Biology Academic Program - Major and Minors - Courses Skip Navigation
Biology

(For 2013–2014 academic year)

Professors Belanger (Chair), Fuller, McHugh, Pruitt
Associate Professors Frey, Hoopes, Ingram, McCay, Meyers
Assistant Professors Ay, Cardelús, Hagos, Holm, Van Wynsberghe, J. Watkins
Visiting Assistant Professors Brashears, Guarnieri
Visiting Instructor C. Woods
Laboratory Instructor LaFave

A major in biology is the traditional undergraduate preparation for students planning to pursue career interests in the biological or health-related sciences. Although the majority of majors ultimately pursue careers in the life sciences, a significant number of individuals with other career interests choose the major within the liberal arts context. The department’s majors are found today in positions of responsibility in many fields outside the life sciences, including business, theology, law, and the performing arts. Biology majors who are interested in pursuing a career in elementary or secondary school teaching should refer to “Educational Studies.”

The Department of Biology offers a major program designed to provide students with a common conceptual foundation through two required courses and an opportunity to pursue breadth and specialization through an extensive selection of elective course offerings, seminars, and research tutorials. Questions about requirements may be directed to the department chair.

Major Program

Students must complete for credit a minimum of nine courses in the department, plus CHEM 101-102 (or CHEM 111). It is strongly recommended that chemistry requirements be taken in the first year, concurrently with beginning biology courses. A biology major can begin the program either by taking a 100-level course or by enrolling in one of the two 200-level required courses (see below). The 100-level courses are generally topic-based courses, and the offering of courses varies from year to year.

All majors are required to take BIOL 211, Evolution, Ecology, and Diversity; and BIOL 212, Molecules, Cells, and Genes. BIOL 212 is generally taken during the second semester of the first year or during the sophomore year because it requires CHEM 101. Students must complete BIOL 211 and BIOL 212 and their credit-bearing laboratory components with a minimum grade of C–. Students are also required to complete a one-credit research tutorial or independent research study (a course numbered BIOL 470 or higher). With prior approval by the biology department, a capstone research experience in another department may be substituted for a course numbered BIOL 470 or higher.

The remainder of the nine biology courses required for the major can be selected from any of the elective courses offered in the department (excluding BIOL 291, BIOL 391, and BIOL 491); at least two of these courses must have laboratories. Normally, elective courses require either BIOL 211 or 212. Only one 100-level course and only one course numbered BIOL 470 or higher can be counted toward the nine courses. The elective courses are found listed as biology 200- and 300-level courses; GEOL 215 also serves as an elective biology course.

Students expecting to attend graduate or professional schools are reminded that these schools frequently recommend or require calculus, statistics, computer science, chemistry (typically through organic), and a year of physics as cognates to the biology major.

Biology majors are strongly encouraged to attend biology seminars that are held approximately biweekly each semester. Students enrolled in 400-level biology courses are expected to attend all biology seminars during the term of enrollment.

Minor Program

A student may plan a minor program in biology in consultation with a member of the department staff. Such a program consists of five biology courses, of which only one can be a 100-level course. The policies regarding minimum grade requirements established for a major apply to the minor program as well. A student entering Colgate as a first-year student may apply for transfer credit toward the minor for one course taken at another institution. A student transferring from another institution with upperclass standing may petition for transfer credit for a second course toward the minor.

Honors and High Honors

With the approval of his or her instructor in a course numbered BIOL 470 or higher, a student may be allowed to stand for honors or high honors in the department. Honors in biology requires an overall GPA of 3.30 in courses counted toward the major, an oral presentation to the department, a review paper, and a research paper submitted to the research adviser based on at least one term of research in a course numbered BIOL 470 or higher. High honors requires an overall GPA of 3.60 in courses counted toward the major, an oral presentation to the department on the student’s research, and a two-chapter thesis submitted to the biology department based on at least two terms of research in biology courses numbered BIOL 470 or higher, or their equivalent. The awarding of high honors will be decided by the faculty in consultation with the adviser and will be based on the quality of the research project, the thesis, and the oral presentation. Research projects submitted for honors or high honors must be carried out on campus or on the NIH study group.

Awards

See “Honors and Awards: Biology” in Chapter VI.

Advanced Placement Policy

An incoming student who submits an AP grade of 4 or 5 will receive credit for BIOL 101. This course can be counted as a 100-level course toward the major requirements. Students with AP credit are encouraged to enter the department’s curriculum with BIOL 211.

Transfer Credit

A maximum of two biology course credits transferred from other institutions may be accepted and applied toward major and area distributions. For incoming first-year students, such courses must be approved by the department’s Transfer and Exemption Committee shortly after students arrive on campus. Students must submit a copy of the course syllabus, lecture and laboratory notes, a course catalogue description, and information about the text used. Matriculated students who plan to transfer a course must supply the department’s Transfer and Exemption Committee with a course catalogue description and course syllabus prior to taking the course to receive approval. Students transferring to Colgate with upperclass standing may petition the department for permission to transfer a third course.

Teacher Certification

The Department of Educational Studies offers a teacher education program for majors in biology who are interested in pursuing a career in elementary or secondary school teaching. Please refer to “Educational Studies.”

Related Majors

Molecular Biology  
The major in molecular biology is designed for students who are interested in biology at the molecular level and who wish to take courses in both biology and chemistry. Many who choose to major in this field pursue graduate work not only in molecular biology but also in other areas of biology where the methods of the molecular biologist are now being applied (e.g., developmental biology, neurobiology, immunology, etc.). Requirements are described under “Molecular Biology.” For further information, contact Professors Belanger, Hagos, Holm, Hoopes, Meyers, Pruitt or Van Wynsberghe.

Environmental Biology  
This major is in affiliation with the Environmental Studies Program (ENST) and is designed for students interested in biology and the environment. Students take a common set of courses in the ENST program as well as courses within the biology department that have an environmental emphasis but also provide breadth in biology. These biology courses include BIOL 211, BIOL 220, BIOL 330, a research course (BIOL course numbered 470 or higher), and three additional courses selected from two lists of ecology and organismal biology courses. The ENST courses focus on interdisciplinary approaches to the ethical, philosophical, and natural/social scientific aspects of environmental issues. For further information, contact Professors Cardelús, Frey, Fuller, Ingram, McCay, or Watkins. See also “Environmental Studies.”

Marine Science — Freshwater Science  
This topical major is offered with the cooperation of the geology department through the Division of Natural Sciences and Mathematics. See program requirements listed under “Marine Science — Freshwater Science.” This major is intended for students who are interested in aquatic sciences and who wish to major in both biology and geology while preparing for certain teaching, museum, and technical positions, and for selected graduate studies programs. For further information, contact Professors Fuller or McHugh. See also “Marine Science — Freshwater Science.”

Other majors and minors 
Certain courses in biology count toward majors in biochemistry, geology, and neuroscience. (See chemistry, geology, and psychology listings in this chapter.)

Mathematical Systems Biology Minor  
See “Mathematical Systems Biology.”

Special Programs in Biology

Australia Study Group (fall term)
An opportunity for junior majors in environmental biology to expand their environmental studies at the University of Wollongong, one hour south of Sydney. See “Off-Campus Study Group Programs” in Chapter VI.

Australia Study Group (spring term)
An opportunity for junior science majors to study at the University of Wollongong, one hour south of Sydney. See “Off-Campus Study Group Programs: Australia” in Chapter VI.

NIH Study Group (fall term)
An opportunity for juniors and seniors interested in careers in the biomedical sciences to spend a research-intensive semester at the National Institutes of Health in Bethesda, Maryland. See
“Off-Campus Study Group Programs: United States” in Chapter VI.

Wales Study Group (spring term)
An opportunity for junior science majors to study at Cardiff University. See “Off-Campus Study Group Programs: United Kingdom: Wales” in Chapter VI.

The biology department also offers international extended study courses and encourages participation in Colgate approved off-campus study programs.

Course Offerings

BIOL courses count toward the Natural Sciences and Mathematics area of inquiry requirement, unless otherwise noted.

All credit-bearing laboratories carry 0.25 course credits unless otherwise noted. Please see the “Academic Credit” section in Chapter VI for additional information and restrictions.

101  Topics in Organismal Biology
R. Fuller, K. Ingram, T. McCay, D. McHugh
This course introduces students to the complexities of biodiversity, from the ecosystem to the genetic level. By examining the factors affecting the structure and function of terrestrial, marine, and freshwater communities students learn about the diversity of organisms in these systems. Students gain an appreciation for the roles of evolutionary and ecological history, as well as modern ecological interactions, in shaping the biodiversity across the globe. This course also exposes students to the many ways that human activities affect biodiversity.

102  Topics in Human Health
K. Belanger, E. Hagos, G. Holm, J. Meyers
Human beings are composed of nearly 100 trillion cells of over 200 different specialized types. In order for an individual to remain alive and healthy, these cells must be effectively organized into tissues and organs that perform specific functions. This course examines external and internal factors that influence both normal and abnormal cell, tissue, and organ function, providing students without an extensive science background with exposure to the biology of human health and disease. Course topics include human diet and nutrition and the cell biology of disease. Students examine how biologists address issues relating to health and disease and how our understanding of basic biology contributes to enhancing human health. The course is composed of lectures and discussions and may include in-class laboratory-based exercises.

103  Topics in Adaptation
N. Pruitt
Nearly every habitat on Earth, from thermal hot springs to the polar ice caps, is home to some form of life. Within those environments, organisms make their living in remarkable and varied ways. This course explores how organisms “work,” with an emphasis on extraordinary feats of survival. The course content crosses many of the traditional hierarchical divisions in biology, integrating cellular biology, physiology, and ecology to come to a greater understanding of how organisms function within their environmental contexts. Course pedagogy includes some lecture, problem-based learning, and group problem solving. This course is an entry for students intending to major in the life sciences and is also for students in other majors with an interest in the life sciences.

211/211L  Evolution, Ecology, and Diversity
C. Cardelús, F. Frey, R. Fuller, K. Ingram, T. McCay, D. McHugh, J. Watkins
This course concentrates on the evolutionary biology of organisms and the ecological processes that influence the distribution and abundance of plants and animals, as well as their interactions. The history of biological diversification (including the origin of life; the evolution of prokaryotes and eukaryotes; and the invasion of land by plants, fungi, and animals) are discussed. In addition, the mechanisms of evolution, including natural selection, adaptation, and extinction, are studied. Topics in population ecology as they relate to evolutionary processes including physiological and behavioral ecology, population growth, and species interactions (e.g., competition, predation, mutualism) are also covered; there is a strong focus on the physical, chemical, and biological factors that affect populations. The credit-bearing laboratory BIOL 211L must be taken concurrently with BIOL 211. Projects in the laboratory and field include experiments designed to understand evolutionary principles and to test ecological hypotheses.

212/212L  Molecules, Cells, and Genes
A. Ay, K. Belanger, E. Hagos, G. Holm, B. Hoopes, R. Metzler, J. Meyers, N. Pruitt, P. Van Wynsberghe
At the level of molecules and cells, the different forms of life on earth are surprisingly similar. This course introduces aspects of life at the cellular and molecular level that are broadly applicable to all living things. The course begins by examining the basic chemistry of life. Building on this chemical foundation we develop an appreciation for cellular structure, the central role of cellular membranes, cellular energetics, and cell growth and reproduction. Special emphasis is placed on proteins and nucleic acids as the informational macromolecules, and how cells use these molecules to encode and express a genetic program. Mechanisms of inheritance are examined from both a classical and a modern molecular perspective. The credit-bearing laboratory BIOL 212L must be taken concurrently with BIOL 212. Laboratories feature experimental approaches in both modern cell biology and genetics. Prerequisite: CHEM 101 or 111, or permission of instructor.

215/215L  Biology of Plants
J. Watkins
The course material covers organisms in three kingdoms: Protista, Fungi, and Plantae. Topics include cell structure, reproduction, transport, and metabolism. There is an emphasis on photosynthesis, diversity, and evolution in fungi, protists, and land plants. Features of seed plant morphology, anatomy, translocation of water and minerals, gas exchange, and reproduction are discussed. The credit-bearing laboratory BIOL 215L must be taken concurrently with BIOL 215. Prerequisite: BIOL 211.

220/220L  Biostatistics
F. Frey, T. McCay
This course explores issues of experimental design, data collection methods, and principles of statistics as they apply to biology. Topics include samples and populations, tests for goodness of fit of frequency data to those expected on the basis of theory, hypotheses about samples drawn from normally distributed populations, the binomial and Poisson distributions, analyses of variance, correlation analysis, linear regression analysis, and elementary statistical modeling. Students learn computer software applications for the analysis and graphing of data. Course material is beneficial to students planning to do research within their major department. Majors in fields other than biology are encouraged to enroll. The course should count as one of the two courses required in mathematics for students interested in the health science professions or graduate school in the sciences. The credit-bearing laboratory BIOL 220L must be taken concurrently with BIOL 220. Prerequisite: one biology course at the 200 level or permission of instructor.

225  Bioinformatics
A. Ay
Recent developments in biological data collection have led to the creation of large-scale experimental data sets of DNA and protein sequences and structures of biological molecules. These data are available for public use from an array of databases, and their analysis is intriguing. This course provides an introduction to the use of computational methods and tools to extract useful information from these large datasets, and focuses on interpreting this expanding biological information. Students discuss the basics of bioinformatics and focus on the identification and characterization of functional elements from protein and DNA sequences. Students also learn to use public databases and web-based sequence analysis tools, focusing primarily on human genome data. Prerequisite: BIOL 212 or permission of instructor.

230  Medical and Forensic Botany
J. Watkins
The great majority of people understand that plants are fundamental to life: They produce life sustaining oxygen, cleanse the air of carbon dioxide, provide material for construction, and more. Yet few people appreciate that modern medicine has its roots in the chemistry of plants. From headaches and malaria to AIDS and hypertension, most modern drug treatments originated from plant extracts. Even in the modern world of sophisticated synthetic chemistry, 25 percent of all prescriptions contain plant extracts or active principles prepared from plants. More than providing pain relief and disease cures, the search of effective medical botany has shaped cultures, created fierce wars, and contributed to the modern issues of bio-prospecting, drug wars, and crime scene investigation. This course delves into issues of medical and forensic botany from multiple perspectives. Students develop a greater understanding of basic plant biology and phytochemistry, and learn how many cultures have utilized plants for curative and destructive means. Students also examine how plant-derived drugs have disrupted both ancient and modern cultures, and have shaped the scientific method and modern drug creation. Finally, the class examines how plants play significant roles in early and modern forensics by focusing on major cases whose decisions have hinged on plant evidence.

254/254L  Invertebrate Zoology
D. McHugh
This course covers the biology of the major animal groups. Attention is given to the phylogenetic history, functional morphology, development, physiology, medical importance, and ecology of representative invertebrates. The credit-bearing laboratory BIOL 254L must be taken concurrently with BIOL 254. Laboratories include field collections of freshwater and terrestrial invertebrates, as well as the study of major groups of marine invertebrates. Prerequisite: BIOL 211 or permission of instructor.

255/255L  Vertebrate Zoology
T. McCay
This course has an evolutionary theme and investigates the diversity of vertebrate animal life. Emphasis is on evolutionary origins and phylogenetic relationships, basic structure and function, development and reproduction, behavior, zoogeography, and interrelationships with the environment. The major vertebrate animal groups are studied, including local species. Students examine the morphology of selected vertebrates in the lab, with dissection of preserved materials. The lab also includes study of vertebrate natural history. The credit-bearing laboratory BIOL 255L must be taken concurrently with BIOL 255. Prerequisite: BIOL 211 or permission of instructor.

311/311L  Comparative Environmental Physiology
N. Pruitt
All animals are faced with similar fundamental problems, namely, acquiring and using energy, exchanging nutrients and wastes with the environment, balancing water and electrolytes, and reproducing. This course is about how animals address these problems in the context of the varied (and sometimes extreme) environments in which they live. With evolution as a unifying theme, both the general principles of animal function (the similarities among different animals) and the exceptions to the general rules are investigated. Topics include size and scaling, energy metabolism, temperature tolerance and regulation, gas exchange, water and osmotic regulation, and animal communication. General principles of animal physiology are also explored using examples of animals that live in extreme environments. When offered, the credit-bearing laboratory BIOL 311L must be taken concurrently with BIOL 311. The laboratory involves hypothesis-guided experimentation with quantitative analysis of data. Prerequisites: BIOL 211 or 212.

321/321L  Molecular Biology
K. Belanger, B. Hoopes, P. Van Wynsberghe
This course provides students an in-depth study of biological processes at the molecular level, including transcription, RNA processing, translation, DNA replication and recombination. Emphasis is on understanding the experiments that have led to our current view of these processes and, in particular, the means by which these processes are regulated. Readings from the scientific literature make up a portion of the course. The credit-bearing laboratory BIOL 321L must be taken concurrently with BIOL 321. The laboratory is a semester-long investigative project that familiarizes students with the molecular techniques used to analyze problems in molecular biology. Prerequisite: BIOL 212.

322  Molecular Biology
K. Belanger, B. Hoopes, P. Van Wynsberghe
This course provides students an in-depth study of biological processes at the molecular level, including transcription, RNA processing, translation, DNA replication and recombination. Emphasis is on understanding the experiments that have led to our current view of these processes and, in particular, the means by which these processes are regulated. Readings from the scientific literature make up a portion of the course. This course does not include a laboratory and is only open to seniors majoring in biochemistry. Prerequisite: BIOL 212.

324/324L  Developmental Biology
K. Belanger, E. Hagos, J. Meyers
This course examines fundamental processes in animal and plant development, including fertilization, the establishment of embryonic polarity, the determination of cell fate in the early embryo, and the mechanisms by which cells generate the specific organizational pattern of a developing embryo. Additionally, potential medical applications resulting from the study of developmental biology are considered. Emphasis is on understanding experimental systems (including sea urchins, fruit flies, frogs, and mice) and approaches (molecular genetics, biochemistry, and classical embryonic manipulations). The credit-bearing laboratory BIOL 324L must be taken concurrently with BIOL 324. Independently designed laboratory projects and oral presentations of current literature are required. Prerequisite: BIOL 212.

325/325L  Plant Evolution
F. Frey
This course provides an understanding of the diverse groups of vascular plants, which are commonly known as the “higher plants” and are the dominant plants in the world today. Course topics focus on the major groups of extant vascular plants and investigate, from an evolutionary perspective, the morphologies, life cycles, reproductive structures and strategies, identification, classification, and economic importance of these groups. Laboratory sessions provide hands-on experience in analyzing plant structures, using identification keys, and working with herbarium specimens. Students lead class critiques of the literature and perform an independent research project as part of the course. The credit-bearing laboratory component BIOL 325L must be taken concurrently with BIOL 325. Prerequisite: BIOL 211 or 212, or permission of instructor.

326  Advanced Cell Biology
K. Belanger
Every living organism is comprised of one or more cells. This course examines how cells grow, reproduce, and maintain themselves, and how cellular activities contribute to the organization and maintenance of multicellular organisms. Course topics include investigating the function of specific organelles and the cytoskeleton, intracellular protein transport, mechanisms of cell cycle regulation and programmed cell death, and cell-cell interactions. The course requires students to critically examine primary journal articles and complete writing assignments that utilize recent primary literature to explore cell structure and function. Prerequisite: BIOL 212.

327/327L  Biology of Stem Cells
J. Meyers
Multi-cellular plants and animals develop from totipotential stem cells that are capable of making both every cell type within the organism and also preserving the information needed to make additional generations. In addition, stem cells within the body contribute cells to organs throughout life and can in many cases regenerate large amounts of tissue following damage. This course examines the biology behind stem cells, both embryonic and adult cells in plants and animals, focusing on the genes and pathways that make stem cells unique in their proliferative and differentiating capacity. Additionally, this course explores the basis for regeneration, including both stem cells and cellular dedifferentiation, and examines what may limit regeneration in certain systems where it does not occur. It also explores what happens when tight control over cell proliferation and differentiation is disrupted, leading to cancer. The course includes reading from the primary literature, and requires oral and written critical analysis of the literature. The credit-bearing laboratory component BIOL 327L must be taken concurrently with BIOL 327. Prerequisite: BIOL 212.

328/328L  Field Ecology

J. Watkins
This course examines the role of plants in the ecological world by studying the biological and historical factors affecting the structure of plant communities, with an emphasis on field and lab work. The topic is approached by viewing plants as individuals, members of populations, communities, and as key integrators of ecosystems. The course examines individual plants from a functional perspective by relating morphological and physiological traits with biological and biochemical processes, to understand spatiotemporal patterns of plant distribution in their natural environments. Beyond the individual, the course explores population and community dynamics and combines this knowledge to understand better the organization of plant communities and the roles they play in ecosystems. The course includes reading from the primary literature and requires oral and written critical analysis of the literature. The credit-bearing laboratory BIOL 328L must be taken concurrently with BIOL 328. Prerequisite: BIOL 211 or permission of instructor.

329/329L  Ecosystem Ecology
C. Cardelús
Ecosystem ecology is the study of both the organisms (biotic) and the environment (abiotic) as an integrated system and the processes that link them: energy transformations and biogeochemical cycling. Emphasizing plant systems, the course introduces students to fundamental ecosystem processes such as primary productivity, decomposition, nutrient cycling, plant-soil interactions, and energy balance. Students also study the major element cycles (carbon, nitrogen, phosphorus) and how these vary among ecosystems as different as the arctic tundra and tropical rainforest. An important theme of the course is the relationship between ecosystem processes and pressing global environmental issues such as global warming, biodiversity loss, and rising carbon dioxide levels. The credit-bearing laboratory, BIOL 329L, must be taken concurrently with BIOL 329. This course is not recommended for first-year students, except by permission of instructor. Prerequisite: BIOL 211.

330  Conservation Biology
C. Cardelús, T. McCay
The widespread loss of species and concerns over how to maintain maximum genetic variability in populations are at the heart of this course. Topics include biological diversity, its measurement, and differences in diversity among habitats. The course also considers threats to biological diversity such as habitat loss, exotic species introductions, pollution, environmental variability, and catastrophic events. This information is used to consider various conservation strategies and sustainable development. Students take a global perspective in this course and consider how globalization affects biodiversity directly and indirectly. Prerequisite: BIOL 211 or permission of instructor.

332  Tropical Ecology
C. Cardelús
This course addresses tropical ecology starting with the discoveries and theories of early explorers to modern theories of biogeography of species richness. Students also learn about human impacts on tropical diversity and the sustainability of tropical ecosystems. Students use seminal papers as readings and discuss questions that are still debated by tropical ecologists: Why are the tropics so diverse? How is this diversity maintained? How do communities respond to disturbance? And how does global warming affect communities and species richness? In this course, students design experiments and write proposals on field projects that are executed during the extended study portion of the course (BIOL 332E), which is required. The 0.5-credit extended study course is a three-week trip to Costa Rica, Central America, where students visit some of the ecosystems studied in the course. The field component includes field work, multiple group projects, laboratory write-ups, and presentations. Corequisite: BIOL 332E. Prerequisite: BIOL 211 and permission of instructor.

332E  Tropical Ecology Extended Study
C. Cardelús
The extended study portion of BIOL 332, Tropical Ecology puts students in the tropical ecosystems studied in the lecture portion. Students stay in and study tropical lowland rainforest, montane cloud forest, and lowland dry forest, and visit a mangrove swamp, secondary forest, and high elevation tropical bog in Costa Rica. In each study site students conduct the research studies proposed and decided on during the lecture course. The extended study includes rigorous field work, individual and group projects, research reports, and presentations — all with the backdrop of the forest. Corequisite: BIOL 332. Prerequisite: BIOL 211 and permission of instructor.

333/333L  Microbiology

G. Holm, P. Van Wynsberghe
This course examines the diversity of microbes in nature and their importance in human affairs from disease to agriculture. It also examines the characteristics of individual microorganisms that enable them to inhabit a particular environment. The credit-bearing laboratory BIOL 333L must be taken concurrently with BIOL 333. Projects in the laboratory include identification of microbes and experiments aimed at understanding their growth, physiology, and genetics. Prerequisite: BIOL 212.

334  Systems Biology
A. Ay
Systems biology is an emerging interdisciplinary field that focuses on system level understanding of complex interactions of biological processes using quantitative approaches. The course focuses on the applications of mathematical techniques such as differential equations, network structure measures, machine learning and modeling (e.g., Boolean and stochastic modeling) to the study of gene regulation, synthetic gene circuits, small- and large-scale biological networks, and signal transduction pathways. Students also learn how to use computer software that is designed for biological data analysis such as GenePattern and COPASI. Prerequisite: MATH 111 or MATH 112 and one of the following: BIOL 212, MATH 113, PHYS 204, or COSC 101, or permission of instructor. This course is crosslisted as MATH 334.

335/335L  Limnology
R. Fuller
This course is an introduction to freshwater ecology, including the study of the effects of physical, chemical, and geographical factors on the structure and function of freshwater lakes and streams. The effects of human activities on water quality are also examined. There are field trips to local lakes and streams. The credit-bearing laboratory BIOL 335L must be taken concurrently with BIOL 335. Laboratories develop skills in water chemistry; sampling, identification, and quantification of algae, aquatic plants, and animals; and the quantitative presentation of data. A small-scale research project is required. Prerequisite: BIOL 211. This course is not recommended for first-year students, except by permission of instructor. Offered in alternate years with BIOL 336.

336/336L  Advanced Ecology
R. Fuller
This course emphasizes the quantitative aspects of ecology by exploring mathematical models of competition and predation, the use of diversity and community similarity indices, population regulation models, island biogeography, key factor analysis, food web analysis, and examining community and ecosystem level processes. In addition to textbook readings, students also read papers from primary literature on topics covered in class. The credit-bearing laboratory BIOL 336L must be taken concurrently with BIOL 336. The laboratory portion includes field trips to examine terrestrial and aquatic communities exposing students early in the semester to field methods; for the remainder of the semester, students design and conduct a small research project. Prerequisite: BIOL 211 or permission of instructor.

337  Cancer Biology
E. Hagos
This course provides students with knowledge of the fundamental principles of the molecular and cellular biology of cancer cells. It focuses on understanding how changes in the normal growth and division processes lead to human cancer. The course highlights multiple areas of cancer biology including the nature of cancer, signals in tumor cells, oncogenes, tumor suppressors, cancer-causing viruses, unregulated cell proliferation, DNA damage, epigenetics, apoptosis, angiogenesis, metastasis, and current therapeutic approaches to cancer treatment. Prerequisite: BIOL 212.

340  Marine Biology
D. McHugh
This course provides students with a comprehensive analysis of marine ecological processes and in-depth examination of the biology of marine organisms. Broad ecological concepts are emphasized in a survey of marine habitats ranging from the intertidal rocky shore to deep sea hydrothermal vents. The diversity of marine organisms is considered in the context of their physical and chemical environments, and their interspecific interactions. In addition, students deliberate in written reports and class presentations on specific ways in which humans impact the marine environment. Prerequisite: BIOL 211 or GEOL 135, or permission of instructor.

341/341L  Animal Behavior
K. Ingram
This seminar covers behavior patterns of select invertebrate and vertebrate groups with emphasis upon their ontogeny, evolution, and adaptive significance. Lecture topics include social organization, communication, territoriality, and mating systems. Students read original literature for discussion in class. Selected laboratory exercises apply data acquisition techniques to the behavior of crickets, crayfish, fish, and birds. A review paper and oral presentation of contemporary literature are required. The credit-bearing laboratory BIOL 341L must be taken concurrently with BIOL 341. Prerequisite: BIOL 211 or permission of instructor. Course open to juniors and seniors only.

350  Biophysics
This course is crosslisted as PHYS 350. For course description, see “Physics: Course Offerings.”

351  Topics in Advanced Cell Physiology
Staff
Cellular function is examined at the molecular and biochemical level. This seminar/discussion course addresses features of the intracellular milieu and the mechanisms by which cells regulate and maintain that milieu in a changing environment. The course addresses the important historical experiments leading to current understanding, as well as the techniques used in the study of cell physiology. Readings are taken from the primary scientific literature but may include advanced textbooks as well. Students are required to write an extensive review of the current literature on one of the topics pertinent to the course. Prerequisite: BIOL 212 or permission of instructor.

352  Animal Evolution
D. McHugh
This seminar involves critical discussions of recent advances in developmental biology, paleontology, molecular systematics, and comparative morphology that are challenging traditional views of animal evolution. Topics include the genetic basis for changes in animal body plans, the phylogeny of invertebrate groups based on analyses of molecular and morphological data, the evolution of social behavior, and the possibility that the Cambrian explosion was one of fossils, not taxa. In addition to reading and discussing primary literature, students are required to provide written critiques of the papers they read and to give oral presentations. Prerequisite: BIOL 211 or GEOL 315, or permission of instructor.

354  Evolutionary Biology
F. Frey, K. Ingram, D. McHugh
Evolutionary biology is a dynamic, interdisciplinary field that influences the way we think about topics as diverse as conservation biology, epidemiology, paleontology, population genetics, adaptive radiations, the evolution of developmental mechanisms, inter-specific competition, and human behavior. The material covered in this course is motivated by the types of questions evolutionary biologists ask about these and other subjects. Emphasis is on the formulation of these questions, the generation of hypotheses, and the testing of predictions. Using primary literature, students critique experiments designed to test competing hypotheses; they also provide informed suggestions for future directions of research through a peer-reviewed research proposal. Prerequisite: BIOL 211 or 212.

355  Advanced Topics in Organismal Biology
Staff
Over the past few decades there has been increasing focus on multicellular organisms at the level of expression of genomes and interactions within and among cells. Recent advances in integration of scientific perspectives from across disciplines are leading to a renewed holistic approach to the study of organismal biology. In this course, the roles of organisms in environments, their functional and behavioral diversity, their evolutionary history, and their representation of physical and living systems are explored through historical and recent literature, case studies, and consideration of how the current growth in integrative science influences our understanding of organismal ecology and evolution. Different groups of organisms are used to illustrate the history, current state of understanding, and emerging principles in the study of whole organisms. Prerequisite: BIOL 211.

364/364L  Population Biology
F. Frey
This course covers current issues in population biology, and draws from the fields of population genetics, evolutionary ecology, community ecology, and biogeography. Students learn the tools of evolutionary genetics, and read original literature for class discussion. Specific course topics include an in-depth study of population and quantitative genetics as well as special investigations of the evolution of parasite virulence, the maintenance of sexual reproduction, the evolution of cooperative behavior, and the evolution of senescence. Students are required to lead class critiques of the literature, and perform an independent research project as an integral part of the course. The credit-bearing laboratory component BIOL 364L must be taken concurrently with  BIOL 364. Prerequisite: BIOL 211 or 212, or permission of instructor.

371/371L  Molecular Ecology
K. Ingram
This course explores the fundamentals of population biology, the molecular methods used to measure critical parameters, and the application of these concepts and techniques to current problems in ecology and evolution. Using detailed case studies from organisms as diverse as dolphins, birds, ants, and humans, students discuss the mechanisms driving ecological and evolutionary patterns. The case studies have been selected to demonstrate the variety of techniques involved in current molecular ecology research from observational studies to gene expression studies. The course is divided into nearly equal parts lecture and discussion, with the case study discussions led by students. The credit-bearing laboratory BIOL 371L must be taken concurrently with BIOL 371. The laboratory introduces students to the basic methodology involved with molecular ecology research, from field collection to experimental hypothesis testing in the laboratory. Prerequisite: BIOL 211 or 212, or permission of instructor.

373/373L  Virology
G. Holm
This course is an in-depth examination of the biology of viruses. Discussions of replication strategies used by specific viruses serve as the basis for understanding virus-host interactions and pathogenicity by particular viruses. Other topics include virus particle structure, vector relations, and viral genetics. Critical reading of the primary virological literature is an important element of the course. The credit-bearing laboratory BIOL 373L must be taken concurrently with BIOL 373. This laboratory introduces students to basic methodology involved in virology research while conducting novel experiments to investigate virus-cell interactions. Prerequisite: BIOL 212.

374  Immunology
G. Holm
This course provides an investigation of the molecular and cellular components of the vertebrate immune system, emphasizing human immunology. It investigates the general principles that govern different components of the immune system and integrates those principles to develop a broad understanding of immune function. Topics include the generation of immunologic memory, consequences of immune system malfunction, manipulation of the immune system to positively impact human health, and methods that facilitate investigation of new questions about immune system function. Prerequisite: BIOL 212.

375/375L  Genetics
B. Hoopes, P. Van Wynsberghe
This course provides students a firm foundation in classical and quantitative genetics and also covers topics in molecular genetics. Topics in the course include Mendelian and non-Mendelian inheritance, genetic mapping in eukaryotes and prokaryotes, molecular aspects of recombination, transposition and gene regulation, and quantitative traits and their analysis. In addition to exams, students are required to review the scientific literature on some topic relevant to the course and present the results in a paper or an oral presentation. The credit-bearing laboratory component BIOL 375L must be taken concurrently with BIOL 375. The laboratory includes a semester-long research project and a required scientific paper. Prerequisite: BIOL 212.

381/381L  Human Physiology
N. Pruitt
This course examines the relationship between structure and function in the human body, starting at the level of molecules and cells, and moving through tissues, organs, and organ systems. Major topics include the endocrine, nervous, and cardiovascular systems; digestive physiology; and water, salt, and pH balance in the body. The credit-bearing laboratory BIOL 381L must be taken concurrently with BIOL 381. Laboratory exercises address the study of the physiology and organ system function in living organisms. Prerequisite: BIOL 212 or permission of instructor.

384  Fundamentals of Neurophysiology
This course is crosslisted as NEUR 384 and PSYC 384. For course description, see “Neuroscience Program under Psychology: Course Offerings.”

385/385L  Neuroethology
This course is crosslisted as NEUR 385/385L and PSYC 385/385L. For course description, please see “Neuroscience Program under Psychology: Course Offerings.”

389  Molecular Neurobiology
J. Meyers
This course examines the cell biology behind the functioning of the nervous system. Students explore how cells make fate decisions during neural development, how neurons elaborate the complex structures they take on, how they form and refine specific connections, and how these together allow the precise transmissions of complex signals. The course also examines the molecular pathways by which sensory systems transduce physical stimuli into electrochemical signals and integrate that information into the nervous system. Prerequisite: BIOL 212 or permission of instructor. This course is crosslisted as NEUR 389.

475  Molecular Analysis of Development
P. Van Wynsberghe
This research tutorial investigates the molecular mechanisms that regulate development in the nematode C. elegans. With the help of the instructor, students design and implement experiments that utilize genetic, molecular, and microscopic techniques to understand how small RNAs, called microRNAs, and the proteins that control their expression regulate development. At weekly meetings, students discuss the primary literature and their research projects. In addition, each student completes a grant proposal based on their research topic, writes a paper summarizing their research, and presents the results of their research to the department. Prerequisite: permission of instructor.

476  Investigations in Biodiversity, Community, and Ecosystem Ecology
C. Cardelús
This research course offers students the opportunity to design their own studies. Research in the lab centers on the causes of species richness patterns and how perturbations (climate change) affect those patterns. Research projects often apply the lens of climate change (e.g., biodiversity loss, global warming, increased carbon dioxide, pollution) and test explicit hypotheses on plant, community, and ecosystem responses (i.e., N deposition, fire frequency) to perturbations. Students have the opportunity to use cutting-edge laboratory, computer, and field-based methods (e.g., mass spectrometry, ecophylogenetics, carbon dioxide flux) to address these questions. Students are expected to develop their own projects, write a grant proposal, execute the lab and field work associated with the projects, write a final paper, and present their work to the department. Prerequisite: permission of instructor.

477  Molecular Control of Neural Development
J. Meyers
This research tutorial explores the molecular and cellular basis of the development and growth of the nervous system. With the guidance of the instructor, students design and carry out an experimental plan that applies techniques from molecular biology and cell biology to open questions in developmental neurobiology. Potential topics include signaling pathways that control neural stem cells, neural plasticity, and control of regeneration following damage. Weekly meetings provide a forum for discussion and research projects and papers from the primary literature. Each student is required to write a peer-reviewed grant proposal, a paper summarizing their results in scientific journal format, and make a formal presentation of their research to the department. Prerequisite: permission of instructor.

478  Animal Systematics, Phylogeny, and Development
D. McHugh
This research tutorial exposes students to the theory and practice of systematics and their application to the study of animal ecology and evolution; it also provides experience in developmental genetics. Topics include life history evolution of marine invertebrates, biogeography of deep-sea hot vent animals, and the developmental evolution of animal body plans. In the laboratory, students pursue independent research projects using molecular techniques, and phylogenetic analytical methods. In addition to reading and discussing primary literature, students are required to give oral presentations on their work, write a peer-reviewed grant proposal, and prepare a final research paper reporting their results. Prerequisite: permission of instructor.

479  Investigations in Evolutionary Ecology
F. Frey
Evolutionary ecology is the study of how ecological interactions among organisms (e.g., pollination, predation, competition, etc.) influence evolutionary change. With the guidance of the instructor, individual students or small teams test novel hypotheses in evolutionary ecology using field and/or laboratory research methods. Projects usually fall under the umbrella of plant-animal interactions, evolutionary genetics, the maintenance of variation in natural populations, or disease ecology. Weekly meetings provide a forum for project and paper discussions. Students are expected to keep a detailed research notebook, submit a peer-reviewed grant proposal, and present their results in the form of a research paper and a formal presentation to the department. Prerequisite: permission of instructor.

480  Cell Cycle Regulation
E. Hagos
In a normal eukaryotic cell cycle, the chromosomal DNA and the centrosome of a cell are replicated once, and only once, during S phase to ensure that each daughter cell receives exactly one complement of genomic material and centrosomes. In this research tutorial, students use cellular and molecular techniques to understand the mechanisms underlying this complex phenomenon. Specifically, they investigate mechanisms through which transcription factors regulate genomic stability, normal centrosome duplication, cellular senescence, autophagy, and DNA repair. Students read and discuss primary journal articles relevant to their research projects. They are also required to write a peer-reviewed grant proposal, write a paper in the format of scientific journal article, and present the results of their research to the department at the end of the semester. Prerequisite: permission of instructor.

481  Modeling of Biological Systems
A. Ay
Quantitative techniques have become a crucial tool in recent years for analyzing biological systems, a field which has been flooded with highly detailed experimental data due to new advanced data acquisition techniques in the biological sciences. This interdisciplinary research tutorial explores the analysis of biological systems using quantitative approaches such as mathematical modeling, statistical learning, and computer programming. With the guidance of the instructor, students choose a biological problem of their interest and analyze it using quantitative techniques. The research topics include (but are not limited to) gene regulation, disease networks, and cell cycle regulation. Students are expected to read the primary literature related to their research project, write a paper describing their research in the format of a scientific journal article, present the results of their research, and write a peer-reviewed grant proposal. Prerequisite: permission of instructor. This course is crosslisted as MATH 481.

482  Adaptation to Environment
N. Pruitt
This laboratory-based, research-oriented course examines the molecular and cellular mechanisms that enable animals to withstand a variety of environmental conditions. Students design, implement, and report on their own original research using various approaches, from classical physiology and biochemistry to modern molecular biology. Students lead weekly discussions of relevant journal articles and submit final papers written in the format of published articles. Students also present the results of their research at a departmental poster session. Prerequisite: permission of instructor.

483  Intracellular Transport
K. Belanger
Most macromolecules expressed in cells must be targeted to specific intracellular locations where they can perform their intended functions. This research tutorial examines the mechanism by which specific proteins undergo regulated transport into and out of the nucleus of eukaryotic cells. Students use classical and molecular genetics to identify genes encoding proteins involved in nuclear transport, and utilize recombinant DNA techniques, biochemistry, and microscopy to characterize the newly identified proteins and their interactions with other nuclear transport factors. Students read and discuss primary literature examining intracellular transport, write a grant proposal and primary journal article based on their research project, and describe the results of their laboratory research in oral and poster presentations at the end of the semester. Prerequisite: permission of instructor.

484  Cellular Responses to Viral Infection
G. Holm
This research tutorial examines the mechanism and regulation of cellular gene expression in response to infection by mammalian reovirus. Students address these questions by conducting independent laboratory research projects using biochemical, molecular biological, and cell biological approaches. In addition, weekly meetings explore the current scientific literature as it pertains to students’ research questions. Students write a grant proposal and scientific journal-style paper based on their research, and formally describe their research to the department in oral or poster presentations at the end of the semester. Prerequisite: permission of instructor.

485  Experimental Animal Behavior
K. Ingram
This research tutorial explores issues, methodology, and experimental designs in fields associated with animal behavior including molecular ecology, behavioral ecology, conservation biology, and behavioral genetics of social insects. Research can involve both field and laboratory work. Students read and discuss relevant primary literature in preparation for a research project that results in a formal presentation. Students write a research proposal and participate in a peer-reviewed research panel. Prerequisite: permission of instructor.

486  Eukaryotic Molecular Genetics
B. Hoopes
This research tutorial allows students to learn a variety of molecular genetic and bioinformatic techniques to address questions of how genetic variation affects function in eukaryotic organisms. With the guidance of the instructor, students design projects to address questions on genetic effects on behavior and body form in dogs or on gene expression. Weekly seminar meetings require students to examine papers from the current scientific literature and to talk about their projects. Each student is required to perform a literature search and write a grant proposal based on the topic of the research. Each student is also required to write a paper describing the research, and make a formal presentation to the department. Prerequisite: permission of instructor.

487  Advanced Aquatic Ecology
R. Fuller
This course provides students with an opportunity to do research in freshwater ecology. Projects are field- or laboratory-oriented investigations of either stream or lake ecology and often require a group effort. In conversation with the instructor, the student designs a study that is of mutual interest to the student and faculty member. Past projects have involved predator-prey relations or competition among stream insects, role of bank-side vegetation in influencing stream macroinvertebrate communities, bacterial/algal interactions in streams, nutrient limitation of algae, effects of insect grazers on stream algae, or the impact of acid deposition on both the structure and function of streams. Weekly meetings discuss papers in the scientific literature, and there are student-directed discussions of individual projects. Each student writes a grant proposal based on the topic of their research. At the end of the semester each student writes a paper in scientific journal format on his or her project and makes a formal presentation to the department (either orally or as part of a poster session). Prerequisite: permission of instructor.

488  Investigations in Terrestrial Ecology
T. McCay
This research tutorial provides students the opportunity to plan, conduct, and present original research in terrestrial ecology. Projects involve investigations in the field, laboratory, or both. Students focus on a particular species or group of species according to interest and feasibility. Potential topics for projects include invasive species, acid deposition, and competition among similar species. Emphasis is placed on the application of ecological, behavioral, and physiological principles to understanding the abundance and distribution of species in real landscapes. Weekly meetings allow students to discuss their projects and relevant papers from the primary literature. Students are expected to keep a research notebook and formally present research findings to the department. Students also complete a report of research activities in scientific format, with the goal of publication in a scientific journal, and a proposal in the format required by the National Science Foundation. Prerequisite: permission of instructor.

489  Research in Plant Physiological Ecology
J. Watkins
This research tutorial uses plants to investigate the relationships between internal events (physiology) and external events (ecology) by combining current readings from the primary scientific literature with laboratory and field experiments. Topics include energetics, reproductive strategies, and seed dormancy and germination. The goal is completion of a project suitable for publication in a scientific journal. Students learn how to search literature, critique articles, design experiments, collect and analyze data, and present information in manuscript form to submit for publication. In addition to weekly meetings, all students complete a National Science Foundation style grant proposal, a significant end of semester term paper, and present a poster at the annual student research forum. Prerequisite: permission of instructor.

291, 391, 491  Independent Study
Staff
Students majoring in biology may, with approval of the department, pursue special problems involving independent, advanced training in areas not adequately covered by formal course work.

393, 493  NIH Study Group Research

295, 395, 495  Transfer Credits and Courses Taken Abroad
These BIOL course numbers are used only for courses taken abroad with a Colgate study group, a non-Colgate study group, or approved by the registrar and the biology department for transfer from another institution of higher learning.