Biology
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Amherst College Biology for 2015-16

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.  Fall semester. Lecturer Levin.   

2014-15: Not offered
Other years: Offered in Spring 2013, Fall 2013, Fall 2015

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 2015-16. Professor Miller.

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

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. Omitted 2015-16. Professor Purdy.

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

114 The Evolution of Human Nature

(Offered as BIOL 114 and ANTH 114.)  After consideration of the relevant principles of animal behavior, genetics, and population biology, it will be shown that extensions of the theory of natural selection---kin selection, reciprocal altruism, parent-offspring conflict, sexual selection, and parental manipulation of sex ratios---provide unifying explanations for the many kinds of social interactions found in nature, from those between groups, between individuals within groups and between genes within individuals. The emphasis throughout will be on the special physical, social and psychological adaptations that humans have evolved, including the instincts to create language and culture, conflict and cooperation within and between the sexes, moral emotions, the mating system and family, kinship and inheritance, reciprocity and exchange, cooking, long distance running, homicide, socioeconomic hierarchies, warfare, patriarchy, religions and religious beliefs, deceit and self-deception, systems of laws and justice and the production, performance and appreciation of art. Along the way, we will consider how misrepresentations of evolutionary theory have been used to support political and social ideologies and, more recently, to attack evolutionary theory itself as scientifically flawed and morally corrupt. This is a reading and writing course in science: no exams or quizzes, and the assigned work consists of two problem sets and several essays. Two ninety-minute lectures per week.

Spring semester.  Professor Emeritus Zimmerman.

Pending Faculty Approval.

2014-15: Not offered
Other years: Offered in Spring 2008, Spring 2010, Spring 2011, Spring 2016

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 15 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.  Omitted 2015-16.

2014-15: Not offered
Other years: Offered in Fall 2007, Fall 2008, 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 and plants. Four classroom hours and three laboratory hours per week.

Spring semester.  Professors Hood, Temeles, and Levin, 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, Spring 2016

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.  Two hours of lecture, two hours of team-based learning, and three laboratory hours per week.

Requisite: Prior completion of, or concurrent registration in, CHEM 161. Fall semester. Professors Goutte and Williamson 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, Fall 2015

201 Introduction to Field Biology: Disease Ecology

Advances in organismal biology hinge upon an understanding of natural history and are enhanced by quantitative observation, hypothesis formation, and experimentation with systems that occur in nature. In this course, we will apply these principles specifically to the study of infectious diseases in natural populations. With a combination of lecture, discussion, and field-based activities, the course will focus on deriving important questions and the variety of approaches to address them. While covering the fundamentals of disease ecology, the applicability of the field-based approaches to other areas of organismal biology will be emphasized as a foundation for further studies. Three classroom hours and three laboratory/field work hours per week.

Requisite: BIOL 181. Limited to 16 students. Fall semester.  Professor Hood.

Pending Faculty Approval.

2014-15: Not offered
Other years: Offered in Fall 2015

211 Plants as Models in Organismal Biology

In their diverse forms, plants play the role of sustaining life on Earth. Plants are also tractable research models, which have facilitated many scientific discoveries and illustrate different approaches to studying organismal biology. This course will strongly integrate lecture, laboratory and field-based material to address plant biology as a foundational discipline in the life sciences. We will include studies on the structures and adaptations that reflect diverse life histories and ecologies, with experimental exercises and work in natural populations. The course will have two three-hour meetings per week with lectures followed by laboratory or field work.

Requisite: BIOL 181. Limited to 16 students.  Omitted 2015-16.  Professor Hood.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2013

221 Developmental Biology

How can a single cell, the fertilized egg, give rise to all the specialized cells of an adult? What gives rise to biological form?  What is the molecular logic of the pathways that progressively refine cellular identities? How do cells "talk" to one another so as to coordinate their behaviors as embryos develop form and function? How can parts of an organism be regenerated with only the appropriate regions remade, structured identically to the missing ones? How does a stem cell differ from a non-stem cell? How can genetically identical organisms be cloned? This course will offer an integrative study of the development of animals, leading to the formulation of the principles of development, including an introduction to experimental embryology and developmental physiology, anatomy, genetics and "evo-devo." Laboratory work explores embryonic development and regeneration in amphibians, sea urchins, nematodes, flatworms, fruit flies, fish, and chickens.  Four classroom hours and three hours of laboratory per week.

Requisite: BIOL 191. Not open to first-year students. Limited to 16 students. Spring semester. Professor Poccia.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2007, Spring 2009, Spring 2010, Fall 2011, Spring 2016

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 equivalent. Not open to first-year students. Limited to 65 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, Fall 2015

240 Mathematical Modeling of Biological Systems

With new experimental techniques leading to large biological data sets of increased quality, the ability to analyze biological systems using mathematical modeling approaches has become an integral part of modern biology. This course aims to provide students interested in the interface between biology and mathematics with an integrated understanding of some of the mathematical and computational techniques used in this field. The mathematical approaches we will use to study biological systems will include discrete and continuous dynamical models as well as probability models and parameter estimation algorithms.

Requisite: MATH 211 and BIOL 181 or 191, or permission of instructor.  Limited to 24 students. Omitted 2015-16. Professor Dresch.

2014-15: Offered in Spring 2015

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. Omitted 2015-16. 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.

Requisite: BIOL 191 or equivalent. Limited to 30 students. Not open to first-year students.  Fall semester. Professors Jeong and Ratner.

2014-15: Not offered
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015

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. Omitted 2015-16. Professor Purdy.

 

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

280 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 per week.

Requisite: BIOL 181. Limited to 14 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, Fall 2015

281 Animal Behavior with Lab

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 16 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, Fall 2015

290, 290H, 490, 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, Fall 2015, Spring 2016

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 Graf.

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2016

301 Molecular Neurobiology

(Offered as BIOL 301 and NEUR 301.)  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.  Four classroom hours and three hours of laboratory per week.

Requisite:  BIOL 191 and CHEM 161.  Not open to first year students. Limited to 24 students. Fall semester.  Professor Graf.

2014-15: Offered in Fall 2014
Other years: Offered in Fall 2010, Fall 2011, Fall 2015

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 30 students. Not open to first-year students. Spring semester.  Professor Miller.

2014-15: Offered in Spring 2015
Other years: Offered in Fall 2011, Fall 2012, Fall 2013, Spring 2016

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. Spring semester.  Professor Miller.

2014-15: Not offered
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2011, Fall 2012, Spring 2016

330 Biochemical Principles of Life at the Molecular Level

(Offered as CHEM 330 and BIOL 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 Jaswal.

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

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. Limited to 45 students. Spring semester. Professor O'Hara (Chemistry) and Professor Williamson (Biology).

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2016

351 Neurophysiology

(Offered as BIOL 351 and NEUR 351.)  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. Open to juniors and seniors. Omitted 2015-16. Professor Trapani.

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

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 2015-16. Professor Emeritus Goldsby.

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

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 191.  This course is designed as an overflow class for those who cannot take BIOL 381 and the combined enrollment for these courses will be 30 students. Omitted 2015-16. 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 2015-16. Professor Hood.

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

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.  Spring semester.  Professor TBA.

2014-15: Offered in Spring 2015
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2016

414 Seminar in Microbiology: Host-Microbe Interactions

In this seminar, we will examine the molecular mechanisms that underlie a broad range of interactions between diverse bacterial species and their multicellular hosts. We will begin the course by exploring the complex molecular "conversations" that help establish mutually beneficial symbiotic relationships. These often involve exchange of metabolites, small molecules, and other cellular components that lead to drastic changes in the physiology, development, and gene expression of both the host and microbial partners. While many examples of such positive interactions exist in nature, as humans, we are perhaps most aware of the bacterial world as a source of disease-causing pathogens. In this context, we will then explore mechanisms of bacterial pathogenesis and draw parallels with mutualistic interactions discussed earlier.  We will focus on bacterial pathogens of humans, particularly as they must survive in the presence of sophisticated innate and adaptive immune responses. This course will rely extensively on readings from the primary literature and will involve a research project and oral presentations.  Three hours per week.

Requisite: BIOL191 and either BIOL 271 or permission of the instructor.  Limited to 15 students. Omitted 2015-16.  Professor Purdy.

 

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

420 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 importance of eukaryotic RNA that is not translated into protein is only now becoming appreciated.  While barely more than 1% of the human genome encodes protein, recent evidence suggests that as much as 98% of our genome is transcribed!  What function, if any, do all those RNA species serve?  Incorporating 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 use of piwi RNAs in genome defense; the origin and possible function of long “antisense” transcripts; modification of RNA transcripts (coding and noncoding) by alternative splicing and editing; and the role of long non-coding RNAs in X chromosome inactivation and other epigenetic phenomena.  Three classroom hours per week. 

Requisite: BIOL 251; alternatively, any two of the following courses: BIOL 220, 241, 291, 331, and 380/1.  Limited to 15 students.  Omitted 2015-16.  Professor Ratner.

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

424 Seminar in Evolution: Sex and Sexual Reproduction

The origin and maintenance of sexual reproduction stands as one of the great mysteries of evolutionary biology.  This seminar will explore the nature of sex and sexual reproduction across organisms, consider hypotheses for its origin and maintenance, and study its diverse consequences in populations.  Readings will incorporate articles from the primary literature and topics for consideration include the molecular machinery and origin of meiosis, variation in sex determination mechanisms (including the evolution of sex chromosomes), sex ratio evolution, mating system variation, sexual conflicts, and the evolutionary ecology of sex differences. Three hours per week.

Requisite: BIOL181, BIOL 191, and one upper level course in Biology. Limited to 16 students. Fall semester. Professor Miller.

Pending Faculty Approval.

2014-15: Not offered
Other years: Offered in Fall 2015

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 this semester 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 2015-16. Professor Temeles. 

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

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. Omitted 2015-16. 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/ENST 210 or permission of the instructor.  Not open to first-year students.  Limited to 14 students.  Fall semester. Lecturer Levin. 

2014-15: Not offered
Other years: Offered in Spring 2012, Fall 2013, Fall 2015

454 Seminar in Tropical Biology

Most biodiversity on our planet can be found in tropical latitudes. Tropical rainforests, for example, which account for less than 10% of the Earth’s surface, may contain 50-75% of all plant and animal species. This course will examine some of the myriad biotic interactions that occur in the tropics using an ecological, evolutionary, and behavioral approach. The course will also touch on important applied issues such as reforestation, sustainable agriculture, and ecotourism. In order to provide students with greater first-hand knowledge, the course will begin with a 2-3 week field trip to Costa Rica (at an additional cost to students; financial aid available; all interested students should contact Professor Clotfelter regardless of financial circumstances) during the January Interterm. The field component will focus on three habitat types: lowland tropical forests, montane cloud forests, and tropical dry forests. While in Costa Rica, we will utilize the expertise of local specialists to learn more about taxonomic groups that are particularly significant in the tropics, such as bats, ants, and epiphytic plants. Students will conduct independent research projects during the field component of the course, as well as a written and oral project during the seminar component of the course. Three hours per week.

Requisite: Two or more of the following courses: Biology 181, 230, 281 or 320/321.  Not open to first-year students.  Limited to 12 students.  Omitted 2015-16. Professor Clotfelter and Lecturer Levin.

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

464 Seminar in Morphology: Animal Form and Function

How does a bird fly? How does a fish breathe under water? How does a cat jump?  These are everyday phenomena, yet we rarely think about their underlying mechanics.  The more we look at the dizzying array of body shapes and physiological systems in the animal kingdom, the more questions come to mind.  How does a butterfly stay dry in the rain?  How does a gecko walk up walls?  Why don’t snakes die from their own venom?  This seminar course takes an integrative approach, drawing from the primary literature in comparative physiology, biomechanics, and functional morphology.  We begin by reviewing concepts in evolutionary biology and physics before moving on to consider the means by which animals move, maintain homeostasis, capture prey, avoid predators, and reproduce.  We will also discuss biomimetics, a field that draws inspiration from biological systems to improve the design of materials from computer displays to ship hulls.  Three hours per week.

Requisites: BIOL 181 (or equivalent) and at least one of the following: BIOL 211, BIOL 220, BIOL 230, BIOL 260, BIOL 280/281, or BIOL 320/321. PHYS 116 is recommended but not required.  Limited to 18 students. Not open to first-year students. Omitted 2015-16. Professor Clotfelter.

 

2014-15: Offered in Fall 2014

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, Fall 2015
 

McGuire Life Sciences Building