Ecology and Evolution In this introduction to ecology and evolutionary biology we will cover the topics of interspecific interactions (competition, predation, mutualism), demography and life-history patterns, succession and disturbance in natural communities, species diversity, stability and complexity, causes of evolutionary change, speciation, phylogenetic reconstruction, and population genetics.   The laboratory component will examine lecture topics in detail (such as measuring the evolutionary response of bacteria, adaptations of stream invertebrates to life in moving water, invasive species and their patterns of spread).  We will emphasize experimental design, data collection in the field and in the laboratory, data analysis, and writing skills. This course is not open to seniors and second semester juniors.

Cell Biology and Genetics In this introduction to modern cellular, genetic, and molecular biology we will explore life science concepts with an emphasis on their integral nature and evolutionary relationships.  Topics covered will include cell membrane structure and function, metabolism, cell motility and division, genome structure and replication, the regulation of gene expression and protein production, genotype to phenotype relationship, and basic principles of inheritance.  Major concepts will be illustrated using a broad range of examples from plants, animals, and microorganisms.  Current topics in biology will be integrated into the course as they arise.

Comparative Vertebrate Biology This course will explore the evolution of the vertebrate classes and the adaptations that allow them to live in almost every habitat on Earth. We will study the phylogeny, anatomy, physiology, and ecology of the major extinct and extant taxa of vertebrates and discuss how each group solves the problems of finding food, finding mates, and avoiding predators. Laboratory exercises will focus on the comparative anatomy of a cartilaginous fish (the dogfish shark) and a mammal (the cat). Students will learn to identify some anatomical structures of the vertebrate body and learn basic functions and the evolutionary homologies for these structures. Occasional field trips will introduce the local vertebrate fauna in their natural habitat.

Biology of Plants Plants have been on Earth for 500 million years and account for over 400,000 of described species. In this course students will explore this incredible diversity of plants from an evolutionary, physiological, and ecological perspective. We will examine unique anatomical, physiological, and developmental characteristics of plants, as well as broad phylogenetic patterns in plant evolution, and engage with primary literature that emphasizes and builds upon lecture material. In lab, we will explore local habitats, identify common local wildflowers, ferns, mosses, and trees, and learn ecophysiological techniques in the lab to measure plant stress and performance. Finally, students will design and conduct a greenhouse experiment that examines the effect of an environmental variable on plant development, performance, and/or growth.

Entomology Insects are one of the most successful animal groups on Earth, accounting for roughly 75% of all animal species. In this course we will examine several aspects of organismal biology in insects and related arthropods, such as comparative anatomy, physiology, reproduction, development, sensory behavior, and evolution. Hands-on experiences with insects will occur in the field and the lab, culminating in an independent research project. Special topics will include medical and veterinary entomology, insect pest management, and the effects of climate change on insect populations. Oral and written reports are required.

Ornithology With over 10,000 species, birds are the most diverse class of terrestrial vertebrates, occupying a wide variety of ecological niches on every continent. Their incredible array of colors and sounds have fascinated scientists for centuries, and birds have played culturally significant roles for millennia. We will discuss the evolution, anatomy, physiology, development, behavior, ecology, and conservation of birds globally. We will learn to identify local bird species by sight and sound using a combination of museum specimens and field trips to various local ecosystems. Field experiments will involve testing bird behavior and assessing ecological relationships. Written and oral reports will be expected.

Experimental Design and Statistical Analysis Experimental design is one of the most important parts of doing science, but it is difficult to do well. How do you randomize mice? How many replicate petri plates should be inoculated? If I am measuring temperature in a forest, where do I put the thermometer? In this course students will design experiments across the sub-areas of biology. We will run student designed experiments, and then learn ways to analyze the data, and communicate the results. Students planning to do independent research are encouraged to take this course. (BIOL 0140 or BIOL 0145).

Animal Behavior The behavior of animals primarily from an ethological perspective, with respect to genetics, physiology, evolution, and other biological factors. The course follows the history and methods of studying individual and social behaviors like feeding, courtship, mating, parental care, defense, predation, and migration. We examine live animals in the field and lab to illustrate such processes as instinct, learning, and communication. Discussion topics address recent research, and students design their own research projects. Oral, and written reports are required. (BIOL 0140 or BIOL 0145) 2.

Evolutionary Biology Why don’t frogs have wings? When did the first eye evolve? The answers to these questions exemplify how evolutionary biology can be used to understand the diversity of the present day and how we can trace important traits back to their origins. In this class, we will learn about the processes that drive diversity, the constraints on evolution, and how the interplay between genes, traits, organisms, and species has sculpted the landscape of life we see today. In addition to lectures, you will read foundational and current primary literature and will lead a project that will use current tools in comparative biology to reconstruct the evolutionary history of a modern-day gene back to its origin in the distant past. (BIOL 140 or 145). 3hrs lect.

Microbes and Social (In)equity Microbes shape our ecosystems and society in unseen but profound ways. This course explores and examines microbial communities in our bodies, environments, and built spaces —and how we, in turn, shape them. Through analysis of scientific literature and other readings, we will interrogate the roles of race and racism, gender, socioeconomic status, and other factors that influence human and environmental microbe interactions. Topics such as pregnancy and birth mode, gut health, food access, and green spaces reveal the surprising ways microbes influence our health and environment. Through discussions, presentations, and creative activities, students will build science communication and critical reasoning skills. The course culminates in a final project based on a student-designed research question. (BIOL 0140 or BIOL 0145) 3 hr. lecture

Human Genetics In this course, we will incorporate both classical and molecular approaches to study the structure and inheritance of the human genome, chromosomes, and genes; gene function; effects of changes in genes and chromosomes; and analysis of the genetic structure of pedigrees and populations. Through lecture, discussion, case studies, and writing projects, we will explore topics including, but not limited to, classical genetics, stem cells and cloning, human migration, the Human Genome Project, human origins, and the future of human genetics. We will also illustrate the consequences of mutation by studying human genetic disease and explore some of the societal, ethical, and legal aspects of human genetics.

Global Change Biology We will examine the effects of global climate change on the earth system. Our emphasis will be on exploring what we know about the impacts of climate change on ecosystems and the organisms that inhabit them. We will examine primary literature-based case studies to reveal how biologists study processes of change on local and global scales, and we will assess how accurately we can predict future changes in species distribution and ecosystem function. In lab, we will apply simulation techniques to predict carbon dioxide and global temperatures into the next century, and couple citizen science platforms (e.g. iNaturalist) with species distribution modeling to predict ecological interactions in future climates. No prior computational modeling experience required/assumed.

The Mighty Mitochondria What are mitochondria and why are they so important to our understanding of many neurological diseases? In this course, we will explore what mitochondria are and their role in different cells and specifically in the cells of the brain. Mitochondria are thought to be the cell’s powerhouse, but they are not found in all cells. Furthermore, their dysregulation, either through genetic mutations or environmental factors, leads to profound consequences for human health. Topics to be covered are the structure and function of mitochondria, cell death, oxidative stress, aging, neurological diseases, and rare genetic diseases. (BIOL 0145; not open to first-year students; open to neuroscience majors and biology majors; others by waiver). 3hrs lecture.

Human Toxicology What makes a substance toxic? This human physiology course integrates perspectives from biology, chemistry, and public health to explore how toxicants cause harm. Students will examine foundational concepts in toxicology at the level of the organism, including absorption, distribution, metabolism, and elimination of toxicants. We will carefully consider dose-response relationships and key mechanisms of toxicity. The impact of toxic exposure on selected target organ systems will then be covered, with particular emphasis on the liver, kidney, lungs, nervous system, immune system, and endocrine systems. For each organ system, a representative toxicant will be studied in depth; students will identify and present information on additional toxicants. Finally, the course will critically examine how the science of toxicology aligns with current regulatory structures to influence public health outcomes. (BIOL 145) 3hrs lecture

Immunology In this course we will explore the human immune system and how it works to protect the body from infection.  Students will be introduced to the cells and molecules of the immune system and how they work together to protect the host from foreign invaders.  We will focus on the cellular and molecular mechanisms of innate immunity before exploring the cellular and genetic principles that underlie the adaptive immune response.  Finally, we will investigate how innate and adaptive immunity work together to combat infection and how disease can arise from inadequacies in this coordinated host response.

Botanical Illustration: The Art of Science, The Science of Art The natural diversity of plants and the adaptations they possess is awe-inspiring and has been the subject of botanical illustration for thousands of years. In this course students will develop fundamental artistic techniques for capturing plant forms using a variety of artistic methods (graphite, charcoal, silver point, ink, watercolor) and a diversity of living plant specimens. Students will learn how to represent the broad scale of botanical diversity, from the shapes of trees via field-based journaling to the cells of mosses via microscopy-to-paper transcription. Students will develop a practice of close observation that challenges their assumptions of how they see the natural world, will master faithful transformation of 3D natural forms to 2D, and will be challenged to apply plant anatomical knowledge and form-function relationships to develop scientifically accurate, publication-quality illustrations in a feedback-rich studio environment.

Advanced Immunology In this course students will be introduced to recent advances in immunology and emerging themes in immunology research via short introductory lectures and in-depth readings from the current primary literature. Topics for in-class discussion will include transplantation tolerance, mucosal immunity, vaccine biology, tumor immunology, immunogenetics, neuroimmunology, antibody engineering, and microbiome-immunity interactions. Students will critically assess the published literature via weekly response papers, active participation in small group discussions, student-led journal club presentations, and a final written project.

Aquatic Ecology In this course we will combine field-based laboratory exercises with classroom activities to examine how humans interact with freshwater ecosystems and how these systems contribute to our understanding of fundamental ecological concepts. We will take frequent field trips to aquatic ecosystems in Vermont and use data and observations collected to connect to broader ecological concepts and environmental issues. Topics covered will include food web structure of aquatic ecosystems, biotic monitoring of water quality, the measurement and interpretation of ecosystem metabolism, and the ecology of emerging contaminants. Evaluation will be based on consistent attendance and engaged participation in class discussions and lab exercises, reports synthesizing the lab exercises, and an original research project. (BIOL 0140).

Developmental Biology Have you ever wondered how an embryo develops from a simple fertilized egg to a complex adult? This course explores this question, examining the preparation and initiation of development (gametogenesis, fertilization, cleavages, and gastrulation), the formation of embryonic structure (morphogenesis), the creation of embryonic pattern (pattern formation), and the control of gene expression during embryogenesis. In a semester when a laboratory section is offered, students will design and carry out experiments at the cutting edge of developmental biology, incorporating modern cellular, molecular, and genetic techniques with classical embryological approaches. Fundamental mysteries of development will be investigated in model organisms that best illustrate each process. This course does not have a lab associated with it every semester.

Mammalogy Thanks to a rogue asteroid, we now live in the Age of Mammals. Mammals fulfill important ecological roles and have adapted to a wide range of habitats – flying, swimming, and scurrying their way to survival. Mammals are also central to numerous livelihoods and cultural practices. We will use the phylogeny of mammals globally to build expertise with evolutionary concepts. Locally, we will work within Vermont to develop a field-based toolkit for studying wild mammals. Experiential learning opportunities may include preparation of salvaged animals, non-invasive monitoring, engagement with trappers/hunters, and introduction to molecular techniques.

Microbiology This course introduces key microbiological principles, providing a foundation for advanced study in modern biology. Students will explore microbial cell structure and function, as well as the roles of microbes in health, biotechnology, agriculture, and the environment. The course integrates both basic and applied microbiology through lectures and hands-on lab experiences. A central component is an independent research project in which students will apply microbiological techniques to either isolate and characterize microorganisms from natural sources or investigate a novel, student-driven research question involving microbes.

Biostatistics II In this course we will explore how to use statistics to help answer questions in biology, building on the foundation set in Biology 211. There will be a focus on real-life data sets which require additional statistical complexity, for example accounting for non-normally distributed data or fixed versus random effects. We will think about the philosophical framework behind statistical methods, particularly considering the recent critique of an over-reliance on p-values. The class will have a “hands-on” approach in which we implement examples of covered material in the statistical programming language R.

Molecular Genetics This course will focus on the structure and function of nucleic acids in both prokaryotes and eukaryotes. Lectures will center on molecular mechanisms of mutation, transposition, and recombination, the regulation of gene expression, and gene control in development, immune diversity and carcinogenesis. Readings from the primary literature will complement the textbook and classroom discussions. The laboratory will provide training in both classic and contemporary molecular-genetic techniques including nucleic acid isolation and purification, cloning, electroporation, nick-translation, Southern/Northern blotting, DNA sequencing, PCR and RT-PCR.

Plant Molecular Physiology When you look at a plant, what do you see? One might observe that plants are green, and they don’t move. Some might question whether plants are truly alive. In this course, we will challenge the notion that plants experience the world passively. Inside a plant, there are many highly active, dynamic processes by which a plant senses aspects of its environment and initiates complex responses that allow it to defend itself, alert its neighbors, or overcome harsh environments. Specifically, in this course we will focus on multiple aspects of plant molecular physiology, including major hormonal responses, developmental stages, vascular transport, nutrient acquisition, and metabolism, all in the context of building our understanding of the genes and proteins that catalyze these essential processes. The lab portion of this course will introduce students to common methods used by plant geneticists to test gene function, including mutational analysis, molecular cloning, and plant transformation, among others. (BIOL 0140 and BIOL 0145) 3 hrs lecture / 3 hrs lab.

Plant Community Ecology This course will explore the structure and dynamics of plant communities, with a particular emphasis on temperate forest communities. We will investigate patterns in community diversity and structure, explore how plant populations and plant communities respond to environmental disturbances, and investigate the effects of anthropogenic influences (climate change, introduced species, habitat conversion) on plant communities. Labs will emphasize fieldwork at local research sites, and will provide exposure to techniques of experimental design in plant ecology and basic approaches to describing plant community structure and dynamics.

Genomics Genomics is a quickly evolving field that analyzes and contextualizes genome sequencing data and high-throughput techniques. Genomics is the study of the nucleic acid content of organisms. In this course students will use national repositories of genomic information, databases, and open-source bioinformatics tools to visualize and manipulate genomic data. We will also explore genomics’ larger social context, particularly as it relates to the environment and medical informatics. In the laboratory we will explore and use the methodology used in genomics to develop and interpret large datasets

Conservation Genomics in Practice: From Genome Assembly to Sequence Analysis Genomic data is increasingly used to inform conservation decision-making in captive and wild populations. In this project-based course, students will gain experience with genomic data generated specifically to address wildlife management needs in Vermont, ultimately contributing to a short peer-reviewed manuscript. We will review a range of sequencing approaches (e.g. Hi-C, RNA, metabarcoding) and how to access public data repositories. Students will actively engage in assembling a genome, including use of the command line and various analysis tools relevant to sequencing technology. Through surveying the primary literature and real-world case studies, students will be able to explore a number of career pathways that bridge molecular biology and conservation science. Note that previous bioinformatics experience is not required. (BIOL 0140 and BIOL 0145; Recommended: BIOL 0211 or BIOL 0314) Ellie Armstrong is a postdoctoral fellow at Washington State University with the Washington Research Foundation. She previously completed her PhD at Stanford University, where she worked on large carnivore genomics (e.g., tigers, lions, bears), genome assembly, and creating genomic-based monitoring tools for conservation./

Mechanisms of Microbial Pathogenesis Many microorganisms have the potential to cause disease. An understanding of the mechanisms that promote bacterial pathogenesis is therefore essential for the development of effective disease prevention and/or treatment strategies. This course will explore the mechanisms by which microbial pathogens adhere to, invade, and persist in the human host. While an emphasis will be placed on microbial mechanisms of disease, the host response to the infectious process will also be discussed. (BIOL 0140 and BIOL 0145) 3 hrs lect/disc.

The Genetics of Cancer  In this course we will examine the molecular and cellular mechanisms that serve to regulate normal cell proliferation, survival, and senescence in order to understand how alterations in these mechanisms can lead to cancer.  Students will develop and propose research projects based on their own specific interests. Topics covered may include: classification of cancers, animal models, oncogenes and tumor suppressors, mitogenic signals, genetic and epigenetic alterations, external causes of cancer, and current treatment protocols.  We will also examine cancer’s far-reaching influence outside the confines of molecular and cell biology.

Receptor Biology In this course we will focus on the wide range of membrane receptors and channels that are critical for cellular communication, neuronal connectivity, and sensory transduction. These complex proteins represent major targets in the pharmaceutical industry, and their study incorporates interdisciplinary techniques in structural biology, electrophysiology, synthetic chemistry, and pharmacology. After thoroughly engaging in the primary literature, we will emphasize discipline-specific writing and learn to summarize and communicate new findings to a wide range of expert and non-expert audiences.

Functional Genomics Functional genomics is the study of how genes and intergenic regions of the genome determine an organism’s physical characteristics (phenotype) and contribute to different biological processes. In this course we will utilize genomic and transcriptomic databases to learn about the core questions and methods of genomics research. Topics include an overview of genomes, sequencing and mapping, transcriptional profiling, and genome editing. We will discuss the Human Genome Project, its contribution to the newly emerging fields of precision medicine and pharmacogenomics, and applications of genomics, from crop improvement to the detection and treatment of infectious pathogens. We will also explore ethical, legal, and social implications of functional genomics research.(BIOL 0140 and BIOL 0145)

Applied Bioinformatics Whether we are identifying cancerous cells, counting animals in an image, or comparing protein functions, we are likely relying on a suite of computational tools. Even then, doing these tasks at a meaningful scale quickly outpaces manual analysis. How, then, are we supposed to identify cancerous cells in 200,000 patients a day or compare proteins across all animal life? In this course, we will learn how to approach biological questions using programmatic thinking. We will refine your data collection strategies, learn the basics of programs and databases for image processing, sequence and phenotypic data, and functional annotation. Lastly, we will apply this knowledge, creating scripts to automate analysis for datasets too large for manual processing. No previous programming experience is necessary. (BIOL 0140 or BIOL 0145).

Endocrinology Endocrinology is a branch of animal physiology devoted to the study of hormones and the endocrine glands that produce them. Hormones are essential for maintaining homeostasis and coordinating biological functions such as growth, reproduction, metabolism, and reaction to stress. This course will cover the diverse mechanisms through which hormones influence physiology and behavior. The endocrine system will provide a window into understanding animal physiology more broadly, with a focus on clinical applications. Lectures will describe the cellular and molecular basis of endocrine regulation and consider the function of each of the major hormone groups produced by the body, such as hypothalamic, pituitary, adrenal, and sex steroids. Weekly journal article discussions will cover current topics in endocrinology, and written work allows students to research endocrine topics of their own interest. .

Molecular Microbial Ecology Molecular microbial ecology (MME) uses leading-edge molecular tools to study the  interactions and diversity of microorganisms in the natural environment. MME covers topics ranging from ancient polar microbes, the human microbiome, and possibly life beyond Earth.  This course will discuss papers that highlight modern technical approaches and form the current theoretical framework in microbial ecology. The laboratory will examine the structure (who is there) and function (what are they doing) of microbial communities in environmental samples. We will cultivate novel microorganisms and analyze nucleic acids via community fingerprinting, functional gene analysis, and the computational exploration of metagenomic datasets.

Animal Physiology This course examines the body functions of animals and humans using general physiological principles and a comparative approach. Lectures will cover the function of each of the major physiological systems (nervous, endocrine, muscular, etc.) and will describe how animal physiology has been shaped by evolution to allow animals to survive in a wide range of environmental conditions. Lectures will focus mainly on physiological processes occurring at the molecular, cellular, and organismal levels. Occasional journal article discussions will provide case studies of current topics in animal physiology. Laboratory exercises, reports and oral presentations emphasize experimental design, analysis and independent study using various methodological approaches including electrophysiology, neurotransmitter manipulations, nutritional analysis, and exercise physiology.  [(BIOL 0140 and BIOL 0145) or NSCI 0251].

Advanced Field Biology: Place-based Global Biology Education In this upper-level biology course, we will conduct field-based scientific observation, sample and data collection, and interpretation of biological phenomena. Students will be deeply engaged in off-campus, place-based learning linking Puerto Rico’s terrestrial landscapes to marine ecosystems, with a focus on the ecology, evolution and biogeochemistry across freshwater to marine system gradients. The course is split between time on-campus and off-campus conducting group research projects integrating field observations with data analysis. Students will collaborate and partner with local community members on intercultural projects with ethical local impact and relevance. Open to BIOL, MBBC, ESBI, BIOL-ECSC majors or waiver.

Sweet Biology: Sugars as Signals and Metabolites Sugars rule the world of life. The acquisition, storage, and efficient usage of sugars are critical throughout biology from animals to plants to single-celled bacteria. In addition to their roles as primary metabolites, sugars can act as regulatory molecules, having major influences on various biological processes. In this course we will examine how different sugars influence the molecular regulation of metabolism and physiology using numerous examples from plants, animals, and unicellular organisms. To accomplish these aims, we will read primary literature on topics including energy storage, growth, and physiology, all in the context of nutrient sensing and signaling. Assignments will include in-class literature discussions, presentations, scientific writing and peer-review, and a final written popular science article. This is a non-lab course. (BIOL0145 and BIOL 0140)  3 hrs lecture.

Conservation Biology        A conservation biologist is a problem-solver who applies tools from disparate fields – e.g., evolutionary biology, genetics, ecology, paleontology, anthropology, and population biology – to address complex real-world dilemmas of relevance to human, wildlife, and ecosystem health. To effectively leverage their data, conservation biologists must also recognize and navigate government regulations, diverse cultural practices, and stakeholder perceptions. This course is international in scope. Emphasis will be placed on current issues such as species reintroduction, detecting extinction, rewilding, novel ecosystems, protected area design, shifting baselines, human-wildlife conflict, and climate change. This course will require engagement with community partners in independent research. Open to juniors and seniors.

Advanced Evolutionary Ecology In 1965, the influential biologist G. Evelyn Hutchinson argued that ecological processes are like a theater in which evolutionary plays are performed. Implicit in his argument was the idea that ecological and evolutionary processes occur at distinct timescales, and can thus be easily separated. We will challenge this notion by studying phenotypic plasticity, ecological speciation, evo-eco dynamics, and other advanced topics through a hybrid of lecture, discussion, and a research experiment conducted as a class. Evaluation will be based on quizzes, discussions of the primary literature, several short written assignments, and the group research project. (BIOL 140 and 211 or waiver).

Hacking Inheritance The Genetic Age is upon us, with the ability to precisely edit the genomes of organisms in our hands. But should we? In this course we will explore the myriad ways gene-editing is used to address global crises in agriculture, public health, and more. Using both primary literature and popular press, we will dive into the history, innovations, and ethical concerns related to gene-editing efforts in medicine, neurobiology, and biotechnology to then predict the next frontiers of the field. Student work will reflect effective scientific communication to experts, non-experts, and policy makers.

Topics in Biotechnology In this seminar course we will discuss primary research articles on current topics in biotechnology, or the harnessing of molecular biology to solve problems and cure diseases. We will look into new developments in therapies, as well as challenges still unsolved, and ethical dilemmas. Topics include DNA and RNA gene therapy, gene editing, the many uses of antibodies, how therapies can be directed to the correct part of the body, and how researchers are targeting proteins that are "undruggable". (BIOL 0145) (Open to juniors & seniors, others with instructor permission)  Elizabeth Stivison is an Assistant Laboratory Professor at Middlebury, and a science writer covering developments in biotechnology research.

Desert Ecology Drylands (deserts, semi-deserts, savannas) account for over 40 percent of Earth’s terrestrial area and are home to two billion people. They represent the most stressful of habitats, but also are home to organisms possessing the most incredible adaptations to survive. In this course we will explore the unique biology of desert ecosystems across the globe, using primary literature, review articles, and nonfiction works to answer: What selective pressures shape physiology and ecology in desert organisms? How have plants and animals evolved to survive in deserts? How are humans and climate change altering dryland ecosystems on local and global scales?

The Living Deserts of North America What does the desert smell like after it rains, and why? How do desert organisms cope with harsh environmental conditions in diverse ways? How have socio-ecological systems shaped desert landscapes? In this course we will explore these types of questions through hands-on, experiential learning and place-based scientific observation. As a class we will gain background knowledge of desert ecology before a 10-day trip to the Mojave, Great Basin, and Colorado Plateau Deserts of Western North America. Students will gain exposure to a diversity of desert landscapes, engage in round-table discussions with local and Indigenous groups around social and environmental issues impacting deserts, and conduct an independent field research project. This course requires participation in a 10-day field trip to the Southwest during spring break. (BIOL 140 and instructor approval).

Extremophiles: conquering Earth’s Extreme Environments Even the most extreme environments are teeming with microbial life. From highly acidic streams to hydrothermal vents with temperatures exceeding 120ºC, microorganisms manage to not only grow, but thrive. How? We will utilize biogeochemistry and cellular biology to characterize these unique microbial processes, and their impact on ecosystems, through critical reading and robust discussion of primary literature. Student-driven research will provide opportunities for advanced oral and written communication skill development.

Topics in Reproduction Reproduction: all life on earth depends on it. In this course we will examine the fundamentals of reproduction and explore reproductive function across the life course. Topics will include fertility, infertility, pregnancy, fetal life, birth, and the neonatal period. We will consider the wide range of factors that can affect reproductive function, along with the many far-reaching impacts of reproduction. Through critical review of the primary literature, writing, presentations, and discussions, students will gain an understanding of key topics in reproduction.

Neuroplasticity In order for the brain to encode, process, and retain new information, it is constantly changing. Neuroplasticity refers to this capacity of the central nervous system to modify its organization in response to a wide variety of endogenous and environmental stimuli. We will discuss the molecular and cellular basis of various forms of neuroplasticity within the adult brain (e.g., synaptic plasticity, synaptogenesis, and neurogenesis). In this course we will explore how neuroplasticity contributes to learning and memory, neural regeneration in response to injury, and various neuroloigcal diseases (e.g., Alzheimer’s disease, schizophrenia, and depression). Evaluation will be based on student-led discussions of the primary literature, article critiques, and a final review paper. [BIOL 0145 and (BIOL 0140 or NSCI 251); open to juniors and seniors] 3hrs sem.

Genes and Disease in the Nervous System Numerous disorders in the nervous system have a genetic component; some are due to a mutation in a single gene while others demonstrate a more complex mode of inheritance. In this course we will focus on understanding the genetic basis of neurological diseases, including Alzheimer’s, Fragile-X, autism spectrum disorder, Huntington’s, motor neuron degeneration, Parkinson’s, and muscular dystrophy. From classical genetics to modern genomics, we will explore the discovery of the genes involved in brain disorders as well the development of animal models to reveal underlying molecular mechanisms. We will cover these topics through a combination of lectures and detailed analyses and discussions of primary research articles.

Graduate Fellowship Writing in the Life Sciences In this course, we will make explicit the otherwise “hidden” curriculum of applying to graduate programs in the life sciences. We will work as a group to demystify how to identify and contact potential PhD advisors/programs, how to translate a resume into a scientific curriculum vitae, how to craft compelling graduate school application materials, and how to write fellowship statements. Course deadlines will provide a structured scaffold for achieving milestones in the application process. Multiple rounds of feedback will be offered by peers during the writing process. Students will complete this course by submitting a National Science Foundation Graduate Research Fellowship proposal (or equivalent). Open to students majoring in BIOL, BIOL/ECSC, BIOL/ENVS or by instructor approval). This course is not intended for pre-health students.

Independent Study In this course students complete individual projects involving laboratory and/or field research or extensive library study on a topic chosen by the student and a faculty advisor. Prior to registering for BIOL 0500, a student must have discussed and agreed upon a project topic with a member of the Biology Department faculty. Additional requirements include attendance at all Biology Department seminars and participation in any scheduled meetings with disciplinary sub-groups and lab groups. This course is not open to seniors; seniors should enroll in BIOL 0700, Senior Independent Study. (BIOL 0211. Approval required) 3 hrs. disc.

Senior Independent Study In this course students complete individual projects involving laboratory and/or field research or extensive library study on a topic chosen by the student and a faculty advisor. Prior to registering for BIOL 0700, a student must have discussed and agreed upon a project topic with a member of the Biology Department faculty. Additional requirements include attendance at all Biology Department seminars and participation in any scheduled meetings with disciplinary sub-groups and lab groups. (BIOL 0211. Approval required; open only to seniors) 3 hrs. disc.

Senior Thesis Seniors majoring in Biology who have completed one or more semesters of BIOL 0500 or BIOL 0700 and who plan to complete a thesis should register for BIOL 0701. In this course students will produce a written thesis, deliver a public presentation of the research on which it is based, and present an oral defense of the thesis before a committee of at least three faculty members. Additional requirements include attendance at all Biology Department seminars and participation in any scheduled meetings with disciplinary sub-groups and lab groups. Open to Biology and joint Biology/Environmental Studies majors. (BIOL 0211 and BIOL 0500 or BIOL 0700 or waiver; instructor approval required for all students) 3 hrs. disc

Reproducible Biology in R Reproducibility is essential at all stages of research and allows for the validation and replication of science, enhancing collaborations and connectivity. The open-source nature of R programming and its ability to analyze and visualize datasets make it a powerful tool in biology. In this course, we will learn the basics of reproducible coding in R and RStudio (no prior knowledge required). Primarily, we will cover: 1) Data structures and creating publication-quality figures; 2) How to ask and answer scientific questions using basic statistics; 3) Creating shareable documents using Rmarkdown; and 4) Reproducibility using GitHub, shell commands, and LaTeX - all within RStudio. Each week will involve a combination of structured lecture, group work, and coding exercises. (Requires BIOL 140 or BIOL 145).

Mountain Ecology In this course we will examine western mountain ranges (Sierra Nevada, Rocky Mountains, and Cascades) and National Parks (e.g., Yellowstone, Grand Teton, Glacier, and Yosemite). These exceptional landscapes will serve as the backdrop for exploring geology, climate, ecology, and natural history of forested and alpine environments. Through lecture, readings, videos, and individual/group activities, we will cover topics including altitude and adaptations, mountains as hotspots for biodiversity, ecosystem services, and effects of climate change on species and habitats. The instructor will share personal experience from releasing wolves into the Idaho wilderness to leading recovery efforts for endangered species, as well as decades of collaborating with federal and state agencies on species of concern and watershed and habitat management issues.  Ray Vizgirdas is a retired biologist with more than 30 years with the US Forest Service and the US Fish and Wildlife Service in California and Idaho. He is also adjunct faculty at Boise State and Northwest Nazarene universities in Idaho teaching advanced and graduate level courses in biology and environmental sciences. /

Nanomachines of Cell Death Correctly orchestrated cell death is essential for organismal life. In this course we will examine the cellular nanomachines that execute cell death processes in mammals through the lens of structural biology and evolution. The course will introduce classical and state-of-the-art structural biology methods including X-ray crystallography, nuclear magnetic resonance, and cryogenic electron microscopy. We will apply an evolutionary analysis to understand conservation of the cell death machinery across the tree of life. Students will complete written and visual assignments, examine case studies from the primary literature, and learn the basic application of structural biology software (Pymol, ChimeraX). Open to Biology, Biochemistry, and MBBC majors, or by waiver. Alex G. Johnson is a postdoctoral research fellow at Harvard Medical School who grew up in Norwich, Vermont. He completed his B.A. in Biochemistry at Reed College in Oregon, and his Ph.D. in Chemical Biology at Stanford University in California./

Animal Communication This course will examine information transfer between animals, including the mechanisms of the production and reception of animal signals in different sensory modalities, and the factors that shape the evolution and structure of communication signals. This course will discuss signal characteristics, signal evolution, honesty and deception, competing interests of signallers and receivers, communication in networks, and methods for identifying and quantifying information in the study of animal communication systems. The goals of this course are: 1) to demonstrate how communication affects the ecology, behavior, neurobiology, and evolution of animal systems; 2) to compare and contrast theoretical and empirical tools used in studying animal communication origins and structure; 3) and to highlight the effects of human-induced change on animal communication.

The Expansive Future of RNA The success of the COVID-19 vaccines has catalyzed a revolution in RNA therapeutics. RNA-based therapies provide a highly versatile and adaptable treatment modality without the risks associated with genomic editing. Currently RNA-based treatments for cancer, infectious diseases, and genetic disorder are under active development. In this course we will explore the scientific discoveries that have made this exciting technological advancement possible. Topics will include eukaryotic transcriptional and translational regulation, RNA structure, RNA modifications, and codon optimality. We will also explore the role of small RNAs (tRNAs, miRNAs, siRNAs) in the regulation of gene expression and RNA therapy. (BIOL 0145)  Ethan Strayer (Middlebury class of 2016) is a doctoral candidate in the laboratory of Dr. Antonio Giraldez at Yale University. His work seeks to understand how cis-regulatory elements encoded in an mRNA modulate transcript stability and translational output. This work has resulted in the filing multiple patents, as well as contributed to the launch of RESA therapeutics, a biotech company focused on the development of novel mRNA therapies.

The Biology of Aging As we grow older, rates of serious disease such as cancer, neurodegeneration, heart disease, and diabetes increase exponentially, with age being the greatest risk factor for their onset. Understanding the biology of aging, and what about aging connects these diseases, has thus received much attention from both scientists and the general public in recent years. In this course, we will examine the scientific theories on what causes aging. A history of aging research will be provided, and students will engage with primary scientific literature to understand how modern scientists study this question. We will conclude with an examination of the ethics of further lifespan extension in the 21st century. (BIOL 0145)  William Nathan is a postdoctoral fellow at the National Cancer Institute/NIH studying genome instability in neurons and cancer cells. He has a DPhil in Biomedical Sciences/Oncology from the University of Oxford and a BA in Biochemistry and Economics from Middlebury College.

Data Science Across Disciplines In this course, we will gain exposure to the entire data science pipeline—obtaining and cleaning large and messy data sets, exploring these data and creating engaging visualizations, and communicating insights from the data in a meaningful manner. During morning sessions, we will learn the tools and techniques required to explore new and exciting data sets. During afternoon sessions, students will work in small groups with one of several faculty members on domain-specific research projects in Anthropology, Biology, Classics, Political Science, and Statistics. This course will use the R programming language. No prior experience with programming is necessary. (Not open to students who have taken STAT 0118, STAT 0201, ANTH 1230, BIOL 1230, CLAS 1230, ECON 1230, ECSC 1230, ENVS 1230, FMMC 1230, GEOG 1230, HARC 1230, HIST 1230, JAPN 1230, LNGT 1230, MATH 1230, NSCI 1230, PSCI 1230, SOCI 1230, STAT 1230, or WRPR 1230.)  ANTH/LNGT: In this section we will explore indigenous political voice in unexpected places. The data we will analyze will consist of bilingual Apache-English and Maidu-English stories, songs and speeches originally recorded by anthropological linguists in the early twentieth century as examples of traditional culture. Students will use R to search this corpora for how indigenous contributors were also making claims on the future in their address to the researcher and to wider anticipated audiences.  BIOL/ECSC 1230: In this section we will work with data collected by elephant seals equipped with oceanographic instruments in the Southern Ocean. Depending on your interests, you can approach the project from different angles: students focusing on biology will explore where the seals travel and what drives their movements, while those interested in earth science will investigate the temperature and salinity profiles gathered during their dives. Working in teams, you’ll combine these perspectives to build a fuller picture of both seal ecology and the oceanographic processes that shape their environment. Along the way, you’ll practice manipulating and visualizing different types of data including maps of seal tracks, temperature and salinity profiles, and cross-sections of ocean properties. We will also bring in satellite  and autonomous float data to place seal activity and the data they collect in a broader context. By the end, you’ll have a sense of how these different data sources fit together and what unique insights we gain from using seals as oceanographers.  CLAS 1230: In this section students will gain hands-on experience with a variety of natural language processing and text mining techniques by exploring the writings of the ancient historian Plutarch, who lived during the first and second centuries AD.  We will focus on the biographies of "great men" in Plutarch’s Lives, which chronicles the history, morals, and virtues of major figures who played parallel roles in ancient Greek and Roman society. The public domain English translation from Project Gutenberg will serve as our main corpus; however, students with a background or interest in Ancient Greek can work with the text in the original language. Using the R programming language, students will transform unstructured text into quantitative data for statistical analysis and morphosyntactic parsing. We will also apply machine learning models to our data to reveal underlying patterns in large amounts of text. No prior experience with R is necessary.  PSCI 1230: Who votes in elections? Who attends protests? Why? In this section we will use the tools of data science to explore these and other questions about political participation in the Americas. We will examine engagement in different forms of participation and the demographic, economic, social, and other factors that shape participation. The class will introduce students to the basics of survey research and the study of political participation.  Students will complete a final group project showcasing the concepts and tools learned in class.   STAT 1230: In this section students will dive into the world of data science by focusing on invasive species monitoring data. Early detection is crucial to controlling many invasive species; however, there is a knowledge gap regarding the sampling effort needed to detect the invader early. In this course, we will work with decades of invasive species monitoring data collected across the United States to better understand how environmental variables play a role in the sampling effort required to detect invasive species. Students will gain experience in the entire data science pipeline, but the primary focus will be on data scraping, data visualization, and communication of data-based results to scientists and policymakers.

Alexis Mychajliw

Alex Johnson

Alex Lyford

Alison Nurok

Amanda Crocker

Andrew Swafford

Carolyn Dash

Casey Schine

Catherine Combelles

David Allen

Elizabeth Stivison

Ellie Armstrong

Emily Putnam

Eric Moody

Erik Solhaug

Erin Eggleston

Ethan Strayer

Glen Ernstrom

Grace Spatafora

Gregory Pask

Heather Christie

Hedya Klein

Jeremy Ward

Kate Gridley

Kirsten Coe

Lauren Ash

Laurence Feyten

Mark Spritzer

Monica Przyperhart

Ray Vizgirdas

Rebekah Keating Godfrey

Sam Byrne

Susan DeSimone

Vickie Backus

William Nathan

Read 515 reviews for Biology courses at Middlebury College. Find the best Biology professors and courses.  Discover your new major today!

This is a hard course, or at least it was for me. The textbook isn't necessarily mandatory to read, but it was very important to me. Without it, I probably wouldn't have understood half the material. Professor Swafford is incredibly understanding and wants to help you succeed. The oral exam was nice because you could tell he wanted you to get the right answer and would try to nudge you in the right direction. 

I took Mol Gen with Prof Swafford and really enjoyed it. He runs his lab much differently than others where you are largely responsible for finding and writing protocols. This can be challenging, but is very helpful in understanding how a lab works. The lectures are split between fast-paced material and lab preparation. He does oral exams where you make a presentation and he asks you questions. While stressful at first, they ultimately provide you with great opportunities to show your learning. Overall an amazing course. 

I really enjoyed our labs and lectures were generally interesting. We got a cheat sheet for exams which was super helpful, although studying was still hard. The lab reports were were tedious and difficult to meet standards, but not horrible.