Biology Course
Descriptions
- BIOL 101(F) The Cell - This course provides an introduction to the
cellular aspects of modern biology. It explains the development of cell structure
and function as a consequence of evolutionary processes, and it stresses the
dynamic properties of living systems. Topics considered include biological
molecules and enzyme action, membrane structure and function, energy exchange
and design of metabolic systems, expression of genetic information, cell signalling,
cell trafficking, the cell cycle, and cancer. In addition to textbook assignments,
articles from the recent biological literature will be assigned and discussed.
Format: lecture/discussion/laboratory, six hours per week. Evaluation will
be based on quizzes, hour tests, a final exam, and weekly lab reports. No
prerequisites. No enrollment limit (expected: 4 sections of 45).
Professors: Hutson,
Lynch Lecture:
9:00 or 10:00 MWF, 8:30 or 9:55 TR Lab: MTWR
- BIOL 102(S) The Organism - This course
uses an evolutionary approach to introduce organismal biology. The course
stresses interrelatedness of different levels of biological organization from
the cell to the organism. Topics include the cell cycle, animal and plant
development, evolutionary mechanisms, speciation, and biodiversity. Examples
are drawn from a broad range of animal, fungal, and plant groups. In addition
to textbook assignments, articles from recent biological literature are assigned
and discussed. Format: lecture/discussion/laboratory, six hours per week.
Evaluation will be based on hour tests, a final exam, weekly lab reports,
and short discussion papers. Prerequisites: Biology 101. No enrollment limit
(expected: 2 sections of 90).
Professors: Ting,
Williams
Lecture: 11:00 MWF, 9:55 TR Lab: MTWR
- BIOL 106(F) Life as an Algorithm - Can computers
reproduce? Can DNA compute? Can evolution give us hints on solving big problems?
Is life's blueprint inefficient? This course looks at the way computers are
shaped by biological thinking, and the way that biologists make use of computational
theories. Topics range from artificial life to identification of genes to
the susceptibility of machines to viruses. Lectures investigate new and novel
ways of thinking about computers and biology. Labs experiment with parameters
of problems of common interest to computer scientists and biologists. Students
will learn to use common programming tools to aid in the manipulation and
analysis of basic biological data. Format: lecture/laboratory. Evaluation
will be based on performance on problem sets, laboratory assignments, and
examinations. No prerequisites. No programming or biology skills are assumed.
This course is not open to students who have completed Computer Science 136
or above. Does not count for major credit in Biology.
- BIOL 132 Human Biology and Social Issues
- From reading the headlines in newspapers and magazines one gets the impression
that human society is on the verge of a wondrous transformation to be brought
about by the application of new biological knowledge. Can science really provide
us with a future that is free of disease and social problems? Is biology the
important underlying dictator of who we are and how we live our lives? Or
are we more than the sum of our biological parts? In lectures, we'll examine
recent scientific advances and/or setbacks in understanding and manipulating
human reproduction, development, inheritance, and health. In particular, research
in the areas of the Human Genome Project, gene therapy, cloning and cancer
will be explored. In addition, in discussion sections we will address the
implications of this current research for individuals and for society as a
whole. Format: lecture/discussion. Evaluation will be based on hour exams,
a final exam, a short paper, and participation on a discussion panel. No prerequisites.
Preference given to seniors, first-years, sophomores, and juniors in that
order. Closed to Biology and Chemistry majors; does not satisfy premedical
requirement in Biology; does not count for Biology major credit.
- BIOL 133 Biology of Exercise and Nutrition
- This class, intended for the non-scientist, focuses on the impact of exercise
and nutrition on the human body. We will discuss topics such as how different
types of training influence exercise performance; the changes that occur in
the cardiovascular system during an exercise routine; the inherent limits
of the body to perform aerobic and anaerobic tasks; and long-term health consequences
of a lifetime of activity or inactivity. We will also examine how nutrition
and metabolism affect body composition. For example, we will rigorously and
scientifically scrutinize the use of "fad" diets as a means to lose weight.
Format: course work will consist of lectures and six hands-on laboratory exercises.
Evaluation will be based on exams and lab reports. No prerequisites. Preference
given to seniors, juniors, sophomores, and first-year students-in that order.
Does not count for major credit in Biology.
- BIOL 134(F) The Tropics: Biology and Social
Issues - Intended for the non-scientist, this course explores the biological
dimensions of social issues in tropical societies, and focuses specifically
on the peoples and cultures of tropical regions in Africa, Asia, Latin America,
Oceanea, and the Caribbean. Tropical issues have become prominent on a global
scale, and many social issues in the tropics are inextricably bound to human
ecology, evolution, and physiology. The course begins with a survey of the
tropical environment of humans, including major climatic and habitat features.
The next section focuses on human population biology, and emphasizes demography
and the role of disease particularly malaria and AIDS. The final part of the
course covers the place of human societies in local and global ecosystems
including the challenges of tropical food production, the importance of organic
diversity, and the interaction of humans with their supporting ecological
environment. Format: lecture/debate, three hours per week. Evaluation will
be based on two hour exams, a short paper, panel preparation, and a final
exam. No prerequisites. Preference given
to seniors, juniors, sophomores, and first-year students- in that order. Does
not count for major credit in Biology.
- BIOL 202(F) Genetics
- Genetics, classically defined as the study of heredity, has evolved
into a discipline whose limits are continually expanded by innovative
molecular technologies. This course covers the experimental basis for
our current understanding of the inheritance, structures, and functions
of genes. It introduces approaches used by contemporary geneticists and
molecular biologists to explore questions about aspects of biology
ranging from embryonic development to aging. The laboratory part of the
course provides an experimental introduction to modern genetic
analysis. Laboratory experiments include linkage analysis, bacterial
transformation with plasmids and DNA restriction mapping. Format:
lecture/laboratory, six hours per week. Evaluation will be based on
biweekly problem sets, weekly laboratory exercises and laboratory
reports, and three examinations; 90% of the final grade is determined
by performance on written exercises and exams. Format:
lecture/laboratory, six hours per week. Evaluation will be based on
biweekly problem sets, weekly laboratory exercises and laboratory
reports, and three examinations; 90% of the final grade is determined
by performance on written exercises and exams. Prerequisites: Biology
101 and 102. No enrollment limit (expected: 85).
Professor: Altschuler
Lecture: 11:00 MWF Lab: MTWR
- BIOL 203(F) Ecology
- This course combines lectures with field and indoor laboratory
exercises to explore factors that determine the distribution and
abundance of plants and animals in natural systems. The course begins
with an overall view of global patterns and then builds from the
population to the ecosystem level. An emphasis is given to basic
ecological principles and relates them to current environmental issues.
Selected topics include population dynamics (competition, predation,
mutalism); community interactions (succession, food chains and
diversity) and ecosystem function (biogeochemical cycles, energy flow).
Format: lecture/laboratory, six hours per week. Evaluation will be
based on problem sets, lab reports, hour exams, and a final exam.
Prerequisites: Biology 101 and 102, or Environmental Studies 101 or
102, or permission of instructor. No enrollment limit (expected: 35).
Required course in the Environmental Studies Program. Satisfies
distribution requirement in major.
Professor: Edwards
Lecture: 9:55 TR Lab: TW
- BIOL 204(F) Animal Behavior
- Making sense of what we see while watching animals closely is both an
enthralling pastime and a discipline that draws on many aspects of
biology. Explanations can be found on many levels: evolutionary theory
tells us why certain patterns have come to exist, molecular biology can
help us understand how those patterns are implemented, neuroscience
gives insights as to how the world appears to the behaving animal,
endocrinology provides information on how suites of behaviors are
regulated. The first part of the course focuses upon how descriptive
studies provide the basis for formulating questions about behavior as
well as the statistical methods used to evaluate the answers to these
questions. We then consider the behavior of individuals, both as it is
mediated by biological mechanisms and as it appears from an
evolutionary perspective. The second half of the course is primarily
concerned with the behaviors of groups of animals from a wide variety
of vertebrate and invertebrate species, concentrating upon the stimuli,
responses, and internal mechanisms that maintain social systems and on
the selection pressures that drive animals toward a particular social
system.
Format: lecture/laboratory, six hours per week. Evaluation will be
based on examinations, lab reports, and a research paper.
Prerequisites: Biology 102, or Psychology 101, or permission of
instructor. Enrollment limit: 28 (expected: 24). Preference given to
seniors, Biology majors, and Neuroscience concentrators.
Satisfies distribution requirement in the major.
Professor: Williams
Lecture: 8:30 MWF Lab: MT
- BIOL 205(S) Physiology - This lecture-based
course examines principles, patterns, and mechanisms of biological function
from the level of cells and tissues to the whole organism. The themes of the
course include structure and function, mechanisms of regulation, control and
integration, and adaptation to the environment. Examples of these themes are
taken from a wide variety of organisms with a focus on vertebrates. Laboratories
provide practical experience in measurement and experimental elucidation of
physiological phenomena and functional analysis of gross structure. Evaluation
will be based on hour exams, laboratory practicals, laboratory reports, and
a final exam. Prerequisites: Biology 101 and 102. No enrollment limit (expected:
60). Satisfies distribution requirement in major.
Professor: Zottoli
Lecture: 11:00 MWF Lab: MTWR
- BIOL 206T Genomes, Transcriptomes and Proteomes
(W) - While determining the complete DNA sequences of organisms continues
at an impressive pace, a sufficient number of eukaryotic and prokaryotic genomes
have been sequenced to consider what has been learned, and, more importantly,
what do we hope to learn in the post-genomic era. This tutorial course, intended
for sophomores, examines the progress and limitations of genome analyses in
enhancing our understanding of biology, as well as more recent investigations
employing DNA, RNA and protein sequence information to gain insights into
fundamental biological processes. Initially in the course, the experimental
approaches and tools used to obtain and analyze DNA sequences are considered.
Subsequently, topics based on recent articles exploring (i) comparative genomic
analyses, (ii) genome-wide changes in expression and mRNA levels (transcriptomes),
and (iii) efforts to analyze proteomes and protein-protein interactions in
cells are examined. The format includes two meetings per week, one general
group meeting and one tutorial meeting between two students and the instructor.
Evaluation is based on five tutorial papers (4-5 pages each), five critiques,
tutorial presentations and general participation. Prerequisite: Biology 202.
Preference given to sophomores.
- Professor: Raymond
- BIOL 210T(S) Evo-Devo: The Evolution of Animal
Design (W)
- What makes a bird a bird and a frog a frog? The key to understanding
the mechanisms that generate biological form and diversity lies in a
new and rapidly growing field, termed "evo-devo," that represents a
synthesis of evolution and development. This course, designed
specifically for sophomores, aims to explore evo-devo in detail by
building on material introduced in Biology 102. Using readings from the
primary literature, the course will consider topics such as how the
modification of developmental mechanisms can create novel traits, why
some traits are resistant to change, how the determination of shared
ancestral traits differs from those that rise independently, and how
ecological considerations impact development to modulate evolutionary
change.
Format: tutorial. Requirements: after an initial group meeting,
students meet weekly with a tutorial partner and the instructor for an
hour each week. Each student will write and present orally a 5-page
paper every other week on the readings assigned for that week. In
alternate weeks the students will question and critique the work of
their colleague. Evaluation will be based on five 5-page papers,
tutorial presentations, and the student's effectiveness as a critic.
Prerequisites: Biology 202. Enrollment limit: 10 (expected: 10).
Preference given to sophomores.
- BIOL 211(S) Invertebrate Paleobiology -
This course offers an introduction to the study of prehistoric life. The fossils
of marine invertebrates provide an excellent foundation for this purpose,
because they are widespread and abundant, they are often well-preserved, and
they have a record that reaches back in time over 600 million years. The intellectual
discovery of fossils as organic relics and the ways in which fossils were
used by earlier generations to support conflicting views on nature are briefly
surveyed. The lecture topics that follow are organized to illustrate the various
directions explored by paleontologists today to solve a broad range of questions.
These include: biological and paleontological views on the species concept
relevant to taxonomy; ongoing debate over the timing and mechanisms of evolution;
biostratigraphy as a means to correlate sedimentary rocks; functional morphology
as a means to reconstruct the biomechanics of extinct species; analysis of
fossil assemblages to interpret the ecology of ancient environments; paleogeography
as related to patterns in biodiversity, and the possible causes of mass extinctions.
Laboratory exercises utilize superb fossil collections to study the processes
of fossilization and to survey the biology and taxonomy of the major invertebrate
phyla. Format: lecture/laboratory; field trip to the Lower Devonian Helderbergs
of New York State. Evaluation will be based on weekly lab reports, a midterm
paper, a midterm exam, a lab practicum, and a final exam. Prerequisites: any
100-level Geosciences course or Biology 101, 102 or 203.
- BIOL 212(F) Neuroscience - A study of the
relationship between brain, mind, and behavior. Topics include a survey of
the structure and function of the nervous system, basic neurophysiology, development,
learning and memory, sensory and motor systems, language, consciousness and
clinical disorders such as schizophrenia, Parkinson's disease, and Alzheimer's
disease. The laboratory focuses on current topics in neuroscience. Format:
lecture, three hours per week; laboratory, every other week. Evaluation will
be based on laboratory reports, a lab practical, two hour exams and a final
exam. Prerequisites: Psychology 101 or Biology 101. Enrollment limit: 144
(expected: 72). Preference given to Biology and Psychology majors. Open to
first-year students who satisfy the prerequisites. Satisfies one semester
of the Division III requirement.
Professors:
Sandstrom, Zottoli
Lecture: 9:55 TR Lab: MTW
Professor: Koegal
- BIOL 220(S) Field Botany and Plant Natural
History
- This field-lecture course covers the evolutionary and ecological
relationships among plant groups represented in our local and regional
flora. Lectures focus on the evolution of the land plants, the most
recent and revolutionary developments in plant systemics and phylogeny,
the sudden appearance and explosive speciation of the flowering plants,
and characteristics of our native plant families and species. The labs
cover field identification, natural history, and ecology of local
species.
No prerequisites. Enrollment limit: 40 (expected: 25). Preference given
to seniors, Biology majors, and Environmental Studies concentrators.
Satisfies distribution requirement in major.
Professor: Edwards Lecture:
10:00 MWF Lab: TW
- BIOL 225(F) Natural History of the Berkshires
- This field-lecture course examines the rich diversity of upland and
wetland communities within a 20-mile radius of the Williams College
campus. Lectures/discussions focus on the biological, geological,
climatological, and historical underpinnings needed to observe,
interpret, and analyze thebiological communities in the region. The
Field/lab sections will engage students in reading the landscape, field
identification of indicator species, natural history, and using
historical documents and materials ranging from photographic images,
tax data, newspaper articles, and other resources. Students will
undertake a series of field projects such as using historical materials
to interpret changes in the landscape and creating interpretive guides
for specific sites. Format: lecture/laboratory, six hours per week.
Evaluation will be based on field quizzes, reading responses, hour
exam, and a final project report.
No prerequisites. Enrollment limit: 18 (expected: 18).
Satisfies distribution requirement in Biology major. Satisfies natural
world requirement for Environmental concentrators.
Professor: Art Lecture:
11:20 TR Lab: TR
- BIOL 231(F,S) Marine Ecology (at Mystic)
- Using the principles of evolutionary biology and experimental ecology, this
course examines the processes that control the diversity, abundance and distribution
of marine organisms. Major marine communities, including estuaries, the rocky
shore, sandy beaches, salt marshes, coral reefs, and the deep sea are discussed
in detail. Format: lecture/laboratory, including coastal and near-shore field
trips, 10 days offshore, and a laboratory or field research project. Requirements:
an hour test, a research project, a presentation, and a final exam. Prerequisites:
Biology 101 or Geosciences/Maritime Studies 104, or permission of instructor.
Satisfies one semester of the Division III requirement.
Professor: Carlton
- BIOL 235T Biological Modeling with Differential
Equations - Many biological phenomena can best be examined through fairly
sophisticated mathematical models. In particular, differential equation models
have been used to explain fluctuations in food webs, the spread of disease,
consequences of certain fishing practices, immune system response to infection,
spatial distribution of species, formation of zebra stripes, and flux across
cell membranes. We will introduce the mathematical machinery needed for these
models, including the theory of ordinary differential equations, phase portrait
dynamics and partial differential equations. We will establish the biological
assumptions that go into these models and examine the consequent dynamics.
Students will work in pairs covering material and explaining it to one another,
presenting worked problems, and critiquing each others presentations. Format:
tutorial. Prerequisites: Mathematics 105 and Biology 101 or equivalents thereof.
- BIOL 297(F) Independent Study - Each student
carries out independent field or laboratory research under the supervision
of a member of the department.
Lecture: TBA
- BIOL 298(S) Independent Study - Each student
carries out independent field or laboratory research under the supervision
of a member of the department.
Lecture: TBA
- BIOL 301(F) Developmental Biology
- Developmental biology has undergone rapid growth in recent years and
is becoming a central organizing discipline that links cells and
molecular biology, evolution, anatomy and medicine. We are now
beginning to have a molecular understanding of fascinating questions
such as how cells decide their fate, how patterns are created, how male
and females are distinguished, and how organisms came to be different.
We have also discovered how the misregulation of important development
regulatory genes can lead to a variety of known cancers and
degenerative diseases in humans. In this course we will examine these
and related topics combining a rich classical literature with modern
genetic and molecular analyses.
Format: lecture/discussion/laboratory, six hours per week. Evaluation
will be based on hour exams, short papers, and a final exam.
Prerequisites: Biology 202 or permission of instructor. Enrollment
limit: 24 (expected: 15).
Professor: Savage
Lecture: 11:20 TR Lab: TW
- BIOL 302 Communities and Ecosystem -
An advanced ecology course that examines how organisms interact with each
other and with abiotic factors. This course emphasizes phenomena that emerge
in complex ecological systems, building on the fundamental concepts of population
biology and ecosystem ecology. Lectures and workshops explore how communities
and ecosystems are defined, and how theoretical, comparative, and experimental
approaches are used to elucidate their structure and function. Field laboratories
emphasize hypothesis-oriented experiments; field trips introduce the diversity
of natural communities and ecosystems in New England. Format: lecture//laboratory,
six hours a week. Evaluation will be based on lab reports, a term project
with presentation, a midterm exam, a midterm paper, and a final exam. Prerequisites:
Biology/Environmental Studies 203 or 220 . Enrollment limit: 28 (expected:
24). Preference given to Biology majors and Environmental Studies concentrators.
- BIOL 303 Sensory Biology - How are important
conditions or changes in the environment received and transduced by organisms?
We will examine the molecular and cellular bases of the transduction and encoding
of physical phenomena such as light, sound,forces and chemicals in a variety
of organisms. The focus will be on questions such as: What properties of the
physical world are sensed (and which ones are ignored)? What mechanisms are
used to convert physical or chemical energy into a changed biological state
within a cell? What are the consequences of this changed state? How are differences
in the attributes of one modality in the physical world represented by differences
in molecular and cellular processes? Among the examples we will consider are:
a comparison of visual structures and pigments in bacteria, arthropods, molluscs,
and primates, sound transduction and its musical consequences, and the olfactory
system of mammals. Format: lecture/discussion/laboratory. Evaluation will
be based on examinations, and a paper. Prerequisites: Biology 212 and permission
of instructor, or Biology 205. Enrollment limit: 24 (expected: 24). Preference
given to seniors, then to Biology majors.
Professor: Williams
Lecture: 8:30 TR Lab: MT
- BIOL 304(S) Neurobiology - This course is
concerned with understanding the biology of the nervous system, focusing primarily
on the cellular bases of neuronal function. Lectures will cover such topics as
nerve resting and action potentials, ion channels, neurotransmitters and synapses,
and the neural correlates of behavior in organisms with simple nervous systems.
Reading original research papers and discussing them constitutes an important part
of the course. Some of the topics that may be covered include: transmitter release
mechanisms, ion permeation through channels, plasticity in the nervous system, and
various clinical disorders. Laboratories are designed to introduce the students to
modern techniques in neurobiology including extracellular and intracellular recording,
histochemistry, and immunohistochemistry. Format: lecture/laboratory, six hours
per week. Evaluation will be based on class participation, laboratory notebooks
and posters, two hour exams and a final exam. Prerequisites: Biology 205. Enrollment
limit: 24 (expected: 16). Preference given to Biology majors and Neuroscience concentrators.
Professor: Zottoli
Lecture: 9:55 TR Lab: T
- BIOL 305(S) Evolution (Q)
- This course offers a critical analysis of contemporary concepts and
controversies in evolution. We focus on the relation of evolutionary
mechanisms (e.g., selection, drift, and migration) to long term
evolutionary patterns (e.g., evolutionary innovations, origin of major
groups, and the emergence of diversity). Topics include
micro-evolutionary models, natural selection and adaptation, sexual
selection, evolution and development, speciation, and the inference of
evolutionary history.
Format: lecture/discussion/laboratory, six hours per week. Evaluation
will be based on two examinations, problem sets and laboratory
assignments, including independent research project using phylogenetic
inference. 85% of the final grade is determined by performance on
written exercises and examinations. 15% on participation in
discussions.
Prerequisites: Biology 202. Enrollment limit: 24 (expected: 24).
Preference given to Biology majors.
Satisfies distribution requirement in major.
Professor: Smith
Lecture: 9:00 MWF Lab: MW
- BIOL 306 Cellular Regulatory Mechanisms
- This course explores the regulation of cellular function and gene expression
from a perspective that integrates current paradigms in molecular genetics,
signal transduction, and genomics. Topics include: transcriptional and post#transcriptional
control, chromatin regulation of gene silencing and imprinting, chromosome
instability, prions and other self-perpetuating protein conformations, protein
degradation, organellar and cytoskeletal dynamics, and the appropriation of
intracellular transport pathways by HIV. A central feature of the course will
be discussion of articles from the primary literature. The laboratory will
consist of a semester-long research project that integrates recombinant DNA
techniques with genomic tools to investigate unanswered questions in eukaryotic
cell biology using yeast as a model organism. Format: lecture/discussion/laboratory.
Evaluation will be based on three take-home tests, in-class discussion of
papers, the laboratory notebook, and a grant proposal. Prerequisites: Biology
202. Preference given to Biology majors.
Professor: Koegel
- BIOL 308(F) Integrative Plant Biology: Fundamentals
and New Frontier
- Plants are one of the most successful groups of organisms on Earth
and have a profound impact on all life. Successful use of plants in
addressing global problems and understanding their role in natural
ecosystems depends on fundamental knowledge of the molecular mechanisms
by which they grow, develop, and respond to their environment. This
course will examine the molecular physiology of plants using an
integrative approach that considers plants as dynamic, functional units
in their environment. Major emphasis will be on understanding
fundamental plant processes, such as photosynthesis, growth and
development, water transport, hormone physiology, and flowering, from
the molecular to the organismal level. Environmental effects on these
processes will be addressed in topics including photomorphogenesis,
stress physiology, mineral nutrition, and plant-microbe interactions.
Discussions of original research papers will examine the mechanisms
plants use to perform these processes and explore advances in the
genetic engineering of plants for agricultural, environmental, and
medical purposes. Laboratory activities stress modern approaches and
techniques used in investigating plant physiological processes.
Format: lecture/discussion/laboratory, six hours per week. Evaluation
will be based on lab reports, a term paper, and exams.
Prerequisites: Biology 202. Enrollment limit: 24 (expected: 12).
Preference given to Biology majors.
Satisfies distribution requirement in major.
Professor: Ting
Lecture: 9:55 TR Lab: WR
- BIOL 310 Neural Development - Development
can be seen as a tradeoff between genetically-determined processes and environmental
stimuli. The tension between these two inputs is particularly apparent in
the developing nervous system, where many events must be predetermined, and
where plasticity, or altered outcomes in response to environmental conditions,
is also essential. Plasticity is reduced as development and differentiation
proceed, and the potential for regeneration after injury or disease in adults
is limited; however, some exceptions to this rule exist, and recent data suggest
that the nervous system is not as hard-wired as previously thought. In this
course we will discuss the mechanisms governing nervous system development,
from relatively simple nervous systems such as that of the roundworm, to the
more complicated nervous systems of humans, examining the roles played by
genetically specified programs and non–genetic influences. We will also
discuss the similarities and differences between development and regeneration,
the extent to which the nervous system is hard-wired, and the controversial
idea that degeneration represents "development in reverse." Format: lecture/discussion/laboratory,
six hours per week. Evaluation will be based on exams, short papers and lab
reports. Prerequisites: Biology 202 and either Biology 205 or Biology 212.
Preference given to Biology majors.
- BIOL 313 Immunology -The rapidly evolving field of immunology examines the complex network of interacting molecules and cells that function to recognize and respond to agents foreign to the individual. In this course, we will focus on the biochemical mechanisms that act to regulate the development and function of the immune system and how alterations in different system components can cause disease. Textbook readings will be supplemented with current literature.
Format: lectures, three hours a week; laboratory, three hours a week. Evaluation will be based on exams, laboratory reports, and a research paper.
Prerequisites: Biology 202. Enrollment limit: 24 (expected: 24). Preference given to senior and then to junior Biology majors.
Professor: Koegel
- BIOL 315(S) Microbiology: Diversity, Cellular
Physiology, and Interactions
- Bioterrorism and the alarming spread of antibiotic resistant bacteria
are but two of the reasons for the renewed emphasis on the biology of
microorganisms. This course will examine microbes from the perspectives
of cell structure and function, genetics, and evolution. A major theme
will be the adaptation of bacteria as they evolve to fill specific
ecological niches, with an emphasis on microbe: host interactions that
lead to pathogenesis. We will consider communication among bacteria as
well as between bacteria and their environment. Topics include:
microbial development, stress response, bioremediation, bacteriophages,
subversion of the immune defenses, and genomics. In the lab, students
will examine the regulation of bacterial gene expression, horizontal
gene transfer, the isolation and characterization of bacteria from
natural environment, and carry out independent projects. Readings will
be supplemented by articles from the primary literature. Evaluation
will be based on three exams, a paper, lab reports, and a presentation.
Prerequisites: Biology 202. Enrollment limit: 24 (expected: 16).
Preference given to junior and then to senior Biology majors.
Professor: Banta
Lecture: 9:00 MWF Lab: TR
- BIOL 316 Neuroethology - Neuroethology is
a comparative biological approach to the study of the neural basis of behavior
which provides insights both into general principles of nervous system function
and into how nervous systems become specialized through evolution to meet
the varied needs of particular animal species. In this class we will focus
on the role of sensory, motor, and integrative systems in selected behaviors
from a wide range of vertebrate and invertebrate animals. The behaviors examined
will include echolocation in bats, prey localization in barn owls, flight
control in locusts, song learning in songbirds, and a variety of others. We
will consider the role of computational modeling in analyzing the function
of such systems. Evaluation will be based on exams, lab reports, and class
participation. Format: Lecture/laboratory, six hours per week. Prerequisites:
Biology 202 and either Biology 205 or Biology 212.
- BIOL 319(F) Integrative Bioinformatics, Genomics,
and Proteomics Lab -
What can computational biology teach us about cancer? In this capstone
experience for the Genomics, Proteomics, and Bioinformatics program,
computational analysis and wet-lab investigations will inform each
other, as students majoring in biology, chemistry, computer science,
mathematics/statistics, and physics contribute their own expertise to
explore how ever-growing gene and protein data-sets can provide key
insights into human disease. In this course, we will take advantage of
one well-studied system, the highly conserved Ras-related family of
proteins, which play a central role in numerous fundamental processes
within the cell. The course will integrate bioinformatics and molecular
biology, using database searching, alignments and pattern matching, and
recombinant DNA techniques to reconstruct the evolution of the RAS gene
family by focusing on the gene duplication events and gene
rearrangements that have occurred over the course of eukaryotic
speciation. By utilizing high through-put approaches to investigate
genes involved in various signal transduction pathways, students will
identify pathways that are aberrantly activated in mammalian cell lines
carrying a mutant, constantly active Ras protein. This functional
genomic strategy will be coupled with microscopic examination of tissue
sections from a variety of human colon tumors, using
phosphorylation-state specific antisera, to test our hypotheses.
Proteomic analysis will introduce the students to de novo structural
prediction and threading algorithms, as well as data-mining approaches
to identify specific amino acids involved in protein-protein contacts.
Phage display and mass spectrometry will be used to study networks of
interacting proteins in normal colon and colon tumor tissue. Format:
lab, with one-hour of lecture per week. Evaluation will be based on lab
participation and several short papers/lab reports.
Prerequisite: Biology 202, or Biology 101/AP biology and Computer
Science 315 or Physics 315 or Computer Science 106, or permission of
instructor. Enrollment: 12 (expected: 12). Preference given to seniors,
then juniors/sophomores.
Professor: Lovett
Lecture: 12:25 W Lab: WR
- BIOL 321(F) Biochemistry I-Structure and Function
of Biological Molecules (Q)
- This course introduces the basic concepts of biochemistry with an
emphasis on the structure and function of biological macromolecules.
Specifically, the structure of proteins and nucleic acids are examined
in detail in order to determine how their chemical properties and their
biological behavior result from those structures. Other topics covered
include enzyme kinetics, mechanism and catalysis and regulation; the
molecular organization of biomembranes and membrane transport; and the
principles of recombinant DNA technologies. In addition, the principles
and applications of the methods used to characterize macromolecules in
solution and the interactions between macromolecules are discussed. The
laboratory provides an opportunity to study the structure of
macromolecules and to learn the fundamental experimental techniques of
biochemistry including electrophoresis and chromatography. Format:
lecture, three hours per week; laboratory, four hours per week.
Evaluation will be based on three hour exams, a final exam, problem
sets and performance in the laboratories including lab reports.
Prerequisites: Biology 101 and Chemistry 251/255 and Chemistry 155/256.
No enrollment limit (expected: 25).
Professor: Kaplan
Lecture: 10:00 MWF Lab: MWR
- BIOL 322(S) Biochemistry II-Metabolism
- This lecture course provides an in-depth presentation of the complex
metabolic reactions which are central to life. Emphasis is placed on
the biological flow of energy including alternative modes of energy
generation (aerobic, anaerobic, photosynthetic); the regulation and
integration of the metabolic pathways including compartmentalization
and the transport of metabolites; and biochemical reaction mechanisms
including the structures and mechanisms of coenzymes. This
comprehensive study also includes the biosynthesis and catabolism of
small molecules (carbohydrates, lipids, amino acids, and nucleotides).
Laboratory experiments introduce the principles and procedures used to
study enzymatic reactions, bioenergetics, and metabolic pathways.
Format: lecture, three hours per week; laboratory, four hours per week.
Evaluation will be based on several exams and performance in the
laboratories including lab reports that emphasize conceptual and
quantitative and/or graphic analysis of the data generated.
Prerequisites: Biology 101 and Chemistry 251/255. Enrollment limit: 40
(expected: 36). Preference given to junior and senior Biology and
Chemistry majors and BIMO concentrators.
Professor: Lynch
Lecture: 10:00 MWF Lab: MW
- BIOL 402T Topics in Ecology: Biological Resources
- A tutorial course investigating the patterns and processes in human-dominated
ecosystems, especially those that produce food and fiber, process wastes,
or provide a context for human activities such as recreation. The course will
draw heavily upon the experiences that students have had in other biology
courses. Topics will include: the relationships among diversity, ecosystem
function, sustainability, resilience, and stability of biological resource
systems, nutrient pools and processing in human-dominated ecosystems. Four
field trips will be taken to biological resource sites in the region. These
experiences will serve as introductions to readings and the topics of papers
to be written by student participants. Each student will write four papers
that deal with questions requiring extensive reading of primary resources.
Paper presentations will alternate with serving as a critic of other student
papers. Students will be given the opportunity to revise and rewrite two of
the four papers in the week following their tutorial presentation thereby
being able to respond to the criticism and discussion of the tutorial group.
Format: tutorial/field trip, one to three hours per week. Evaluation will
be based on writing assignments, tutorial presentation, performance in the
role of paper critic, and course participation. Prerequisites: Biology 203
or Biology 302 or Environmental Studies 203 or permission of instructor. Open
to juniors and seniors, with preference given to senior Biology majors who
have not taken a 400-level course. Satisfies the distribution requirement
in the Biology major and the Natural World distributional requirement of the
Environmental Studies program.
- BIOL 409(F) Molecular Physiology
- This discussion-based course is an advanced physiology course that
examines mammalian organ function at the molecular level. Important
proteins and biochemical events that dictate subcellular and cellular
processes will be discussed for many organ systems. Material will be
presented and discussed in the context of the molecular basis of
pathophysiological states of human disease. Topics will include
numerous genetic predispositions and diseases including Type II
diabetes, hypertension, and obesity. Student-led discussions will come
from the original literature.
Format: discussion. Evaluation will be based on class participation and
four papers (four pages each).
Prerequisites: Biology 202, Biology 205, or permission of instructor.
Enrollment limit: 2 sections of 12 (expected: 2 sections of 12 ). Open
to juniors and seniors, with preference given to senior Biology majors
who have not taken a 400-level course.
Professor: Swoap
Lecture: 8:30, 9:55 TR
- BIOL 410 Cell Dynamics in Living Systems
- Far from being static entities, individual cells can exhibit dynamic behaviors,
sometimes migrating great distances or structurally reorganizing as in the
formation-or reformation-of neuronal synapses. The ability of cells to move
and reshape underlies a vast array of normal biological processes, including
immune function, embryonic development, and memory formation, as well as abnormal
processes such as cancer growth and metastasis. It is through precise regulation
of polymerization, depolymerization, and contraction of the cellular cytoskeleton
that motility is achieved, and we are just beginning to understand the genetic
and biophysical bases of how this regulation occurs. Not surprisingly, imprecise
regulation of the cytoskeleton can have serious consequences, and several
disorders arise from defects in this process. In this course we will review
the primary literature covering migration and motility. Format: discussion,
three hours per week. Evaluation will be based on class participation and
several short papers. Prerequisites: Biology 202 and either Biology 205 or
Biology 212.
- BIOL 412 Biochemical Regulatory Mechanisms
- All biological systems are subject to regulation; in recent years, we have
come to understand a great deal about a wide range of regulatory systems.
This course, which will explore the biochemical mechanisms by which regulatory
molecules control cellular processes, is designed to provide a synthetic view
of regulatory events in the living cell. Topics will include the cell cycle;
cell signaling; mechanisms of action of regulatory molecules; and the molecular
mechanisms of cancer, with the aim of describing cancer as a derangement of
normal regulatory events that control cell growth, division, and differentiation.
Class discussions will focus on readings in the original literature. Format:
discussion. Evaluation will be based on class participation and short papers.
Prerequisites: Biology 202.
- BIOL 413(S) Molecular Basis of Biological Clocks
- Circadian rhythms have been described in all organisms studied,
including humans, a wide range of other eukaryotes and several
prokaryotes. With periods of about 24 hours, these rhythms regulate
biochemical, cellular, physiological and behavioral activities.
Circadian rhythms are generated by cellular clocks-genetically
determined internal pacemakers that maintain their oscillations in the
absence of environmental cues but may be reset by periodicities in the
environment, especially the light-dark cycle. Only recently have we
begun to understand how circadian rhythms are generated and controlled
at the cellular level. This course will explore the basic biochemical
features of biological clocks with the aim of understanding their
crucial role in regulating key biological parameters, such as enzyme
levels, levels of hormones and other regulatory molecules, and activity
and sleep cycles. Class discussions will focus on readings in the
original literature. Format: discussion, three hours per week.
Evaluation will be based on class participation and several short
papers.
Prerequisites: Biology 202. Enrollment limit: 12 (expected: 12 ). Open
to juniors and seniors, with preference given to senior Biology majors
who have not taken a 400-level course. Professor: DeWitt
Lecture: 9:55 or 11:20 TR
- BIOL 414 Life at Extremes: Molecular Mechanisms
- All organisms face variability in their environments, and the molecular
and cellular responses to stresses induced by environmental change often illuminate
otherwise hidden facets of normal physiology. Moreover, many organisms have
evolved unique molecular mechanisms, such as novel cellular compounds or macromolecular
structural modifications, which contribute to their ability to survive continuous
exposure to extreme conditions, such as high temperatures or low pH. This
course will examine how chaperonins, proteases, and heat- and cold-shock proteins
are regulated in response to changes in the external environment. We will
then consider how these and other molecular mechanisms function to stabilize
DNA and proteins -and, ultimately, cells and organisms. Other extreme environments,
such as hydrothermal vents on the ocean floor, snow fields, hypersaline lakes,
the intertidal zone, and acid springs provide further examples of cellular
and molecular responses to extreme conditions. Biotechnological applications
of these molecular mechanisms in areas such as protein engineering will also
be considered. Class discussions will focus upon readings from the primary
literature. Format: discussion, three hours per week. Evaluation will be based
on class participation and several short papers. Prerequisites: Biology 202.
Open to juniors and seniors, with preference given to senior Biology majors
who have not taken a 400-level course.
- BIOL 416(S) Epigenetics -
After decades of studies emphasizing the role of DNA in heredity,
scientists are now turning their attention from genetics to a variety
of heritable phenomena that fall under the heading of epigenetics,
heritable changes that do not result from an alteration in DNA
sequence. Research reveals that stable changes in cell function can
result from, for example, stable changes in protein conformation,
protein modification, DNA methylation, or the location of a molecule
within the cell. Using readings from the primary literature, we will
explore the epigenetic nature and molecular mechanisms underlying a
diverse array of phenomena such as prion propagation, genetic
imprinting, dosage compensation, transvection, centromere formation,
synapse function, and programmed genome rearrangements. The
significance of epigenetic processes for development, evolution, and
human health will be discussed. Format: discussion, three hours per
week. Evaluation will be based on class participation and several short
papers. Prerequisites: Biology 202. Enrollment limit: 12 (expected:
12). Open to sophomores, juniors and seniors, with preference given to
senior Biology majors who have not taken a 400-level course, then to
juniors.
Professor: Altschuler
Lecture: 8:30 TR
- BIOL 418(S) Viral Pathogenesis and the Immune Response
Viruses have an absolute requirement for a host in order to replicate. Whether that replication process causes disease in the host is a secondary byproduct of the ultimate goal of reproduction. Pathogenesis can be caused by the virus directly, or as a result of the host immune response. This course will focus on the molecular and cellular interactions between eukaryotic viruses and their hosts and how that interaction causes disease. With a primary focus on human pathogens, we will examine how viruses evade and modulate the immune response and the challenges that creates for the development of anti-viral treatments and vaccines.
Format: discussion, three hours per week. Evaluation will be based on class participation and several short papers.
Prerequisites: Biology 202. Enrollment limit: Two sections of 12 (expected: 12 per section). Open to juniors and seniors, with preference given to senior Biology majors who have not taken a 400-level course.
Professor: Roseman
- BIOL 420 Evolutionary Genetics- Why are some
amphibian genomes more than ten times larger than our own? Did humans and
Neanderthals ever interbreed? What kinds of genetic changes cause speciation
to occur? The field of evolutionary biology has seen a recent explosion in
the use of new genetic tools and techniques to study the process of evolution.
In this course we will discuss current issues in evolutionary genetics including
the molecular basis of adaptation and diversification, genome evolution, the
genetics of speciation, and the interpretation of population genetic patterns
of variation. Class discussions will focus on readings from current primary
literature. Format: discussion, three hours per week. Evaluation will be based
on participation in class discussions and several short papers. Prerequisite:
Biology 305 or permission of instructor. Open to juniors and seniors, with
preference given to senior Biology majors who have not taken a 400-level course.
- BIOL 425T(S) Coevolution -
Coevolution, defined as reciprocal adaptation between species, is
central to understanding biological phenomena ranging from global
patterns of biodiversity to the molecular mechanisms of host-parasite
evolution. The focus of this tutorial will be on coevolution as a
paradigm for integrating across scales of biological organization.
Topics will include adaptive radiation, evolutionary dynamics and
conservation, molecular coevolution of human disease (e.g., HIV) and
evolution of sex mediated by a sperm-egg arms-race. Format: tutorial.
Evaluation will be based on 5 (4-5 page) papers, tutorial
presentations, and the student's effectiveness as a critic.
Prerequisites: Biology 203 or 302 or 305 or Environmental Studies 203
or permission of instructor. Enrollment limit: 10 (expected: 10). Open
to juniors and seniors, with preference given to senior Biology majors
who have not taken a 400-level course.
Professor: Morales
Lecture: TBA
- BIOL 493(F) Senior Thesis - Each student
prepares a thesis under the supervision of a member of the department. Thesis
work can begin either in the spring of the junior or the fall of the senior
year, and includes the Winter Study period of the senior year.
Lecture: TBA
- BIOL 494(S) Senior Thesis - Each student
prepares a thesis under the supervision of a member of the department. Thesis
work can begin either in the spring of the junior or the fall of the senior
year, and includes the Winter Study period of the senior year.
Lecture: TBA
- BIOL W031 Senior Thesis - Each student
prepares a thesis under the supervision of a member of the department. Thesis
work can begin either in the spring of the junior or the fall of the senior
year, and includes the Winter Study period of the senior year.
Lecture: TBA