Biology
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Amherst College Biology for 2009-10

03 Chemical Basis of Biological Processes

(Offered as Chemistry 03 and Biology 03.) 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 Mathematics 5 or Mathematics 11 (Intensive), and who are enrolled in a Mathematics course but not in Chemistry 11. Admission with consent of the instructor. Fall semester. Professors Goutte and O'Hara.

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

06 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.

This course is for non-majors and will not count toward the Biology major. Fall semester. Professor Miller.

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

08 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 2009-10.  Professor Goldsby. 

2014-15: Not offered
Other years: Offered in Fall 2007, Spring 2009, Fall 2010, Fall 2011

14 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.

Spring semester.  Professor Emeritus Zimmerman.

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

18 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 Hood.

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

19 Molecules, Genes and Cells

An introduction to the molecular and cellular processes common to life. A central theme is the genetic basis of cellular function. Four classroom hours and three laboratory hours per week.

Requisite: Prior completion of, or concurrent registration in, Chemistry 12 or permission from the instructor. Fall semester. Professor Poccia and Visiting Professor Springer.

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

22 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, and genetics. Four classroom hours and four hours of laboratory per week.

Requisite: Biology 19. Spring semester. Professor Poccia.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2007, Spring 2009, Spring 2010, Fall 2011

23 Ecology

(Offered as Biology 23 and Environmental Studies 21.) 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 ecosytems, and the effects of humans and other organisms on population, community, and global stability. Three hours of lecture per week.

Requisite: Biology 18 or Environmental Studies 12 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

24 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: Biology 19. 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

25 Molecular Genetics

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: Biology 19. Limited to 30 students. Not open to first-year students.  Omitted 2009-10.  Professor Ratner.

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

27 Genome Biology

A study of the architecture and interactions of genetic systems. Advances in genomics are resulting in new approaches to a variety of important issues, from conservation biology to disease prevention and treatment. We will address how heritable information is organized in diverse types of organisms and the consequences for shaping species traits and long-term evolutionary potential. We will cover the major challenges of this emerging research field, including techniques for dealing with vast amounts of DNA sequence data. We will also critically review the concept of the genome as a “cooperative assemblage of genetic elements.”  Three hours of lecture and three hours of laboratory per week.

Requisite: Biology 18 and 19. Limited to 30 students. Fall semester.  Professor Hood.

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

29 Cell Structure and Function

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: Biology 19 and completion of, or concurrent registration in, Chemistry 12. Spring semester. Visiting Professor Springer.

2014-15: Not offered
Other years: Offered in Spring 2009, Spring 2010, Spring 2011

30 Biochemistry

(Offered as Biology 30 and Chemistry 30.) 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.

Requisite: Chemistry 21 and Biology 19; Chemistry 22 is a co-requisite. Anyone who wishes to take the course but does not satisfy these criteria should obtain permission from the instructor. Spring semester. Professors Williamson (Biology) and Jaswal (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

32 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. 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 and four hours of laboratory work each week.

Requisite: Biology 18; Biology 19 recommended. Limited to 24 students. Not open to first-year students. Spring semester. Professor Miller.

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

33 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: Biology 19 and Biology 25, 29, 30 or permission from the instructor. Limited to 25 students. Spring semester. Professor Goldsby.

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

34 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--Biology 22, 24, 25, 27, 29, 30, 33, or 37. Limited to 20 students. Open to juniors and seniors or permission from the instructor. Fall semester. Professor Goldsby.

2014-15: Not offered
Other years: Offered in Fall 2008, Fall 2009, Spring 2011

35 Neurobiology

Nervous system function at the cellular and subcellular level. Ionic mechanisms underlying electrical activity in nerve cells; the physiology of synapses; transduction and integration of sensory information; the analysis of nerve circuits; the specification of neuronal connections; trophic and plastic properties of nerve cells; and the relation of neuronal activity to behavior. Four classroom hours per week.

Requisite: Biology 18 or 19 and Chemistry 11; Physics 17 or 24 is recommended. Spring semester. Professor S. George.

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

37 Structural Biochemistry

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: Biology 19 and Chemistry 12; Chemistry 21 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

39 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: Biology 18. Limited to 24 students. Not open to first-year students. Fall semester. Professor Clotfelter.

2014-15: Offered in Spring 2015
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Fall 2011, Fall 2013

42 Seminar in Evolution: Plant Sexual Diversity

The diversity of reproductive strategies and sexual systems among angiosperm species is extraordinary and perhaps unmatched by any other group of organisms. This course will provide a comprehensive introduction to plant sexual diversity through lectures and discussion of the primary literature. Topics will include the evolution and maintenance of sexual polymorphisms, temporal and spatial segregation of gender function in hermaphrodites, self-incompatibility systems, plant-pollinator coevolution, pollinator-mediated selection, hybridization, tradeoffs with asexual modes of reproduction, and the evolution and functional significance of sexual dimorphism. Readings will emphasize integrative studies that use developmental, ecological, population genetic, and phylogenetic approaches to uncover the mechanisms underlying this rich morphological and functional diversity. Three classroom hours per week.

Requisite: Biology 23 or 32 or permission from the instructor. Limited to 15 students. Omitted 2009-10. Professor Miller.

2014-15: Not offered
Other years: Offered in Spring 2008

44 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: Biology 23 or 32 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

45 Seminar in Molecular Genetics: DNA Makes RNA

If the basic tenants of eukaryotic molecular biology have followed the prokaryotic paradigm (DNA makes RNA makes protein) established decades ago, the diverse ways in which our genes are regulated continue to surprise.  In particular, the extent to which eukaryotic genomes are transcribed but not translated contributes to the growing appreciation of RNA as a regulatory molecule.  Using articles from the recent scientific literature, this course will focus on topics such as: the diverse roles of micro RNAs in regulating gene expression; the extent and possible function of “antisense” transcripts; modification of RNA transcripts (including those not encoding protein) by alternative splicing and editing; and the role of non-coding RNAs in X chromosome inactivation and other epigenetic phenomena.  Three classroom hours per week.    Requisite: Biology 25 or two courses from the following list: Biology 22, 24, 27, 29, 30 and 34.  Limited to 12 students.  Fall semester.  Professor Ratner.

2014-15: Offered in Spring 2015
Other years: Offered in Fall 2009

46 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 Biology 18, 23, 32, 39 or consent of the instructor.  Not open to first-year students. Limited to 14 students.  Spring semester. Professor Temeles.

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

47 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: Biology 23 or 32 or permission from the instructor. Limited to 14 students. Not open to first-year students. Fall semester. Professor Temeles.

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

48 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. To date, efforts to safeguard biological diversity for future generations have largely failed. This seminar will focus on emerging cutting-edge solutions to those challenges and will involve the integration of biological, economic, technological, and socio-political threats and opportunities. The course will include readings from the primary literature, group discussions, problem-solving exercises, and presentations. Topics will include environmental markets, biodiversity banking, "re-wilding," invasive species, and environmental psychology. Three classroom hours per week.

Requisite: Biology 23 or 32 or permission from the instructor. Limited to 14 students. Not open to first-year students. Spring semester. Copeland Fellow Donlan.

2014-15: Not offered
Other years: Offered in Spring 2009, Spring 2010

77, 78D 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

97, 98, 97H, 98H Special Topics

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

Fall semester.

2014-15: Not offered
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010

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