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Amherst College Biology for 2012-13

104 Food, Fiber, and Pharmaceuticals

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

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

2016-17: Offered in Fall 2016
Other years: Offered in Spring 2013, Fall 2013, Fall 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.   Spring semester.  Professor Purdy.

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

131 Chemical Basis of Biological Processes

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

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

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

2016-17: Not offered
Other years: Offered in Fall 2009, Fall 2010, Fall 2011, Fall 2012, Fall 2013

181 Adaptation and the Organism

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

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

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.  Four classroom hours and three laboratory hours per week.

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

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

210 Experimental Design and Data Analysis in the Life Sciences

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

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

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

230 Ecology

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

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

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

241 Genetic Analysis of Biological Processes

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

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

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2010, Spring 2011, Spring 2012, Spring 2013, Spring 2014, Spring 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. Fall semester. Professor Purdy.

 

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

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

310 Structural Biochemistry

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

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

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

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

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. Spring semester. Limited to 45 students. Professors Williamson (Biology) and Bishop (Chemistry).

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

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

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

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

360 Neurobiology of Disease

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

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

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

380 Genome Biology

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

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

2016-17: Not offered
Other years: Offered in Fall 2007, Fall 2009, Fall 2010, Spring 2012, Spring 2013, Spring 2014

395 Physical laws and biological processes

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

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

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

400 Molecular and Cellular Biophysics

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

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

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

410 Seminar in Disease Biology

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

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

2016-17: Not offered
Other years: Offered in Spring 2008, Spring 2010, Spring 2011, Spring 2012, Spring 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. Spring semester. Professor Temeles. 

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

450 Seminar in Physiology: Classic Papers in Neurophysiology

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

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

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

490, 290 Special Topics

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

Fall and spring semester.

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

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.

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