields of biology. This course is open only to graduate students, subsequent to passing their qualifying examination; it may be elected for credit more than once. This course carries two course credits and should be elected by students electing only departmental colloquia in addition to research. Guerinot and the staff of the Department.

299. Graduate Research II: Level III

All terms: Arrange

An original individual experimental or theoretical investigation beyond the undergraduate level in one of the fields of biology. This course is open only to graduate students, subsequent to passing their qualifying examination; it may be elected for credit more than once. This course carries three course credits and should be elected by students conducting research exclusively in any one term. Guerinot and the staff of the Department.

(Footnotes)

* If Biology 77 is elected then you must also take Chemistry 51, 52 as additional prerequisites.