Courses

Students who are thinking of majoring in Biology are encouraged to take Biology 101 and 102 during their first year at Williams. This allows them to take BIOL 202, a prerequisite for many other BIOL courses, during fall of their sophomore year. Students who begin the major in their sophomore year and who spend part of junior year in a study away program will have less flexibility in course choices and may need to take two or more Biology courses during a few semesters.

Research Courses

Students can take research courses (BIOL 297, 298, 493 or 494) for academic credit. Independent research is not required for completion of the major–however, students thinking of attending graduate school are strongly advised to pursue at least one semester of independent research. A research course can count as an elective. [Research courses do not satisfy the 300- or 400-level requirements for the major.] Only one semester of research can count toward the nine courses required to complete the major. In addition, students can enroll in a WSP course to do an off-campus research internship (BIOL 22 or a WSP 99 project).

Pre-Med Requirements

All Courses

Please note that courses in gray are not being offered this year.

BIOL 101(F)The Cell

This course investigates cell structure and function as a consequence of evolutionary processes, and it stresses the dynamic properties of living systems. Topics include an introduction to biological molecules and enzyme action, membrane structure and function, energy exchange and design of metabolic systems, expression of genetic information, cell signaling, cell trafficking, the cell cycle, and cancer. Student-designed laboratory experiments and discussions based on primary biology literature will highlight how biological knowledge is created and understood. [ more ]

BIOL 102(S)The Organism

This course focuses upon the developmental and evolutionary processes that have given rise to a wide diversity of multicellular organisms. We consider many levels of biological organization, from molecular and cellular to individuals and populations in our examination of evolutionary concepts. Topics include meiosis and sexual reproduction, developmental and evolutionary mechanisms, and speciation with representative examples from a diversity of plants and animals. Readings are drawn from a variety of sources, including the recent primary literature. [ more ]

BIOL 120(F)Biology Through The Media

This course explores the foundational concepts examined in Williams's Introduction to Biology series through their expression in mass media: news outlets, television and feature films. Each topic will be presented through the lens of a "media story," either based in fact or fictional. The first half of the course investigates cell structure and function, paying special attention to how information is conveyed in a cell. The focus then shifts to the developmental and evolutionary processes that have given rise to the diversity of life. This is a qualitative-focused, non-majors course and, as such, the students are not expected to have much, if any, background in biology. [ more ]

BIOL 133Biology of Exercise and Nutrition

Last offered Fall 2017

This class, intended for the non-scientist, focuses on the impact of exercise and nutrition on the human body. We will discuss topics such as how different types of training influence exercise performance; the changes that occur in the cardiovascular system during an exercise routine; the inherent limits of the body to perform aerobic and anaerobic tasks; and the long-term health consequences of a lifetime of activity of inactivity. We will also examine how nutrition and metabolism affect body composition. For example, we will rigorously and scientifically scrutinize the use of "fad" diets as a means to lose weight. [ more ]

BIOL 134(F)The Tropics: Biology and Social Issues

Biology and Social Issues of the Tropics explores the biological dimensions of social issues in tropical societies, and focuses specifically on the peoples of tropical regions in Africa, Asia, Latin America, Oceania, and the Caribbean. Tropical issues have become prominent on a global scale, and many social issues in the tropics are inextricably bound to human ecology and the tropical environment. Each section provides the science behind the issues and ends with possible solutions. The course highlights differences between the tropics and areas at higher latitudes. It begins with a survey of the tropical environment, including a global climate model, variation in tropical climates and the amazing diversity of tropical biomes. The next section focuses on human population biology, and emphasizes demography and the role of disease particularly malaria, AIDS and Covid-19 (SARS-CoV-2). The final part of the course covers the place of human societies in local and global ecosystems including the challenges of tropical food production, the interaction of humans with their supporting ecological environment and climate change. This course fulfills the DPE requirement. Through lectures, debates and readings, students confront social issues and policies from the perspective of biologists. This builds a framework for lifelong exploration of human diversity in terms of difference, power and equity. [ more ]

BIOL 135Evolution as Fact and Theory

Last offered Fall 2019

This course examines evolution as a science and its current and historical importance. Lectures focus on the evidence for evolution, the main evolutionary forces (natural selection and others) and the diversification processes that generate biodiversity. We will also explore recent evolutionary trends and discussions such as human evolution, heritability, personalized genomics, antibiotic and pesticide resistance, climate change, and the conflict between creationists and evolutionists. Includes a trip to the American Museum of Natural History in NYC. [ more ]

BIOL 136Studying Human Genetic Diversity: Individuals, Populations, and 'Races'--Dangerous Biology

Last offered Spring 2014

Scientists are rapidly acquiring DNA sequence information on thousands of individuals from a wide variety of human populations. This information can be used to illuminate human history and evolution. It can also be used in the field of medicine to develop new drugs and as a first step toward tailoring treatments to match individuals' genomes. This information can also create new ethical and social dilemmas. Do such studies support or refute the idea of a biological basis for 'race'? Can the data be used to justify societal inequities? Do the data have any use outside of scientific circles? Through reading scientific articles we'll explore genome sequencing data to determine the types of DNA differences that exist among humans. We'll examine the data in the light of human population history (migration, population bottlenecks, selection) to understand how these variations come about. Throughout we'll discuss the implications of these studies for individuals and for society. In particular we'll critique the use of such information in guiding policy and practice in areas such as genetic screening and eugenics, ancestry testing, 'race-based' medicine, forensics. [ more ]

BIOL 165Coral Reefs: Ecology, Threats, & Conservation

Last offered Fall 2020

Coral reefs are a fascinating ecosystem found throughout the world's tropical oceans. Corals can thrive in nutrient-poor oceans because of the mutualistic relationship with algal symbionts. And as a foundational species, corals provide a habitat for numerous species, possibly the highest diversity found on the planet. However, these complex and beautiful ecosystems are declining worldwide from a variety of local and global threats. In this course, we will explore coral reef ecology through an in-depth examination of the biotic and abiotic factors contributing to the ecosystem's functioning. We will also investigate the causes and consequences of threats to coral reefs, such as ocean warming, ocean acidification, and resource extraction. Finally, we will identify the many efforts worldwide to conserve coral reefs and promote their resilience. In this seminar course, offered remotely, you will demonstrate your proficiency through knowledge assessments, short writing reflections, a virtual coral fragmentation experiment, and a creative advocacy project. This course aims to deepen your awareness of the complex species interactions on coral reefs and the physical factors affecting coral survival while fostering hope through current conservation efforts. [ more ]

BIOL 202(F)Genetics

Genetics, classically defined as the study of heredity, is today a multidisciplinary field whose principles provide critical insight and tools to most areas of biology and medicine. This course covers the experimental basis for our current understanding of the inheritance, structures, and functions of genes. It introduces approaches used by contemporary geneticists and molecular biologists to explore questions in areas of biology ranging from evolution to medicine. A primary focus of the course is on students developing familiarity with problem solving, the logic and quantitative reasoning required to understand how genetic mechanisms lead to biological patterns. The laboratory part of the course provides an experimental introduction to modern genetic analysis as well as introductions to interpreting genetic reasoning in the primary research literature. Laboratory experiments include investigating chromosome structure using microscopy, integrating multiple streams of evidence to map a mutation to the genome, determining the structure of a DNA plasmid using molecular tools. [ more ]

BIOL 203(F)Ecology

This course combines lectures & discussion with field and indoor laboratory exercises to explore factors that determine the distribution and abundance of plants and animals in natural systems. The course begins with an overview of global environmental patterns and then builds from the population to ecosystem level. Throughout the course, we will emphasize the connection between basic ecological principles and current environmental issues. Selected topics include population dynamics (competition, predation, mutualism); community interactions (succession, food chains and diversity) and ecosystem function (biogeochemical cycles, energy flow). Laboratory activities are designed to help students build skills in data analysis and scientific writing. [ more ]

BIOL 204(S)Animal Behavior

Making sense of what we see while watching animals closely is both an enthralling pastime and a discipline that draws on many aspects of biology. Explanations can be found on many levels: evolutionary theory tells us why certain patterns have come to exist, molecular biology can help us understand how those patterns are implemented, neuroscience gives insights as to how the world appears to the behaving animal, endocrinology provides information on how suites of behaviors are regulated. The first part of the course focuses upon how descriptive studies provide the basis for formulating questions about behavior as well as the statistical methods used to evaluate the answers to these questions. We then consider the behavior of individuals, both as it is mediated by biological mechanisms and as it appears from an evolutionary perspective. The second half of the course is primarily concerned with the behaviors of groups of animals from a wide variety of vertebrate and invertebrate species, concentrating upon the stimuli, responses, and internal mechanisms that maintain social systems and on the selection pressures that drive animals toward a particular social system. [ more ]

BIOL 205(S)Physiology

This lecture-based course examines principles, patterns, and mechanisms of biological function from the level of cells and tissues to the whole organism. The themes of the course include structure and function, mechanisms of regulation, control and integration, and adaptation to the environment. Examples of these themes are taken from a wide variety of organisms with a focus on vertebrates. Laboratories provide practical experience in measurement and experimental elucidation of physiological phenomena and functional analysis of gross structure. [ more ]

BIOL 210Mathematical Biology

Last offered Fall 2020

This course will provide an introduction to the many ways in which mathematics can be used to understand, analyze, and predict biological dynamics. We will learn how to construct mathematical models that capture essential properties of biological processes while maintaining analytic tractability. Analytic techniques, such as stability and bifurcation analysis, will be introduced in the context of both continuous and discrete time models. Additionally, students will couple these analytic tools with numerical simulation to gain a more global picture of the biological dynamics. Possible biological applications include, but are not limited to, single and multi-species population dynamics, neural and biological oscillators, tumor cell growth, and infectious disease dynamics. [ more ]

BIOL 211(S)Paleobiology

The fossil record is a direct window into the history of life on Earth and contains a wealth of information on evolution, biodiversity, and climate change. This course investigates the record of ancient life forms, from single-celled algae to snails to dinosaurs. We will explore how, why, when, and where fossils form and learn about the major groups of fossilized organisms and how they have changed through time. In addition, we will cover a range of topics central to modern paleobiology. These include: how the fossil record informs our understanding of evolutionary processes including speciation; the causes and consequences of mass extinctions; how fossils help us tell time and reconstruct the Earth's climactic and tectonic history; statistical analysis of the fossil record to reconstruct biodiversity through time; analysis of fossil morphology to recreate the biomechanics of extinct organisms; and using fossil communities to reconstruct past ecosystems. Laboratory exercises will take advantage of Williams' fossil collections as well as published datasets to provide a broad understanding of fossils and the methods we use to study the history of life on Earth, including using the programming language R (no previous experience is required). We will also view a diversity of fossils in their geologic and paleo-environmental context on our field trip to Eastern New York. This course is in the Sediments and Life group for the Geosciences major. [ more ]

BIOL 212(F)Neuroscience

This course is designed to give an overview of the field of neuroscience progressing from a molecular level onwards to individual neurons, neural circuits, and ultimately regulated output behaviors of the nervous system. Topics include a survey of the structure and function of the nervous system, basic neurophysiology and neurochemistry, development, learning and memory, sensory and motor systems, and clinical disorders. Throughout the course, many examples from current research in neuroscience are used to illustrate the concepts being considered. The lab portion of the course will emphasize a) practical hands-on exercises that amplify the material presented in class; b) interpreting and analyzing data; c) presenting the results in written form and placing them in the context of published work; and d) reading and critiquing scientific papers. [ more ]

BIOL 214 TMathematical Ecology

Last offered Spring 2016

Using mathematics to study natural phenomena has become ubiquitous over the past couple of decades. In this tutorial, we will study mathematical models comprised of both deterministic and stochastic differential equations that are developed to understand ecological dynamics and, in many cases, evaluate the dynamical consequences of policy decisions. We will learn how to understand these models through both standard analytic techniques such as stability and bifurcation analysis as well as through simulation using computer programs such as MATLAB. Possible topics include fisheries management, disease ecology, control of invasive species, and predicting critical transitions in ecological systems. [ more ]

BIOL 219 TDangerous Exposures: Environment, Immunity, and Infectious Disease

Last offered Fall 2020

Global reports of emerging infectious diseases and old diseases with new pathogenic properties incite fears for personal safety as well as national security. The specter of a contagious pandemic has captured the public imagination through the mass news media, movies, and even popular online and board games. In this tutorial course, we will explore the ecology and evolution of several recently emergent diseases such as Ebola hemorrhagic fever, dengue, and AIDS. Topics to be considered include transmission dynamics, epidemiological modeling of vaccination strategies, and wildlife reservoirs that contribute to human virus exposure. We will examine progress in preventing the parasitic disease malaria and why such diseases have proven so refractory. We will also discuss the science behind the recent development of the vaccine against the human papillomavirus, which causes cervical cancer, and the intriguing and highly unusual transmissible cancers in dogs and Tasmanian devils. Finally, we will think about the contributions of inadequate diagnostic capacities world-wide and broader issues of resource shortages in driving the global emergence of drug resistance in tuberculosis and other diseases. One common theme in each of these case studies will be the interplay between the host immune response and the evolution of the pathogen. Although the primary focus of the course is on biology rather than policy, each week's readings will have implications for public health and/or conservation biology. [ more ]

BIOL 220(S)Field Botany and Plant Natural History

This field-lecture course covers the evolutionary and ecological relationships among plant groups represented in our local and regional flora. Lectures focus on the evolution of the land plants, the most recent and revolutionary developments in plant systematics and phylogeny, characteristics of plant families, the cultural and economic uses of plants and how plants have shaped our world. The labs cover field identification, natural history and the ecology of local species. [ more ]

BIOL 222(S)Essentials of Biochemistry

This course will explore the biochemistry of cellular processes and contextualize these processes in healthy and diseased states. Lecture topics in this one semester course will include the structure and function of proteins (enzymes and non-enzymatic proteins), lipids, and carbohydrates. Lectures will also survey the major metabolic pathways (carbohydrates, lipids, and amino acids) with particular attention to enzyme regulation and the integration of metabolism in different tissues and under different metabolic conditions. In the discussion/laboratory component of the course a combination of primary literature, hypothesis-driven exercises, problem solving, and bench work will be used to illustrate how particular techniques and experimental approaches are used in biochemical fields. [ more ]

BIOL 225 TSustainable Food & Agriculture

Last offered Fall 2018

A tutorial course investigating patterns, processes, and stability in human-dominated, food production systems. The course will examine sustainable food and agriculture from an ecological perspective. Topics will include: changes in diversity, concentration, and scale, flows of energy, circulation (or not) of fertilizer nutrients, carbon balances in soils, and stability of food production, processing, and distribution ecosystems. A day-long field experience will take place on a local farm. [ more ]

Taught by: Henry Art

Catalog details

BIOL 231(F, S)Marine Ecology

We have explored only a fraction of the ocean, with about 10% of marine species classified and 20% of the ocean mapped. Many discoveries remain to be made, and marine ecology is one technique to uncover new insights. The field of marine ecology, rooted in the theory of evolution, describes the mechanisms and processes that drive the diversity, abundance, and distribution of marine organisms. The goal is to document natural patterns and make predictions about how species will respond to environmental changes by investigating the relationship between the abiotic environment and biotic interactions. This course will take a deep dive into the unique challenges to life in the ocean. You will compare and contrast different marine ecosystems, such as coral reefs, kelp forests, and the deep sea. You will also practice a marine ecologist's skillset as you design, carry out, and analyze your own research project, which will improve your scientific writing, data analysis, and communication skills. Importantly, you will connect your research and course topics to larger marine conservation issues and broader societal impacts. [ more ]

BIOL 234 TBiology of our Sexes: The Genetic and Epigenetic Regulation of Sex Determination

Last offered Spring 2018

Many physical and behavioral characteristics that are associated with male and female anatomy, physiology, and behavior are initially the products molecular choices arising from the action of our chromosomes in early development. The embryonic assignment of sex can also lead to intersex or hermaphroditic outcomes in many different organisms with extraordinary and illuminating biological effects. We will explore the molecular mechanisms and evolutionary basis of sex determination in both plants and animals, as well as the physical and behavioral expression of sex by the organism discussed, and experiments that create and characterize traits and behavior of mosaic/intersex organisms. Additionally, the epigenetic regulation of the X chromosome in mammals has a canonical role in our understanding of sex determination, but whole genome studies and investigations of autosomes and the Y chromosome have raised new layers of complexity for understanding the molecular basis of human sex and sexuality. [ more ]

BIOL 297(F)Independent Study: Biology

Biology 200-level independent study. Each student carries out independent field or laboratory research under the supervision of a member of the department. [ more ]

BIOL 298(S)Independent Study: Biology

Biology 200-level independent study. Each student carries out independent field or laboratory research under the supervision of a member of the department. [ more ]

BIOL 301Developmental Biology

Last offered Fall 2014

Developmental biology has undergone rapid growth in recent years and is becoming a central organizing discipline that links cells and molecular biology, evolution, anatomy and medicine. We are now beginning to have a molecular understanding of fascinating questions such as how cells decide their fate, how patterns are created, how male and females are distinguished, and how organisms came to be different. We have also discovered how the misregulation of important development regulatory genes can lead to a variety of known cancers and degenerative diseases in humans. In this course we will examine these and related topics combining a rich classical literature with modern genetic and molecular analyses. [ more ]

BIOL 302Communities and Ecosystems

Last offered Fall 2019

An advanced ecology course that examines how species interact with each other and their environment and how communities are assembled. This course emphasizes phenomena that emerge in complex ecological systems, building on the fundamental concepts of population biology, community ecology, and ecosystem science. This foundation will be used to understand specific topics relevant to conservation including invasibility and the functional significance of diversity for ecosystem stability and processes. Lectures and labs will explore how to characterize the emergent properties of communities and ecosystems, and how theoretical, comparative, and experimental approaches are used to understand their structure and function. The lab component of this course will emphasize hypothesis-oriented field experiments as well as "big-data" analyses using existing data sets.The laboratory component of the course will culminate with a self-designed independent or group project. [ more ]

BIOL 305(S)Evolution

This course offers a critical analysis of contemporary concepts in biological evolution. We focus on the relation of evolutionary mechanisms (e.g., selection, drift, and migration) to long term evolutionary patterns (e.g., evolutionary innovations, origin of major groups, and adaptation). Topics include micro-evolutionary models, natural and sexual selection, speciation, the inference of evolutionary history, evolutionary medicine among others. [ more ]

BIOL 306Cellular Regulatory Mechanisms

Last offered Spring 2015

This course explores the regulation of cellular function and gene expression from a perspective that integrates current paradigms in molecular genetics, intracellular trafficking, genomics, and synthetic biology. Selected topics include: the contribution of nuclear organization to genome regulation, mechanisms to maintain genomic integrity, transcriptional and post-transcriptional regulation, nuclear export, cell cycle and cell signaling. A central feature of the course will be discussion of articles from the primary literature, with an emphasis on the molecular bases for a variety of human pathologies such as cancer and aging. The laboratory will consist of a semester-long project that incorporates fluorescence-based approaches, quantitative PCR analysis of transcriptional patterns, bioinformatics, and protein analysis. [ more ]

BIOL 308(S)Integrative Plant Biology: Fundamentals and New Frontiers

Plants are one of the most successful groups of organisms on Earth and have a profound impact on all life. Successful use of plants in addressing global problems and understanding their role in natural ecosystems depends on fundamental knowledge of the molecular mechanisms by which they grow, develop, and respond to their environment. This course will examine the molecular physiology of plants using an integrative approach that considers plants as dynamic, functional units in their environment. Major emphasis will be on understanding fundamental plant processes, such as photosynthesis, growth and development, water transport, hormone physiology, and flowering, from the molecular to the organismal level. Environmental effects on these processes will be addressed in topics including photomorphogenesis, stress physiology, mineral nutrition, and plant-microbe interactions. Discussions of original research papers will examine the mechanisms plants use to perform these processes and explore advances in the genetic engineering of plants for agricultural, environmental, and medical purposes. Laboratory activities stress modern approaches and techniques used in investigating plant physiological processes. [ more ]

BIOL 310Neural Development and Plasticity

Last offered Fall 2016

Development can be seen as a tradeoff between genetically-determined processes and environmental stimuli. The tension between these two inputs is particularly apparent in the developing nervous system, where many events must be predetermined, and where plasticity, or altered outcomes in response to environmental conditions, is also essential. Plasticity is reduced as development and differentiation proceed, and the potential for regeneration after injury or disease in adults is limited; however some exceptions to this rule exist, and recent data suggest that the nervous system is not hard-wired as previously thought. In this course we will discuss the mechanisms governing nervous system development, from relatively simple nervous systems such as that of the fruitfly, to the more complicated nervous systems of humans, examining the roles played by genetically specified programs and non-genetic influences. [ more ]

BIOL 311Neural Systems and Circuits

Last offered Fall 2020

This course will examine the functional organization of the mammalian brain, emphasizing both neuroanatomy and neurophysiology. How do specific populations of neurons and their connections encode sensory information, form perceptions of the external and internal environment, make cognitive decisions, and execute movements? How does the brain produce feelings of reward/motivation and aversion/pain? How does the nervous system regulate homeostatic functions such as sleep, food intake, and thirst? We will explore these questions using a holistic, integrative approach, considering molecular/cellular mechanisms, physiological characterizations of neurons, and connectivity among brain systems. Journal article discussions will complement course topics, providing experience in reading, understanding, and critiquing primary research papers. Writing an original literature review article will provide experience in expository writing and anonymous peer review. Laboratory sessions will provide experience in examining macroscopic and microscopic neural structures, as well as performing experiments to elucidate the structure and function of neural systems using classical and cutting-edge techniques. [ more ]

BIOL 312(F)Sensory Biology

How do animals sense properties of the physical world? How do they convert physical or chemical energy to a signal within a cell that carries information? How is that information represented? What are the limits on what can be sensed? We will look for answers to these questions by investigating the molecular and cellular mechanisms of sensory transduction and how these mechanisms constrain the types of information that the nervous system encodes and processes. We will also ask how natural selection shapes the type of sensory information that animals extract from the world, and what adaptations allow some species to have "special" senses. Some of the examples we will consider are: bat echolocation (hair cells in the ear), detecting visual motion (amacrine cells in the mammalian retina), the constant reshaping of the olfactory system (chemical mapping of odors), what makes a touch stimulus noxious, and enhanced color vision (in birds, bees, and shrimp). Laboratory exercises will focus on the nematode C. elegans, an important model system, to explore and extend how we understand touch, temperature sensation, chemosensation, and light sensation. [ more ]

BIOL 313Immunology

Last offered Spring 2021

The rapidly evolving field of immunology examines the complex network of interacting molecules and cells that function to recognize and respond to agents foreign to the individual. In this course, we will focus on the biochemical mechanisms that act to regulate the development and function of the immune system and how alterations in different system components can cause disease. Textbook readings will be supplemented with current literature. [ more ]

BIOL 315(S)Microbiology: Diversity, Cellular Physiology, and Interactions

Bioterrorism and the alarming spread of antibiotic resistant bacteria are but two of the reasons for the resurgence of interest in the biology of microorganisms. This course will examine microbes from the perspectives of cell structure and function, genomics, and evolution. A central theme will be the adaptation of bacteria as they evolve to fill specific ecological niches, with an emphasis on microbe: host interactions that lead to pathogenesis. We will consider communication among bacteria as well as between bacteria and their environment. Topics include: microbial development, population dynamics, metagenomics, bioremediation, plant and animal defenses against infection, and bacterial strategies to subvert the immune system. In the lab, major projects will focus on the mammalian gut microbiome and the isolation and characterization of bacteria from natural environments. The lab experience will culminate in multi-week independent investigations. Readings will be comprised primarily of articles from the primary literature. [ more ]

BIOL 319Integrative Bioinformatics, Genomics, and Proteomics Lab

Last offered Spring 2021

What can computational biology teach us about cancer? In this lab-intensive experience for the Genomics, Proteomics, and Bioinformatics program, computational analysis and wet-lab investigations will inform each other, as students majoring in biology, chemistry, computer science, mathematics/statistics, and physics contribute their own expertise to explore how ever-growing gene and protein data-sets can provide key insights into human disease. In this course, we will take advantage of one well-studied system, the highly conserved Ras-related family of proteins, which play a central role in numerous fundamental processes within the cell. The course will integrate bioinformatics and molecular biology, using database searching, alignments and pattern matching, and phylogenetics to reconstruct the evolution of gene families by focusing on the gene duplication events and gene rearrangements that have occurred over the course of eukaryotic speciation. By utilizing high through-put approaches to investigate genes involved in the inflammatory and MAPK signal transduction pathways in human colon cancer cell lines, students will uncover regulatory mechanisms that are aberrantly altered by siRNA knockdown of putative regulatory components. This functional genomic strategy will be coupled with independent projects using phosphorylation-state specific antisera to test our hypotheses. Proteomic analysis will introduce the students to de novo structural prediction and threading algorithms, as well as data-mining approaches and Bayesian modeling of protein network dynamics in single cells. Flow cytometry and mass spectrometry may also be used to study networks of interacting proteins in colon tumor cells. [ more ]

BIOL 321(F)Biochemistry I: Structure and Function of Biological Molecules

This course introduces the foundational concepts of biochemistry with an emphasis on the structure and function of biological macromolecules. Specifically, the structure of proteins and nucleic acids are examined in detail in order to determine how their chemical properties and their biological behavior result from those structures. Other topics covered include catalysis, enzyme kinetics, mechanism and regulation; the molecular organization of biomembranes; and the flow of information from nucleic acids to proteins. In addition, the principles and applications of the methods used to characterize macromolecules in solution and the interactions between macromolecules are discussed. The in-person laboratory provides further opportunity to study macromolecules and to learn the fundamental experimental techniques of biochemistry including electrophoresis, chromatography, and principles of enzymatic assays. A laboratory section will also be provided for remote students, which will examine similar topics and techniques through literature and data analysis. [ more ]

BIOL 322(S)Biochemistry II: Metabolism

This lecture course provides an in-depth presentation of the complex metabolic reactions that are central to life. Emphasis is placed on the biological flow of energy including alternative modes of energy generation (aerobic, anaerobic, photosynthetic); the regulation and integration of the metabolic pathways including compartmentalization and the transport of metabolites; and biochemical reaction mechanisms including the structures and mechanisms of coenzymes. This comprehensive study also includes the biosynthesis and catabolism of small molecules (carbohydrates, lipids, amino acids, and nucleotides). Laboratory experiments introduce the principles and procedures used to study enzymatic reactions, bioenergetics, and metabolic pathways. [ more ]

BIOL 326(F)Cellular Assembly and Movement

This course will focus on how multi-protein complexes are assembled to control key cellular processes in eukaryotic systems: 1) protein sorting and trafficking, 2) establishment and maintenance of cell architecture, and 3) mitosis, cell migration and tissue morphogenesis that require coordination of the membrane transport and cytoskeleton. The course will highlight involvement of these processes in pathological conditions. Laboratories will use mammalian tissue culture as a model system to study cellular functions. Important techniques in cell biology will be introduced in the first half of the semester; in the second half of the term, students will conduct a multi-week independent project. Textbook readings will be supplemented with primary literature. [ more ]

BIOL 329Conservation Biology

Last offered Fall 2020

This course examines the application of population genetics, population ecology, community ecology, and systematics to the conservation of biological diversity. The overarching theme of the course is on the role of stochastic processes for small populations. Lecture/discussion topics will include extinction, the genetics of small populations, metapopulations, and importantly, conservation strategies. Labs will include a mixture of computer and lab projects. [ more ]

BIOL 330(S)Genomes: Structure, Function, Evolution

Genome sequencing technologies have opened the "book of life" to biologists. But making sense of genomes is still a work in progress. This course will examine central features of genomes, their evolution, and their contribution to human diseases such as cancer. Genome biology is a new field, and this presents the opportunity to learn science as it is being done. Biologists working today started out knowing nothing about core features of genomes, such as why most of the DNA is repetitive, or why segments of genes get removed in the RNA, or why silenced genes wake up in cancer cells. They began to find meaning by adopting dual perspectives of function and neutral evolution. Students will learn to walk these same paths and learn to evaluate for themselves what genome complexity means. In lab, students will develop hands-on and computational skills for investigating genome structural variation, then apply them in the second half of the semester in independent lab investigations. [ more ]

BIOL 335(F)Chronobiology

Internal clocks control nearly all aspects of physiology and behavior and allow organisms to anticipate the dramatic environmental changes between day and night. In this course we will focus on the organization of internal clocks at the molecular, organ and physiological levels. We will explore fundamental properties of biological clocks, how internal rhythms are synchronized with the environment and the means by which clocks drive physiological rhythms. Subsequently, we will investigate how endogenous clocks help organisms cope with rhythmic changes in our environment, and how disruption of our internal rhythms compromises health and wellbeing. Lectures will alternate with discussions of primary literature. During laboratory sessions we will explore the characteristics of the circadian system in a group of mice, followed by the design and execution of a research project in a small group of students. Working with mice will require time outside of regular scheduled class times, including the weekends. Grading will be based on 2 reports and 2 presentations of the lab components as well as 2 intermediate and 1 final exam. [ more ]

BIOL 337(F)Evolutionary Ecology

Evolutionary ecology is an interdisciplinary field that integrates concepts in genetics, adaptation, and ecology to understand how evolution operates in the context of ecological communities. This course provides an overview of the discipline including foundational concepts in evolutionary demography, phenotypic plasticity, and population genetics. It also explores how breakthroughs in these topics provide a framework for advances in our understanding of the evolution of reproductive timing and ageing, interspecific interactions (e.g. competition, predation), cooperation, and altruism. The course combines lectures, readings, in-class discussion, and a lab section that includes a mixture of field, computer, and lab projects. Laboratories will give students practical, hands-on experience in how to develop, plan, and carry out evolutionary ecology research from start to finish. [ more ]

BIOL 402Rapid Evolution in Ecology

Last offered Spring 2018

Darwin believed that evolution was a slow process. Until recently, the impact of evolutionary changes on short-term ecological studies was considered to be minimal. However, empirical documentation of rapid, directly observed evolution has changed this view and has led to an increased focus on the joint dynamics of evolution and ecology including community genetics, niche construction, and evolutionary rescue. In this course, we first focus on the literature presenting the evidence for rapid evolutionary change in natural and experimental populations. Then, we explore the consequences of rapid evolutionary change for our understanding of population, community, and ecosystem ecology including the impacts that evolutionary changes have for conservation efforts and predicting the response of organisms to global environmental and climate change. [ more ]

BIOL 405 TSociobiology

Last offered Fall 2014

Sociobiology, or the study of social behavior, has challenged the limits of evolutionary theory since Darwin described the non-reproducing castes among social insects (i.e., eusociality) as "one special difficulty." Inclusive fitness theory and Hamilton's rule--that an altruistic act can evolve where the benefit to related individuals exceeds the cost to the actor--potentially resolves Darwin's paradox. Nevertheless, explanations including delayed fitness benefits and ecological constraints have been suggested as alternatives to inclusive fitness theory. Moreover, the theoretical justification for inclusive fitness theory has recently been vigorously challenged. This course will use readings from the primary literature to examine the evidence for inclusive fitness as a potential explanation for topics including the evolution of helping behavior, eusociality and its relationship to extraordinary sex ratios, and spiteful behavior. Other topics that we will cover include the evolution of deceit and self deception. [ more ]

BIOL 406Dynamics of Internal Membrane Systems

Last offered Fall 2014

Eukaryotic cells build and maintain a diverse set of internal membrane compartments, such as the endoplasmic reticulum, the Golgi compartment, and lysosomes, which exist as parts of an interconnected and dynamic membrane system. Each of these membrane compartments has unique functions despite a high rate of exchange between the different organelles. This course will mechanistically examine how the identity of organelles is achieved via highly regulated membrane trafficking events and investigate the importance of membrane trafficking in specialized biological processes including neurotransmission, glucose homeostasis, and immune cell killing. We will read classic and current primary literature articles and discuss the essential techniques, experimental design, and models of cell biology. [ more ]

BIOL 407(S)Neurobiology of Emotion

Emotion is influenced and governed by a number of neural circuits and substrates, and emotional states can be influenced by experience, memory, cognition, and many external stimuli. We will read and discuss articles about mammalian neuroanatomy associated with emotion as defined by classic lesion studies, pharmacology, electrophysiology, fMRI imaging, knockout mouse studies, as well as new opti-genetic methods for investigating neural circuit function in order to gain an understanding of the central circuits and neurotransmitter systems that are implicated in emotional processing and mood disorders. [ more ]

BIOL 408RNA Worlds

Last offered Spring 2016

Ribonucleic acids (RNAs) serve as genomes, catalysts, messengers, adaptors, regulators, structural components, and evolutionary substrates. Non-coding RNAs such as microRNAs, ribozymes, and small interfering RNAs control a diverse range of biological processes including plant and animal development, translation, epigenetic chromosome silencing, and cancer. This course explores recently discovered non-coding RNAs and considers evidence for their mechanisms of action. Through extensive reading of primary literature, we will analyze experimental investigations that reveal our current understanding of the functions and evolution of non-coding RNAs in all three domains of life. [ more ]

BIOL 409 TCultural Evolution in Biological Systems

Last offered Fall 2017

The evolution of genetically transmitted traits has been the subject of extensive study since the "modern synthesis" combined Darwin's and Mendel's ideas--later enriched by molecular approaches to developmental biology. More recently, the study of evolution has been extended to traits that are transmitted via social learning. The cultural evolution that occurs in such behavioral traits has many parallels with evolution based on genes: errors and innovation correspond to genetic mutations, immigration may bring in new forms of the behavior, and population bottlenecks can result in loss of behavioral traits. However, there is also a crucial difference between genetic and social transmission of traits: social learners can potentially acquire traits from many members of their population, including unrelated individuals. This difference has many implications, including the acceleration of the evolutionary time scale. We will explore the ways socially learned behaviors evolve, using systems such as tool use (primates, crows), vocal learning (songbirds, orcas), and social organization (baboons). Among the topics we will consider are the role of neutral models and random processes, how neural constraints guide social learning, how social status influences the choice of tutors, and how competition and sexual selection drive changes in learned behavior. We will also consider how these processes interact and how they generate differences as well as parallels between cultural and genetic evolution. [ more ]

BIOL 410Nanomachines in Living Systems

Last offered Spring 2021

Through reading and discussing the primary literature, this course will explore how nanometer-sized biological molecules like proteins perform functions that require integration of information and transmission of force at much larger scales, microns and above. These nanoscale proteins will be considered as nanomachines that can transform a chemical energy into a mechanical one. We will focus on the cytoskeleton, which gives cells their shape, organizes the internal parts of cells and provides mechanical support for essential cellular processes like cell division and movement. An emphasis will be placed on how the biochemical properties of actin, actin-binding proteins and motors are used to generate mechanical force necessary for the respective biological function. Topics will include some controversial and emerging hypotheses in the field: sliding versus depolymerizing hypotheses for constriction of the contractile ring in cytokinesis, roles of cytoskeleton in pathogen entry and propagation, organelle dynamics, polarity establishment in cell migration, immunological synapse and neuronal function. [ more ]

BIOL 411 TDevelopmental Biology: From Patterning to Pathogenesis

Last offered Fall 2020

A small number of developmental regulators coordinate the interplay between cell proliferation and specification of cell fates during animal development. The genetic basis of many of the cancer and degenerative diseases are, in fact, due to these same developmental regulators whose expression is misregulated in the adult. Through the reading of primary literature, this course in developmental biology will examine the mechanisms of gene expression of key regulators, the biological processes they mediate in the embryo, and how they become misregulated in proliferative and degenerative diseases. [ more ]

BIOL 412Neural and Hormonal Basis of Hunger

Last offered Spring 2018

Hunger and satiety are highly regulated behavioral states that maintain energy homeostasis in animals. This course will focus on readings from the primary literature to track numerous recent advances in how the brain and endocrine systems regulate appetite. Topics include how organ systems communicate with the brain to regulate appetite, how different populations of neurons in the brain interact to regulate appetite, how brain systems that regulate appetite affect other behaviors, and how the neural and hormonal basis of hunger compare with brain systems that regulate other homeostatic systems such as thirst. By tracing the advances in appetite regulation within the past decade, we will also trace the advent of cutting-edge molecular, genetic, and optical-based tools that are transforming multiple fields within physiology and neuroscience. Students in this class will have the opportunity to improve skills in written and oral scientific presentation. [ more ]

BIOL 413Global Change Ecology

Last offered Fall 2019

Plants and animals are increasingly faced with rapid environmental change driven by human activities across the globe. How do they cope with challenges imposed by climate change, altered nutrient cycling, biological invasions, and increased urbanization? What are the impacts of organismal responses at the population and community level? This course uses an integrative approach to understand the impacts of global change at multiple levels of biological organization in both aquatic and terrestrial environments. We examine how global-scale environmental changes affect the distribution and abundance of species and alter community organization. We also consider the physiological and behavioural mechanisms underlying species responses and the role of acclimation versus adaptation in coping with rapid environmental change. Finally, we learn the analytical tools used to predict future responses to global change. Class discussions will focus on readings drawn from the primary literature. [ more ]

BIOL 414(F)Life at Extremes: Molecular Mechanisms

All organisms face variability in their environments, and the molecular and cellular responses to stresses induced by environmental change often illuminate otherwise hidden facets of normal physiology. Moreover, many organisms have evolved unique molecular mechanisms, such as novel cellular compounds or macromolecular structural modifications, which contribute to their ability to survive continuous exposure to extreme conditions, such as high temperatures or low pH. This course will examine how chaperonins, proteases, and heat- and cold-shock proteins are regulated in response to changes in the external environment. We will then consider how these and other molecular mechanisms function to stabilize DNA and proteins- and, ultimately, cells and organisms. Other extreme environments, such as hydrothermal vents on the ocean floor, snow fields, hypersaline lakes, the intertidal zone, and acid springs provide further examples of cellular and molecular responses to extreme conditions. Biotechnological applications of these molecular mechanisms in areas such as protein engineering will also be considered. Class discussions will focus upon readings from the primary literature. [ more ]

BIOL 416Epigenetics

Last offered Spring 2015

After decades of studies emphasizing the role of DNA in heredity, scientists are now turning their attention from genetics to a variety of heritable phenomena that fall under the heading of epigenetics, heritable changes that do not result from an alteration in DNA sequence. Research reveals that stable changes in cell function can result from, for example, stable changes in protein conformation, protein modification, DNA methylation, or the location of a molecule within the cell. Using readings from the primary literature, we will explore the epigenetic nature and molecular mechanisms underlying a diverse array of phenomena such as prion propagation, genetic imprinting, dosage compensation, transvection, centromere formation, vernalization, and programmed genome rearrangements. The significance of epigenetic processes for development, evolution, and human health will be discussed. [ more ]

BIOL 417(S)Translational Immunology: From Bench to Bedside

Recent advances in the field of immunology have led to the development of new approaches to prevent and treat diseases that affect millions of people worldwide. Drugs that modulate the body's natural immune response have become powerful tools in treating major diseases--infection, autoimmunity and cancer. This course will use readings from the primary literature to explore central themes involved in translating basic research to new clinical and therapeutic approaches. Topics will include vaccine development, autoimmunity and cancer immunotherapy. [ more ]

BIOL 418Signal Transduction to Cancer

Last offered Spring 2020

Division of normal cells is a highly regulated process based on input from both intrinsic and extrinsic signals. The cell's response to its environment affects all aspects of cell behavior: proliferation, death, differentiation and migration. The goal of the course is to understand the molecular mechanisms of signal transduction that guide normal cell behavior and how disruptions in this process can lead to cancer. We will focus on the Hedgehog-Gli signaling pathway that is activated in 30% of all known cancers. Genetic studies will serve as an introduction to the components of the pathway, followed by an examination of the molecular mechanisms of signal reception, transduction of intracellular information, scaffolding and transcriptional targets. The final section of the course will investigate how high throughput screens, medicinal chemistry studies and mouse models are used to identify small molecular inhibitors of pathway components. We will consider the effectiveness of these inhibitors in pharmacological studies, clinical trials and potential cancer treatments. [ more ]

BIOL 419Secrets of Enzymes: Fidelity, Promiscuity, and Disease

Last offered Spring 2020

Living organisms have spent the past 4 billion years evolving proteins and enzymes that perform basic cellular functions to support life. Over time, duplications and mutations of these enzymes have led to novel reactions, pathways, and chemistries. To gain an appreciation for these molecular catalysts, we will start by considering how enzymes are synthesized, how errors are introduced and corrected, and how proteins are degraded. We will then analyze the effects of beneficial errors on the evolution of new function and the effects of undesirable errors in human disease. The final section of this course will focus on how enzymes such as CRISPR/Cas9 act as 'molecular scissors' to cut DNA and how these enzymes can be used to correct errors. We will explore the implications of this field in active areas of biomedical research, including antibiotic resistance and personalized medicine. Discussions and writing assignments will focus on reading and critiquing the scientific literature. [ more ]

BIOL 421 TThermoregulation: From Molecules to Organisms

Last offered Fall 2019

Thermal physiology involves the study of molecular events, organ systems, and organism-environmental interactions that are involved with heat production and temperature maintenance. The area of thermal physiology has been around for over 100 years. However, only in the last 5-7 years has the science progressed to understanding basic fundamental mechanisms for generating and regulating heat production. This tutorial will focus on four questions: 1) how do organisms generate heat? 2) how do organisms sense the temperature in the environment? 3) how do organisms integrate information about the environment (temperature, humidity, time of day, etc.) with internal information (deep body temperature, energy stores, etc.) to regulate their metabolic production of heat? 4) how do animals make "the decision" to enter a state of torpor? [ more ]

BIOL 425 T(F)Coevolution

Coevolution, defined as reciprocal adaptation between species, is central to understanding biological phenomena ranging from global patterns of biodiversity to the molecular mechanisms of evolution. The focus of this tutorial will be on coevolution as a paradigm for understanding species diversification. [ more ]

BIOL 426 TFrontiers in Muscle Physiology: Controversies

Last offered Fall 2013

While an active muscle produces force, contraction of muscle is far from the only function of this intriguing organ system. Muscle plays a major role in metabolic regulation of organisms, acts as a glucose storage facility, regulates blood pressure in mammals, and produces numerous hormones. The mechanism for contractile activity varies not only among different organisms, but also among different muscles within the same organism. Controversies, disagreements, and arguments pervade the muscle biology literature perhaps because of the integrative nature of the science. In this tutorial course, we will utilize molecular, physiological, comparative, and evolutionary aspects of muscle biology to address current controversies of this dynamic tissue. Some questions that will be addressed include: 1) Lactic acid generated by skeletal muscle is / is not involved with fatigue at high exercise intensity, 2) Satellite cells are / are not obligatory for skeletal muscle hypertrophy, 3) Do mammals possess the same "stretch activation" of skeletal muscle as seen in insect flight muscle?, 4) Are smooth and skeletal muscles from the same lineage of cells, or do they represent convergent evolution on the tissue level? After an initial group meeting, students meet weekly with a tutorial partner and the instructor for an hour each week. Every other week at this tutorial meeting, students present a written and oral critical analysis of the assigned research articles. Students not making a presentation question and critique the work of their colleague. [ more ]

BIOL 428Forests of the Future--Understanding Global Change through 'Big Science' Experiments

Last offered Spring 2021

Increases in atmospheric CO2 and warming temperatures associated with global climate change affect the growth and physiology of plants and microorganisms and the cycling and storage of carbon and nutrients within terrestrial ecosystems. These changes cross scale and encompass complex feedbacks that are challenging to predict and understand. Over the past several decades, scientists have used large-scale global change experiments to depict the future of organisms and ecosystems in a CO2-enriched, warmer world. In this course, we will trace the progress of these experiments and evaluate our understanding of the effect of global changes on plant growth and physiology, microbial community composition and activity, and ecosystem nutrient cycling processes. We will then consider the interactive effects of multi-factor global changes and assess the promises and challenges of interpreting biological responses at the ecosystem level. Finally, we will investigate how experimental results can be integrated within models that describe and predict ecosystem function at a global scale. Throughout the course, we will consider how understanding gained from manipulative experiments can be used to inform and prioritize climate change mitigation strategies. Discussions and writing assignments will focus on reading and critiquing the scientific literature. Writing assignments will include two short writing assignments (3 pages each) and a final research proposal (6 pages), as well as formal written peer review. Students will gain experience revising scientific writing. [ more ]

BIOL 430 TGenome Sciences: At the Cutting Edge

Last offered Spring 2020

Research in genomics has integrated and revolutionized the field of biology, including areas of medicine, plant biology, microbiology, and evolutionary biology. Moreover, recent developments in "metagenomics" (genomic studies of entire communities of microorganisms in natural environments, such as the mammalian gut and the deep sea) and "metatranscriptomics" (studies of genome wide changes in expression and mRNA levels in natural communities of organisms) have generated unprecedented knowledge about the genomic potential of a community and the in situ biological activity of different ecological niches. In this course we will explore how research in these and related areas, including proteomics, have advanced our fundamental understanding of (1) organisms in the three domains of life, and their interactions and evolutionary relationships; (2) biological systems and environments, such as the human body, extreme environments, and the oceans; (3) strategies for solving global challenges in medicine, agriculture, energy resources, and environmental sciences. During the course, students will meet each week for one hour with a tutorial partner and the instructor. Every other week, students will present a written and oral critical analysis of the assigned research articles. On alternate weeks, students will question/critique the work of their colleague. [ more ]

BIOL 432Evolutionary Genetics

Last offered Fall 2017

The synthesis of evolutionary processes with the mechanistic understanding of genetics has lent insight into many mysteries of life. The goal of this course is to explore the interface between evolution and genetics to make sense of fundamental biological processes. For example, why do we expect that male and female offspring occur in 50:50 ratios? How and why do unusual sex-ratios occur? Other topics include: conflict among genes, evolution of allelic dominance, adaptation at the molecular level, and genetics of speciation. Class discussion and written assignments will emphasize critical evaluation and synthesis of the scientific literature. [ more ]

BIOL 435Causes of the obesity epidemic

Last offered NA

The prevalence of a host of metabolic diseases has increased dramatically in recent decades. The causes underlying these increases remain hotly contested. During this course we will discuss primary literature to better understand the mechanisms by which our body regulates energy metabolism and how this is shaped by genetics and evolution. Subsequently, we will explore how our metabolic environment has been altered in modern society and try to figure out what mechanisms should be targeted to reverse the obesity epidemic. [ more ]

Taught by: TBA

Catalog details

BIOL 454Climate Change Physiology

Last offered Fall 2020

Animals are increasingly faced with rapid climate change driven by human activities across the globe. How do they cope with challenges imposed by increasing temperature? And, how might physiological mechanisms at the organismal level scale up to influence population processes? This course uses an integrative approach to understand the impacts of climate change at multiple levels of biological organization in both terrestrial and aquatic environments. We examine physiological mechanisms underlying animal responses and the role of acclimation versus adaptation in coping with rapidly shifting thermal environments. We then consider the impacts of these mechanisms on whole organism performance and their consequences for population persistence. Finally, we learn the analytical tools used to incorporate physiological mechanisms into ecological models to predict future responses to global climate change. Class discussions will focus on readings drawn from the primary literature. [ more ]

BIOL 455Neural Regeneration

Last offered Spring 2021

Injury to the human nervous system can cause lasting impairment, but non-mammalian animals have prodigious capacity to regenerate neurons, regrow axons, and repair scars. What accounts for these differences? Regeneration can occur in multiple modes: replacement of injured neurons, repairs such as axonal regrowth to reconnect to a target structure, or repurposing existing neurons for new tasks through neural plasticity. We will explore the molecular foundations that underlie neuronal proliferation, neural plasticity, and inflammatory responses. We will consider the potential for translating these findings to inform treatments for humans who suffer from neural injury or neurodegenerative disease. Class discussions will focus on readings from the primary literature. [ more ]

BIOL 493(F)Senior Thesis Research: Biology

Each student prepares a thesis under the supervision of a member of the department. Thesis work can begin either in the spring of the junior or the fall of the senior year, and includes the Winter Study period of the senior year. The number of Biology Department faculty available to mentor research students and the number of students each can accommodate in their lab vary from year to year. Although the department will make every effort to provide an opportunity for students to conduct Honors research, you should be aware that it may not be possible to assign all applicants to a laboratory. This is part of a full-year thesis (493-494). [ more ]

BIOL 494(S)Senior Thesis Research: Biology

Each student prepares a thesis under the supervision of a member of the department. Thesis work can begin either in the spring of the junior or the fall of the senior year, and includes the Winter Study period of the senior year. The number of Biology Department faculty available to mentor research students and the number of students each can accommodate in her/his lab vary from year to year. Although the department will make every effort to provide an opportunity for students to conduct Honors research, you should be aware that it may not be possible to assign all applicants to a laboratory. This is part of a full-year thesis (493-494). [ more ]

BIOL 499Biology Colloquium

Last offered Spring 2018

Scientists from around the country who are on the cutting edge of biological research come to talk about their work. Students of Biology at any level are welcome. [ more ]