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Amherst College Biology for 2016-17

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.   

2016-17: Offered in Fall 2016
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 2016-17. Professor Miller.

2016-17: Not offered
Other years: Offered in Spring 2008, Fall 2009, Spring 2012, Spring 2015

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 2016-17. Professor Purdy.

2016-17: 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. Two problem sets, three essays, two in-class examinations, and two 90-minute lectures per week.

Omitted 2016-17. Professor Emeritus Zimmerman.

 

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2010, Spring 2011, Spring 2016

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.

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, 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 Purdy and Lab Coordinator Emerson.

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013, Fall 2014, 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. Omitted 2016-17. Professor Hood.

 

2016-17: 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 2016-17.  Professor Hood.

2016-17: Not offered
Other years: Offered in Fall 2013, Fall 2014

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. Omitted 2016-17. Professor Poccia.

2016-17: Not offered
Other years: Offered in Fall 2007, Spring 2009, Spring 2010, Fall 2011, Fall 2014, 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 50 students. Fall semester. Professor Temeles.

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2007, Fall 2008, Fall 2009, Fall 2010, Spring 2012, Fall 2012, Fall 2013, Fall 2014, Fall 2015

240 Mathematical Modeling of Biological Systems

(Offered as MATH 240 and BIOL 240.)  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 the instructor.  Limited to 24 students. Omitted 2016-17.

2016-17: Not offered
Other years: Offered in Spring 2015

241 Genetic Analysis of Biological Processes

In this course we will explore genetic analysis as a means of probing the mysteries of the molecular world. Scientists often turn to the study of genes and mutations when trying to decipher the molecular mechanisms that underlie such diverse processes as the making of an embryo, the response of cells to their environment, or the defect in a heritable disease. All of the reading in the course will be from the primary literature, where students will engage with data from genetic experiments that shed light on the workings of a signal transduction pathway. Students will learn from these examples how to use genetic analysis to formulate models that explain the molecular function of a gene product. In the laboratory students will apply these approaches to their own semester-long project, taking responsibility for experimental design and execution as well as data interpretation and analysis. Three hours of lecture and four hours of laboratory per week;the laboratory projects will require time outside of class hours.

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

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015

251 Molecular Genetics

(Offered as BIOL 251 and BCBP 251) 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. Professor Jeong

 

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2008, Fall 2010, Fall 2011, Fall 2013, Fall 2015

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.

2016-17: 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. Spring semester. Professor Purdy.

 

2016-17: Not offered
Other years: Offered in Fall 2012, Fall 2013, Spring 2015

280 Animal Behavior

Shaped by millions of years of evolution, animals have evolved myriad abilities to respond to their environment, their potential predators and prey, and members of their own species. This course examines animal behavior from both a mechanistic and a functional perspective. Drawing upon examples from a diverse range of taxa, and using articles from the primary scientific literature, we will discuss topics such as behavioral endocrinology, sexual selection and mating systems, animal communication, and kinship and cooperation.  Four classroom hours.

Requisite: BIOL 181. Limited to 14 students. Not open to first-year students. Fall semester. Professor Clotfelter.

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Fall 2011, Fall 2013, Spring 2015, Fall 2015

281 Animal Behavior with Lab

Shaped by millions of years of evolution, animals have evolved myriad abilities to respond to their environment, their potential predators and prey, and members of their own species. This course examines animal behavior from both a mechanistic and a functional perspective. Drawing upon examples from a diverse range of taxa, and using articles from the primary scientific literature, we will discuss topics such as behavioral endocrinology, sexual selection and mating systems, animal communication, and kinship and cooperation.  Four classroom hours and three laboratory hours per week; the laboratory projects will require additional time outside of class.

Requisite: BIOL 181. Limited to 16 students. Not open to first-year students. Fall semester. Professor Clotfelter.

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Fall 2011, Fall 2013, Spring 2015, Fall 2015

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.

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2011, Fall 2012, Spring 2013, Fall 2013, Spring 2014, Fall 2014, Spring 2015, 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 Poccia.

2016-17: Not offered
Other years: Offered in Spring 2012, Spring 2013, Spring 2014, Spring 2015, 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. Admission with consent of the instructor.  Limited to 24 students. Fall semester. Professor Graf.

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2010, Fall 2011, Fall 2014, Fall 2015

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 for addressing how specific biological problems are solved at the atomic level. Three classroom hours per week plus one hour discussion.

Requisite: BIOL 191 and CHEM 161; CHEM 221 would be helpful but is not required. Spring semester.  Professor Williamson.

2016-17: Not offered
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 30 students. Not open to first-year students. Spring semester.  Professor Miller.

2016-17: Not offered
Other years: Offered in Fall 2011, Fall 2012, Fall 2013, Spring 2015, 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.

2016-17: 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 40 students with 20 students per discussion section.  Fall semester.  Professors O'Hara (Chemistry) and Williamson (Biology).

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2011, Fall 2012, Fall 2013, Fall 2014, 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. Professors Jeong and O'Hara.

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2009, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, 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 lecture hours, plus a fourth Discussion hour to be used for group work, paper presentations, and review sessions. 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. Admission with consent of the instructor. Fall semester. Professor Trapani.   

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2007, Fall 2008, Spring 2010, Fall 2012, Fall 2013

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. Spring semester.  Professor Hood.

2016-17: 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 2016-17. Professor Hood.

2016-17: 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.

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Fall 2011, Fall 2012, Fall 2013, Spring 2015, Spring 2016

404 Seminar in Biochemistry

(Offered as BIOL 404 and BCBP 404) 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 18 students.  Fall semester.  Professor Williamson. 

2016-17: Offered in Fall 2016
Other years: Offered in Spring 2011

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 2016-17. Professor Purdy.

2016-17: Not offered
Other years: Offered in Spring 2014

420 Seminar in Molecular Genetics: DNA Makes RNA

(Offered as BIOL420 and BCBP 420.) 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, there is evidence 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; and the role of long non-coding RNAs in gene regulation, X chromosome inactivation, and other epigenetic phenomena. Riboswitches and CRISPR count, too. Three classroom hours per week.

Requisite: BIOL 251; alternatively, any two of the following courses: BIOL 220, 241, 291, 330/1, and 380/1. Limited to 15 students. Spring semester. Professor Ratner.

2016-17: Not offered
Other years: Offered in Fall 2009, Spring 2015

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.

 

2016-17: Offered in Fall 2016
Other years: Offered in Fall 2015

434 Seminar in Ecology: 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.  The main topics that we will discuss in this seminar include pollination, fruit and seed dispersal, deception, herbivory, and phytocarnivory, considering both ecological and evolutionary perspectives.  We will also examine the biodiversity consequences of the loss of these associations via human-induced environmental change.  Class readings emphasize the relevant primary literature.  Students will have the opportunity to lead discussion and present independent literature research in both oral and written format.  Three classroom hours per week.

Requisite: One of the following Biology courses: BIOL 201, 211, 230, 280/1, 320/1, or instructor permission. Limited to 15 students. Not open to first-year students. Omitted 2016-17. 

2016-17: Not offered
Other years: Offered in Fall 2007, Fall 2009, Fall 2011, Spring 2013, Fall 2014, Spring 2016

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.

2016-17: Offered in Fall 2016
Other years: Offered in Spring 2012, Fall 2013, Fall 2015

450 Seminar in Physiology: Classic Papers in Neurophysiology

(Offered as BIOL 450 and NEUR 450.)  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 one of NEUR 226, BIOL 260, BIOL 351, or consent of the instructor. Limited to 18 students. Not open to first-year students. Spring semester.  Professor Trapani.

2016-17: Not offered
Other years: Offered in Spring 2013

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: BIOL 181, 230, 281 or 320/321. Not open to first-year students. Limited to 12 students. Spring semester. Professor Clotfelter and Lecturer Levin.

2016-17: Not offered
Other years: Offered in Spring 2014, Spring 2015

470 Seminar in Biology of Metals: a molecular/cellular perspective 

Metals are required for the function of about one third of all proteins and are involved in vital biological processes such as photosynthesis, respiration, gene regulation, DNA replication and repair, signal transduction, and antioxidant defense. However, essential metals are potentially toxic due to the same properties that make them indispensable. To cope with such a paradox, metals must be tightly regulated.

This advanced seminar will focus on the molecular and cellular biology of metals. Topics of discussion will include metal homeostasis strategies (e.g. import/export, chelation, subcellular compartmentalization), metal cofactors of biochemical processes, inherited metal metabolism disorders, and genetics of hyperaccumulators. We will also discuss prospects of manipulating metal homeostasis to aid human health and environmental sustainability. The course will consist of discussions of primary literature and student presentations. Assignments will include written reviews of literature.

Requisite: One of the following courses, BIOL 241, 251, 291, 330, 331, or permission from instructor. Limited to 15 students. Omitted 2016-17. Professor Jeong.

2016-17: Not offered
Other years: Offered in Spring 2016

499D, 498 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.  Spring semester. The Department.

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2009, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 2015, Spring 2016