Biology
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Amherst College Biology for 2012-13

104 Food, Fiber, and Pharmaceuticals

It is perhaps impossible to experience a day without plants.  From the air we breathe, the bed we sleep in, the soap we wash with and clothes we put on, to the foods we consume and the medicines we take, we are very much dependent upon plants and their products.  Through a combination of lecture, discussion, and observation, we will explore how, why, and when plants became vital to people and their societies.  Several economically important plant groups will be studied, including those that provide food and beverages, medicines and narcotics, spices, perfumes, fuels, and fiber.  What are the characteristics of these groups enabling their exploitation, and what is the history of these associations?  How and when were plants domesticated and what are the consequences of large-scale agriculture?  What impacts do human population growth and habitat destruction have on the ways that people interact with plants now and in the future?  Finally, we will explore the role of technology in efforts to both improve and synthesize plant products.  Three classroom hours per week.  Two local field trips.

Limited to 26 students. This course is for non-majors. Students majoring in Biology will be admitted only with permission from the instructor.  Spring semester.  Visiting Professor Levin.   

2014-15: Not offered
Other years: Offered in Spring 2013, Fall 2013

106 Why Sex?

Perhaps no subject in biology is as troublesome (or as fraught with contradictions) as sex. Why should organisms devote so much of their time and energy to attracting mates, when they can reproduce much more efficiently by cloning themselves? Similarly, why not pass on all your genes, rather than just half? Darwin was among the first to realize that competition for mates is sometimes as important as competition for survival. Sex is an exceedingly powerful ecological and evolutionary force, responsible for generating a tremendous diversity of morphologies and behaviors. In this course, we will draw upon examples from microbes to mosses to mammals in order to address these most basic biological questions: Why did sex evolve and what are its consequences? Three hours of lecture and one hour of discussion per week.

Limited to 30 students. This course is for non-majors. Students majoring in Biology, Chemistry, or Psychology will be admitted only with permission from the instructor.  Omitted 2012-13.  Professor Miller.

2014-15: Not offered

108 The Biology of Catastrophe: Cancer and AIDS

AIDS, the acquired immunodeficiency syndrome, is caused by HIV infection and is the result of a failure of the immune system. Cancer is the persistent, uncontrolled and invasive growth of cells. A study of the biology of these diseases provides an opportunity to contrast the normal operation of the immune system and the orderly regulation of cell growth with their potentially catastrophic derangement in cancer and AIDS. A program of lectures and readings will provide an opportunity to examine the way in which the powerful technologies and insights of molecular and cell biology have contributed to a growing understanding of cancer and AIDS. Factual accounts and imaginative portraits will be drawn from the literature of illness to illuminate, dramatize and provide an empathetic appreciation of those who struggle with disease. Finally, in addition to scientific concepts and technological considerations, society's efforts to answer the challenges posed by cancer and AIDS invite the exploration of many important social and ethical issues. Three classroom hours per week.

Limited to 50 students. This course is for non-majors. Students majoring in Biology, Chemistry, or Psychology will be admitted only with permission from the instructor.  Omitted 2012-13.

2014-15: Not offered

110 Contagion

Infection by contagious microorganisms remains a leading cause of death in many parts of the world.  This course will explore the biological mechanisms of infectious diseases, as well as the challenges associated with fighting their emergence and spread. We will focus on diseases of global health importance, such as HIV/AIDS, cholera, and tuberculosis, to discuss the strategies pathogens have evolved that ensure their successful transmission. In light of their ability to effectively outwit our own immune systems, we must devise new means to overcome these disease-causing microbes. Here, the challenges are legion. We will see that the answer lies not only with an understanding of biology to formulate treatments and prevention measures, but this knowledge must be integrated with awareness of complex societal issues to inform and implement solutions. Discussions will focus upon the many perspectives from which infectious diseases are encountered, drawing on resources from the literature on microbiology, ethics, and policy, as well as personal accounts and current news stories.  Three hours of lecture and discussion per week.  This course is for non-science majors and will not count toward the Biology major.

Limited to 40 students.   Spring semester.  Professor Purdy.

2014-15: Not offered
Other years: Offered in Spring 2013, Spring 2014

114 Evolution of Human Nature

Recent extensions of the theory of natural selection provide a unified explanatory framework for understanding the evolution of human social behavior and culture.  After consideration of the relevant principles of genetics, population biology, developmental biology and animal behavior, the social evolution of animals--especially that of our nearest relatives, the apes--will be discussed and illustrated.  With this background, many aspects of human social, psychological and cultural evolution will be considered:  the instinct to create and acquire language; aggression and cooperation within and between the sexes; the human mating system; the origin of patriarchy; systems of kinship and inheritance; incest avoidance; rape; reciprocity and exchange; conflict between parents and offspring; homicide; warfare; moral emotions; deceit and self deception; the evolution of laws and justice; and the production and appreciation of art and literature.  Three hours of lecture and films per week, and several guest speakers.

Omitted 2012-13.  Professor Emeritus Zimmerman.

2014-15: Not offered

131 Chemical Basis of Biological Processes

(Offered as CHEM 131 and BIOL 131.) What are the natural laws that describe how biological processes actually work?  This course will use examples from biology such as human physiology or cellular signaling to illustrate the interplay between fundamental chemical principles and biological function.  We will explore how bonding plays a central role in assembling simple biological building blocks such as sugars, amino acids, and fatty acids to form complex carbohydrates, proteins, and membranes.  What underlying thermodynamic and kinetic principles guide systems to biological homeostasis or reactivity?  What is pH, and how are proton gradients used to generate or change an organism's response?  Emphasis is on using mathematics and physical sciences to understand biological functions. Three classroom hours and three hours of laboratory per week.

Enrollment is limited to first-year students who are interested in science or premedical study, who are recommended to begin with either MATH 105 or MATH 111 (Intensive), and who are enrolled in a Mathematics course but not in CHEM 151.

Admission with consent of the instructor.  Fall semester. Professor Poccia and Postdoctoral Fellow Hebda.

2014-15: Not offered
Other years: Offered in Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013

181 Adaptation and the Organism

An introduction to the evolution, ecology, and behavior of organisms and how these relate to the diversity of life. Following a discussion of the core components of evolutionary theory, we'll examine how evolutionary processes have shaped morphological, anatomical, physiological, and behavioral adaptations in organisms that solve many of life's problems, ranging from how to find or acquire food and avoid being eaten, to how to attract and locate mates, and how to optimize reproduction throughout a lifetime. We'll relate and compare characteristics of animals, plants, fungi, protists, and bacteria, examining how and why these organisms have arrived at various solutions to life's problems. Laboratory exercises will complement lectures and will involve field experiments on natural selection and laboratory studies of vertebrates, invertebrates, bacteria, and plants. Four classroom hours and three laboratory hours per week.

Spring semester. Professors Clotfelter and Miller, and Lab Coordinator Emerson.

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014

191 Molecules, Genes and Cells

An introduction to the molecular and cellular processes common to life with an emphasis on control of energy and information flow.  Central themes include metabolism, macromolecular function, and the genetic basis of cellular function.  We examine how membranes work to establish the internal composition of cells, how the structure of proteins including enzymes affects protein function, how energy is captured, stored and utilized by cells, and how cells communicate, move and divide.  We explore inheritance patterns and underlying molecular mechanisms of genetics, the central dogma of information transfer from DNA replication to protein synthesis, and recombinant DNA methods and medical applications.  Laboratories include genetic analyses, enzyme reaction kinetics, membrane transport, and genomic analysis.  Four classroom hours and three laboratory hours per week.

Requisite: Prior completion of, or concurrent registration in, CHEM 161. Fall semester. Professors Graf and Ratner and Lab Coordinator Emerson.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013

210 Experimental Design and Data Analysis in the Life Sciences

Organisms--even members of the same species--differ from one another in structure, genetics, physiology, biochemistry, and behavior.  Life scientists’ observations contain variability not only because of measurement error or imprecision, but also because of real differences within the samples being studied. How is this variation best described quantitatively?  What inferences about a population can be made from measurements on a sample of the population?  If our aim is to detect differences between groups, such as experimental and control groups, how do we go about designing a study that has a reasonable chance of finding a meaningful difference if one exists, subject to considerations of time and cost?  How is experimental design affected by ethical considerations in the treatment of animal and human subjects?  Once the data are obtained, how likely is it that an observed difference between experimental and control groups could have arisen by chance because of variability in the samples chosen for study even if there were no actual effect of the experiment?  The course will include study of the principles and methods of data analysis, practice in using these methods, and discussion of examples of successes and failures in the design of experiments and the use of statistics.

Not open to first-year students. Spring semester. Professor S. George.

2014-15: Not offered
Other years: Offered in Spring 2013

220 Developmental Biology

A study of the development of animals, leading to the formulation of the principles of development, and including an introduction to experimental embryology and developmental physiology, anatomy, developmental genetics and "evo-devo."  Four classroom hours per week.

Requisite: BIOL 191. Omitted 2012-13.  Professor Poccia.

2014-15: Not offered

230 Ecology

(Offered as BIOL 230 and ENST 210.) A study of the relationships of plants and animals (including humans) to each other and to their environment. We'll start by considering the decisions an individual makes in its daily life concerning its use of resources, such as what to eat and where to live, and whether to defend such resources. We'll then move on to populations of individuals, and investigate species population growth, limits to population growth, and why some species are so successful as to become pests whereas others are on the road to extinction. The next level will address communities, and how interactions among populations, such as competition, predation, parasitism, and mutualism, affect the organization and diversity of species within communities. The final stage of the course will focus on ecosystems, and the effects of humans and other organisms on population, community, and global stability. Three hours of lecture per week.

Requisite: BIOL 181 or ENST 120 or permission from the instructor. Not open to first-year students. Fall semester. Professor Temeles.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Spring 2012, Fall 2012, Fall 2013

241 Genetic Analysis of Biological Processes

This course will explore the application of genetic analysis toward understanding complex biological systems. Scientists often turn to the study of genes and mutations when trying to decipher the mechanisms underlying such diverse processes as the making of an embryo, the response of cells to their environment, or the defect in a heritable disease. By reading papers from the research literature, we will study in detail some of the genetic approaches that have been taken to analyze certain molecular systems. We will learn from these examples how to use genetic analysis to formulate models that explain the molecular function of a gene product. The laboratory portion of this course will include discussions of the experimental approaches presented in the literature. Students will apply these approaches to their own laboratory projects. Three hours of lecture and four hours of laboratory per week; the laboratory projects will require additional time outside of class hours.

Requisite: BIOL 191. Limited to 24 students. Not open to first-year students. Spring semester. Professor Goutte.

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2008, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014

251 Molecular Genetics

(Offered as BIOL 251 and BCBP 281) A study of the molecular mechanisms underlying the transmission and expression of genes. DNA replication and recombination, RNA synthesis and processing, and protein synthesis and modification will be examined. Both prokaryotic and eukaryotic systems will be analyzed, with an emphasis upon the regulation of gene expression. Application of modern molecular methods to biomedical and agricultural problems will also be considered. The laboratory component will focus upon recombinant DNA methodology. Four classroom hours and four hours of laboratory per week; some laboratory exercises may require irregular hours.

Requisite: BIOL 191 or equivalent. Limited to 30 students. Not open to first-year students.  Omitted 2012-13. Professor Ratner.

2014-15: Not offered

260 Animal Physiology

This course will examine the function of tissues, organs, and organ systems, with an emphasis on the relationship between structure and function. Building outward from the level of the cell, we will study bodily processes including respiration, circulation, digestion and excretion. In addition, the course will address how different organisms regulate these complex processes and how ion and fluid balance is maintained. We will also study the nervous system in the context of sensory systems, focusing on how external stimuli are transformed into meaningful neuronal signals and processed by the brain. Weekly discussions will include readings from primary literature. Four classroom hours per week.

 Requisite: BIOL 191 and either BIOL 181 or NEUR 226.  Spring semester.  Professor Trapani.

2014-15: Not offered
Other years: Offered in Fall 2011, Spring 2013

271 Microbiology

Microbes inhabit the world's oceans, deserts, lakes, soils, and atmosphere, and play a vital role in the Earth's biogeochemical cycles.  As humans, we harbor a diverse microbial flora estimated to outnumber our own human cells.  During this course, we will explore this microbial world by investigating the structure, physiology, genetics, and evolution of microorganisms with a focus on bacteria, but including discussions of archaea, viruses, and microbial eukaryotes. The goal of the course is to gain an understanding of the unique properties of microbes that enable their persistence and diversification.  We will also pay special attention to microbial interactions with eukaryotic organisms, by studying both host and microbe contributions to virulence, mutualism, and symbiotic relationships. Laboratory exercises will include explorations of microbial functions and diversity in a variety of contexts using both classical and molecular approaches. Three hours of lecture, three hours of laboratory and one hour of discussion per week.

Requisite: BIOL 181 and 191. Limited to 28 students. Not open to first-year students. Fall semester. Professor Purdy.

 

2014-15: Offered in Spring 2015
Other years: Offered in Fall 2012, Fall 2013

281 Animal Behavior

Shaped by millions of years of natural and sexual selection, animals have evolved myriad abilities to respond to their biotic and abiotic environment. This course examines animal behavior from both a mechanistic and a functional perspective. Drawing upon examples from a diverse range of taxa, we will discuss topics such as sensory ecology, behavioral genetics, behavioral endocrinology, behavioral ecology and sociobiology. Three classroom hours and four laboratory hours per week; the laboratory projects will require additional time outside of class hours.

Requisite: BIOL 181. Limited to 24 students. Not open to first-year students. Omitted 2012-13. Professor Clotfelter.

2014-15: Not offered

290, 490, 290H, 490H Special Topics

Independent reading or research courses. Full course as arranged. Does not normally count toward the major.

Fall and spring semesters.

2014-15: Offered in Fall 2014 and Spring 2015
Other years: Offered in Fall 2011, Fall 2012, Spring 2013, Fall 2013, Spring 2014

291 Cell Structure and Function

(Offered  as BIOL 291 and BCBP 291)  An analysis of the structure and function of cells in plants, animals, and bacteria. Topics to be discussed include the cell surface and membranes, cytoskeletal elements and motility, cytoplasmic organelles and bioenergetics, the interphase nucleus and chromosomes, mitosis, meiosis, and cell cycle regulation. Four classroom hours and three hours of laboratory per week.

Requisite: BIOL 191 and completion of, or concurrent registration in, CHEM 161.  Limited to 24 students. Spring semester. Professor Poccia.

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2012, Spring 2013, Spring 2014

301 Molecular Neurobiology

An analysis of the molecules and molecular mechanisms underlying nervous system function, development, and disease.  We will explore the proteins that contribute to the unique structure and function of neurons, including an in-depth analysis of synaptic communication and the molecular processes that modify synapses.  We will also study the molecular mechanisms that control brain development, from neurogenesis, neurite growth and synaptogenesis to cell death and degeneration.  In addition to analyzing neural function, throughout the course we will also study nervous system dysfunction resulting when such molecular mechanisms fail, leading to neurodevelopmental and neurodegenerative disease.  Readings from primary literature will emphasize current molecular techniques utilized in the study of the nervous system.  Three classroom hours and three hours of laboratory per week.

Requisite:  BIOL 191 and CHEM 161.  Limited to 24 students. Omitted 2012-13.  Professor Graf.

2014-15: Not offered

310 Structural Biochemistry

(Offered as BIOL 310 and BCBP 310.) This course will concentrate on the structure of proteins at the atomic level. It will include an introduction to methods of structure determination, to databases of structural information, and to publicly available visualization software. These tools will be used to study some class of specific structures, (such as membrane, nucleic acid binding, regulatory, structural, or metabolic proteins). These proteins will provide the framework for discussion of such concepts as domains, motifs, molecular motion, structural homology, etc., as well as addressing how specific biological problems are solved at the atomic level. Four classroom hours per week plus one hour discussion .

Requisite: BIOL 191 and CHEM 161; CHEM 221 would be helpful but is not required. Limited to 20 students. Fall semester.  Professor Williamson.

2014-15: Offered in Spring 2015
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Fall 2012

320 Evolutionary Biology

Evolution is a powerful and central theme that unifies the life sciences. In this course, emphasis is placed on microevolutionary mechanisms of change, and their connection to large-scale macroevolutionary patterns and diversity. Through lectures and readings from the primary literature, we will study genetic drift and gene flow, natural selection and adaptation, molecular evolution, speciation, the evolution of sex and sexual selection, life history evolution, and inference and interpretation of evolutionary relationships. Three hours of lecture and one hour of discussion each week.

Requisite: BIOL 181; BIOL 191 recommended. Limited to 14 students. Not open to first-year students. Fall semester.  Professor Miller.

2014-15: Offered in Spring 2015
Other years: Offered in Fall 2011, Fall 2012, Fall 2013

321 Evolutionary Biology With Lab

Evolution is a powerful and central theme that unifies the life sciences. In this course, emphasis is placed on microevolutionary mechanisms of change, and their connection to large-scale macroevolutionary patterns and diversity. Through lectures and readings from the primary literature, we will study genetic drift and gene flow, natural selection and adaptation, molecular evolution, speciation, the evolution of sex and sexual selection, life history evolution, and inference and interpretation of evolutionary relationships. The laboratory investigates evolutionary processes using computer simulations, artificial selection experiments, and a semester-long project that characterizes phenotypic breeding relationships among individuals and integrates these results with analyses of molecular sequence variation for genes contributing to mating recognition. Three hours of lecture, one hour of discussion and four hours of laboratory work each week.

Requisite: BIOL 181; BIOL 191 recommended. Limited to 16 students. Not open to first-year students.  Fall semester.  Professor Miller.

2014-15: Not offered
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2011, Fall 2012

330 Biochemical Principles of Life at the Molecular Level

(Offered as BIOL 330 and CHEM 330) What are the molecular underpinnings of processes central to life?  We will explore the chemical and structural properties of biological molecules and learn the logic used by the cell to build complex structures from a few basic raw materials. Some of these complex structures have evolved to catalyze chemical reactions with enormous degree of selectivity and specificity, and we seek to discover these enzymatic strategies. We will consider the detailed balance sheet that shows how living things harvest energy from their environment to fuel metabolic processes and to reproduce and grow.  Examples of the exquisite control that permits a cell to be responsive and adapt its responses based on input from the environment will be considered.  We will also consider some of the means by which cells respond to change and to stress.  A student may not receive credit for both CHEM 330 and BCBP/BIOL/CHEM 331.

Requisite:  BIOL 191 and CHEM  221.  Limited to 30 students.  Fall semester.  Professor O'Hara.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2011, Fall 2012, Fall 2013

331 Biochemistry

(Offered as BIOL 331, BCBP 331, and CHEM 331.) Structure and function of biologically important molecules and their role(s) in life processes. Protein conformation, enzymatic mechanisms and selected metabolic pathways will be analyzed. Additional topics may include: nucleic acid conformation, DNA/protein interactions, signal transduction and transport phenomena. Four classroom hours and four hours of laboratory work per week. Offered jointly by the Departments of Biology and Chemistry. A student may not receive credit for both BCBP/BIOL/CHEM 331 and CHEM 330. 

Requisite: CHEM 221 and BIOL 191; or consent of the instructor. CHEM 231 is a co-requisite. Spring semester. Limited to 45 students. Professors Williamson (Biology) and Bishop (Chemistry).

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014

340 The Cell and Molecular Biology of Cancer

While still mysterious, cancer is now recognized as a set of diseases resulting from molecular aberrations that are traceable to mutations in the genome. Molecular biology and cell biology have emerged as key approaches in the continuing effort to gain a fundamental understanding of the origin, development and pathogenesis of cancer. In this course we will explore the experimental and conceptual foundations of current views of oncogenes, tumor suppressors, multistep carcinogenesis, cancer stem cells, immune responses to cancer and the rational design of targeted chemotherapeutic agents. The work of the course will include lectures and discussions, critical reading of the primary literature of cancer research, and one-on-one tutorials. Three classroom hours per week and regularly scheduled tutorial meetings with the instructor.

Requisite: At least one but preferably two or more courses from the following list--BIOL 220, 241, 251, 291, 310, 331, 370, or 381. Limited to 20 students. Open to juniors and seniors or permission from the instructor.  Omitted 2012-13.

2014-15: Not offered

351 Neurophysiology

This course will provide a deeper understanding of the physiological properties of the nervous system. We will address the mechanisms underlying electrical activity in neurons, as well as examine the physiology of synapses; the transduction and integration of sensory information; the function of nerve circuits; the trophic and plastic properties of neurons; and the relationship between neuronal activity and behavior. Laboratories will apply electrophysiological methods to examine neuronal activity and will include experimental design as well as analysis and presentation of collected data. Throughout the course, we will focus on past and current neurophysiology research and how it contributes to the field of neuroscience. Three classroom hours and three hours of laboratory work per week.

Requisites: BIOL 191 and CHEM 151; PHYS 117 or 124 is recommended. Limited to 24 students.  Fall semester.  Professor Trapani.

2014-15: Not offered
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2012, Fall 2013

360 Neurobiology of Disease

How translational research applies neuroscience knowledge to seek to understand the pathophysiology, prevent, treat, and cure brain diseases.   After reviewing basic neuroanatomy, neuropathology, and neuronal cell biology, we will study Parkinson's, Huntington's, and Alzheimer's diseases, epilepsy, multiple sclerosis, neurologic complications of AIDS and cancer, cerebrovascular disease, trauma, alcoholism and other intoxications, motor neuron disease including amyotrophic lateral sclerosis, and prion diseases.  Several Amherst alumni who are doing translational neuroscience research will serve as guest lecturers in the course.  How are animal models of these diseases developed?  What promises and problems arise in using animal models?   How are pharmacological and other therapeutic strategies derived?  How do we assess genetic influences on human nervous system diseases, and how should we use such knowledge?  Three classroom hours per week.   

Requisite: BIOL 191 and either NEUR 226 or BIOL 301 or BIOL351, or consent of the instructor.  Additional upper-level courses in biology recommended.  Fall semester. Limited to 20 students.  Croxton Lecturer Koo. 

2014-15: Not offered
Other years: Offered in Spring 2011, Fall 2012

370 Immunology

The immune response is a consequence of the developmentally programmed or antigen-triggered interaction of a complex network of interacting cell types. These interactions are controlled by regulatory molecules and often result in the production of highly specific cellular or molecular effectors. This course will present the principles underlying the immune response and describe the methods employed in immunology research. In addition to lectures, a program of seminars will provide an introduction to the research literature of immunology. Three classroom hours per week.

Requisite: BIOL 191, 251, 291, 331 or permission from the instructor. Limited to 25 students. Omitted 2012-13.

2014-15: Not offered

380 Genome Biology

A study of the architecture and interactions of genetic systems. Advances in genomics are providing insights into a variety of important issues, from the structural limits of DNA-based inheritance to the discovery of novel infectious and genetic diseases. We will address how heritable information is organized in different groups of organisms. We will also cover a major challenge of this emerging field--the application of vast amounts of genetic data to understanding genomic integrity and regulation. We will critically assess the genome as a "cooperative assemblage of genetic elements" and conclude by discussing the consequences of genomic structure for shaping species traits and long-term evolutionary potential.  Three hours of lecture per week. 

Requisite: BIOL 181 and BIOL 191.  Spring semester. Professor Hood.

2014-15: Not offered
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Spring 2012, Spring 2013, Spring 2014

381 Genome Biology with Lab

A study of the architecture and interactions of genetic systems. Advances in genomics are providing insights into a variety of important issues, from the structural limits of DNA-based inheritance to the discovery of novel infectious and genetic diseases. We will address how heritable information is organized in different groups of organisms. We will also cover a major challenge of this emerging field--the application of vast amounts of genetic data to understanding genomic integrity and regulation. We will critically assess the genome as a "cooperative assemblage of genetic elements" and conclude by discussing the consequences of genomic structure for shaping species traits and long-term evolutionary potential.  Three hours of lecture, and three hours of laboratory per week.  Lab activities will require work outside of the scheduled meeting times.

Requisite: BIOL 181 and 191. Limited to 18 students. Omitted 2012-13.  Professor Hood.

2014-15: Not offered

395 Physical laws and biological processes

Reading and discussion of historical and contemporary scientific literature at the interface between physics and the life sciences.  Topics will include (1) how observations on human physiology contributed to the formulation of the laws of thermodynamics; (2) whether an intelligent being (a so-called Maxwell’s demon) could thwart the entropy increases called for in the second law of thermodynamics by sorting individual molecules using information about each molecule’s position or motion; and (3) to what extent non-classical physical phenomena such as quantum tunneling must be invoked to explain biological processes including enzyme catalysis, neuronal information processing, and consciousness.

Requisite: PHYS 116 and 117, or 123 and 124; BIOL 181; CHEM 161 or PHYS 230. Spring semester. Professor S. George.

2014-15: Not offered
Other years: Offered in Spring 2013

400 Molecular and Cellular Biophysics

(Offered as PHYS 400, BIOL 400, BCBP 400, and CHEM 400.) How do the physical laws that dominate our lives change at the small length and energy scales of individual molecules? What design principles break down at the sub-cellular level and what new chemistry and physics becomes important? We will answer these questions by looking at bio-molecules, cellular substructures, and control mechanisms that work effectively in the microscopic world. How can we understand both the static and dynamic shape of proteins using the laws of thermodynamics and kinetics? How has the basic understanding of the smallest molecular motor in the world, ATP synthase, changed our understanding of friction and torque? We will explore new technologies, such as atomic force and single molecule microscopy that have allowed research into these areas. This course will address topics in each of the three major divisions of Biophysics: bio-molecular structure, biophysical techniques, and biological mechanisms.

Requisite: CHEM 161, PHYS 116/123, PHYS 117/124, BIOL 191 or evidence of equivalent coverage in pre-collegiate courses.  Fall semester. Professors Carter and Williamson.

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013

404 Seminar in Biochemistry

(Offered as BIOL 404 and BCBP 405) The topic of this advanced seminar will be cholesterol.  It has been said that more Nobel prizes have been awarded for the study of cholesterol than any other biological topic, yet it is astonishing how much we have learned only in the last few years, and how much we still don't understand.  The topics in this course will include biosynthesis, transport, regulation, physiology, and biophysics of cholesterol.  In many cases, these subjects illuminate or are illuminated by cholesterol-related diseases, so the biochemical bases for high cholesterol medications and for a genetic propensity for getting heart disease from eating broccoli are likely to come up.  The course will be based on the scientific literature, and will include writing and presentation assignments.

Requisite:  BIOL 191 and 291 or 331 or equivalent.  Limited to 15 students.  Omitted 2012-13.  Professor Williamson.

2014-15: Not offered

410 Seminar in Disease Biology

The majority of organisms on earth cause disease or are parasitic, and it could be said that a thorough understanding of biology should necessarily involve the study of infectious disease. Yet only within the past two decades has there been a realization that diseases may regulate populations, stabilize ecosystems, and be responsible for major biological features such as reproductive systems or genomic structures. Disease is of course responsible for large amounts of human misery and death, and it is all the more remarkable that our understanding of disease as an ecological and evolutionary force is in its infancy. In this course we will discuss our historical and current understandings of infectious disease biology. We will include studies of human, animal, and plant diseases, as well as their impacts on wild and domestic populations. Three classroom hours per week.

Requisite: BIOL 230 or 321 or permission from the instructor. Limited to 15 students. Spring semester.  Professor Hood. 

2014-15: Not offered
Other years: Offered in Spring 2008, Spring 2010, Spring 2011, Spring 2012, Spring 2013

430 Seminar in Behavioral Ecology

This course will explore the relationship between an animal's behavior and its social and ecological context. The topic for 2010 will be the evolution of sexual dimorphism in animals. Sexual dimorphism is widespread in animals, yet its causes remain controversial and have generated much debate. In this seminar, we will examine a variety of sexual dimorphisms in different groups of animals and consider hypotheses for how these sexual dimorphisms may have evolved. We will then consider how such hypotheses are tested in an attempt to identify the best approaches to studying the evolution of sexual dimorphisms. Then we will look at evidence that either supports or refutes various hypothesized mechanisms for the evolution of sexual dimorphisms in different animal groups. Finally, we will consider whether some mechanisms for the evolution of sexual dimorphism are more common among certain kinds of organisms (predators) than others (herbivores).  Three hours per week.

Requisite:  One or more of BIOL 181, 230, 281, 321 or consent of the instructor.  Not open to first-year students. Limited to 14 students. Omitted 2012-13.  Professor Temeles. 

2014-15: Not offered

434 Seminar in Ecology

The topic is the ecology and evolution of plant-animal interactions. Most animals on Earth obtain their energy from green plants, and thus it is not surprising that interactions between plants and animals have played a prominent role in our current understanding of how ecological processes such as predation, parasitism, and mutualism shape evolutionary patterns in plants and animals. In this course we will start our analysis with a consideration of how plant-animal relationships evolve by studying examples from both extant systems and the fossil record. Next we will examine the different kinds of plant-animal interactions (pollination, seed dispersal, seed predation, and herbivory, to mention a few) that have evolved on our planet, and the ecological processes promoting reciprocal evolution of defenses and counter-defenses, attraction, and deceit. Finally, we will turn our attention to global change and the implications of human alteration of the environment for the future of plant-animal relationships, such as pollination, which are of vital importance to life on Earth. Three classroom hours per week.

Requisite: BIOL 230 or 321 or permission from the instructor. Limited to 14 students. Not open to first-year students. Spring semester. Professor Temeles. 

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2007, Fall 2009, Fall 2011, Spring 2013

440 Seminar in Conservation Biology.

Conservation biology is a highly interdisciplinary field, requiring careful consideration of biological, economic, and sociological issues. Solutions to biodiversity conservation and environmental challenges are even more complex. Yet, conservation is a topic of timely importance in order to safeguard biological diversity. Utilizing articles from the primary literature, course topics will include invasive species, restoration, climate change, and biodiversity banking, as well as how to determine appropriate conservation priorities. Three classroom hours per week.

Requisite: BIOL 230 or 321 or permission of the instructor.  Not open to first-year students.  Limited to 14 students.  Omitted 2012-13.  Visiting  Professor R. Levin. 

2014-15: Not offered

444 Seminar in Developmental Genetics

Much of our molecular understanding of developmental biology stems from genetic analysis of mutants in model systems. In this seminar we will consider a range of developmental events, such as cell specialization and cell communication, in the well-studied Drosophila and C. elegans model systems. Reading from scientific journals, we will follow a variety of genetic approaches that have uncovered the molecular mechanisms responsible for these developmental events. Class discussions will focus on experimental design, data interpretation, and model building. Assignments will include scientific writing and oral presentations.

Requisite: BIOL 220, 241, 251, or 291.  Limited to 15 students.  Omitted 2012-13.  Professor Goutte.

2014-15: Not offered

450 Seminar in Physiology: Classic Papers in Neurophysiology

Concentrating on reading and interpreting primary research, this course will focus on classic and soon-to-be classic neurophysiology papers. We will discuss the seminal experiments performed in the 1950s that led to our understanding of action potentials; experiments in the 1960s and 1970s that unlocked how synapses function; and more recent research that combines electrophysiology with optical methods and genetic techniques to investigate the role of many of the molecular components predicted by the work from the earlier decades. Assignments will include written reviews of literature as well as oral presentations.

Requisite: PHYS 117 or PHYS 124 and either NEUR 226, BIOL 260, BIOL 351, or consent of the instructor. Limited to 15 students. Not open to first-year students. Spring semester. Professor Trapani.

2014-15: Not offered
Other years: Offered in Spring 2013

498, 499D Senior Departmental Honors

Honors students take three courses of thesis research, usually, but not always, with the double course load in the spring. The work consists of seminar programs, individual research projects, and preparation of a thesis on the research project.

Open to seniors. Fall semester. The Department.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013
 

McGuire Life Sciences Building