Courses
Biology 101 - Topics in Biology I
One-unit semester course, taught by several staff members. The course furnishes an understanding of biological principles and the properties of life. Among topics considered are structure and function of plants and animals, relations of organisms to each other and to their environment, energy relations of organisms, integrative and coordinating mechanisms of organisms, cell biology principles, genetics, molecular biology, reproduction, development and growth, and the evidence for organic evolution. The laboratory deals with the descriptive and experimental aspects of the topics covered in the lectures. BIOL 101 and 102 comprise a full year of introductory biology, and may be taken in either order. Lecture-laboratory.
Biology 102 - Topics in Biology II
One-unit semester course, taught by several staff members. The course furnishes an understanding of biological principles and the properties of life. Among topics considered are structure and function of plants and animals, relations of organisms to each other and to their environment, energy relations of organisms, integrative and coordinating mechanisms of organisms, cell biology principles, genetics, molecular biology, reproduction, development and growth, and the evidence for organic evolution. The laboratory deals with the descriptive and experimental aspects of the topics covered in the lectures. BIOL 101 and 102 comprise a full year of introductory biology, and may be taken in either order. Lecture-laboratory.
Biology 113 - Lichens of the Pacific Northwest
One-unit semester course. This course will explore Pacific Northwest lichens as simultaneous ecosystems and organisms, allowing an introductory setting and study system for student investigation into biological and ecological thinking. Topics will include natural history of lichens, lichen biology (structure, life history, diversity, reproduction, physiology, and ecology), ethnobotany, bioindication, and lichens as ecosystem engineers. Students will learn the ways in which living things are interconnected and interact with one another, using lichens to explore biological and ecological concepts and the local environment. Students will build natural history skills through place-based campus observations, form an understanding of basic lichen biology and ecology, and examine current topics in lichenology through academic literature. This course will include outdoor field-based components (class time as well as potential off-campus field trips). Students must be prepared to spend time in unpredictable field conditions. Conference.
Biology 131 - Introduction to Computational Biology
One-unit semester course. This course provides an integrated survey of fundamental questions in molecular biology and the computational tools that are used to solve them. Elements of molecular biology and computer programming are presented in parallel throughout the semester. Topics include molecular sequence analysis (identifying repeats, regulatory/binding motifs, and genetic variation) using pattern-matching operations on text strings. Assignments will include writing Python programs to analyze human DNA, RNA, and protein sequences. Prerequisite: BIOL 101 or 102, or consent of the instructor. Lecture-laboratory.
Biology 172 - Cells and Society
One-unit semester course. This course explores the role cells play in society and will simultaneously building foundational knowledge about how cells function. Topics will include the role of mitochondria in neurodegenerative diseases, common mutations linked to cancer and how they affect the cell cycle, cell migration and its relationship to metastasis, and the biology and therapeutic potential of stem cells. The course will feature combination of lectures and conferences, allowing students both to learn the foundations of cell biology and, through close reading of the primary literature, to develop an understanding of how those basic principles dictate how cells function in normal and diseased states. Conference.
Biology 181 - Introduction to Neurobiology
One-unit semester course. This course will explore nervous system functions and the biological processes underlying these functions. Topics will include nervous system structure and function, sensory processing, generating behaviors, and how evolution has shaped diverse nervous system functions that support animal survival. The course will focus on basic biological rules that contribute to, and constrain, nervous system function. Students will explore major neurobiological concepts, unanswered questions, and common experimental techniques through careful readings of primary research articles. Conference.
Biology 211 - Introduction to Scientific Literature and Discourse
One-half-unit semester course. In parallel with the biology department seminar series, this conference course explores current topics in biology through reading and discussion of primary literature. The course is designed to deepen understanding of the many forms of biological inquiry; students will learn to evaluate biology scholarship, pose questions, and participate in scientific discourse. Prerequisite: BIOL 101 and 102 and sophomore standing, or consent of the instructor. Credit/no credit only. Conference.
Biology 273 - Evolution
One-unit semester course. This course will focus on the central, unifying tenet of biology—evolution. Despite its centrality, evolution is often misunderstood. Learning objectives 1) provide an accurate and integrative understanding of evolutionary biology, generally; 2) introduce patterns of micro- and macroevolution, as well as the use of phylogenetic analysis to understand relatedness; 3) connect biological phenomena (e.g., adaptation or horizontal transfer) to their evolutionary consequences; 4) review evolutionary theory and debate (e.g., selectionist vs. neutralist); 5) learn to read papers detailing experimental evolution and evaluate evidence for evolutionary change in populations; 6) explore human origins and evolution; 7) confront the problematic and racist roots of evolutionary biology as a field; 8) examine the current-day issues related to the acceptance of evolution in society; and 9) discuss the relevance of evolution in other contexts (e.g., the COVID-19 pandemic). Prerequisite: BIOL 101 or 102, or consent of the instructor. Lecture-conference.
Biology 301 - Ecology
One-unit semester course. This course examines fundamental concepts in ecology such as limits to distribution, behavioral ecology, population ecology, species interactions, community ecology, and ecosystem ecology, and will examine the relevance of such topics for addressing contemporary applied issues of global change, human health, and sustainability. Central objectives of this course are to 1) evaluate the evidence that supports major theories in ecology and 2) actively participate in the process by which theories are tested, falsified, and refined. Weekly laboratories will help facilitate the latter objective. Lectures and laboratories will emphasize how ecologists gain inference from experiments, observations, and ecological models. Prerequisite: BIOL 101 and 102, or consent of the instructor. Lecture-laboratory.
Not offered 2023–24.
Biology 303 - Leaves to Landscapes
One-unit semester course. This is a field experience–based course that examines the underlying structure, function, diversity, and ecology of Pacific Northwest (PNW) Forests. The heart of this course is the weekly and extended (weekend) natural history field trips that allow for exploration of our amazing native forests and the identification of all the major tree species in the PNW. These trips provide an outdoor classroom for us to discuss topics such as plant water and carbon relations, plant life history and resource use, resilience of trees and forests to disturbance, and plant responses to global change. In addition, we will explore how our forests operate as complex socio-ecological systems through direct interaction with the natural resource managers, conservationists, and decision makers who steward these lands. In the latter part of the semester, an independent course project will be undertaken that focuses on (1) building skills for testing hypotheses about the patterns and processes of trees and forests and (2) employing a translational-science approach that connects decision-makers to the scientific process. It is important to note that this is a FIELD-BASED COURSE. As often as possible, class will occur outdoors. As such, the course requires the willingness to spend considerable time in challenging and unpredictable field conditions. Prerequisite: BIOL 101 and 102. Lecture-laboratory.
Not offered 2023–24.
Biology 308 - Restoration Ecology
One-unit semester course. This is a project-based field course that examines the biological concepts that drive our efforts to restore natural ecosystems. Successful restoration projects require a multiscale biological approach, from understanding the role of local genetic adaptations in individual species to making predictions about the response of whole ecosystems to disturbance and global change. In the lab portion of the class, students will have the opportunity to directly apply the concepts covered in lecture as they take on the role of ecological consultants for a local restoration site. Working in small groups and interacting with local restoration professionals, students will design a monitoring plan to shed light on the patterns and processes that affect restoration potential at the field site. Methods will include biodiversity monitoring, demographic analyses, species behavioral observations, and soil and water quality testing. Students will learn to collect and analyze the data in the context of setting management goals, identifying uncertainties and trade-offs, and practicing adaptive decision-making. This class effort will be synthesized into a management plan that would aid the landowner in the restoration of the site. Note that this is a field-based course, and requires the willingness to spend time in unpredictable field conditions. Prerequisite: BIOL 101 and 102. Lecture-laboratory.
Not offered 2023–24.
Biology 313 - Forest Canopy Ecophysiology
One-unit semester course. This course will explore of the physiological and ecological principles that govern the responses of forest trees to dynamic local, regional, and global environmental conditions. Importantly, study of forest ecosystems has historically taken place from the forest floor. Yet many of the processes that drive forest ecosystem function take place far above the ground in the complex intersection of branches that forms the forest canopy environment. This course will leverage recent advances for studying this unique and important environment, such as arborist-style tree climbing and drone-based technologies for sampling and surveying the canopy. Students will learn the underlying structure-function relationships and other biological theories that describe ecophysiological patterns and processes, as well as develop skills for asking important research questions and test hypotheses that advance this exciting and important field. Prerequisite: BIOL 101 and 102. Lecture-laboratory.
Biology 331 - Computational Systems Biology
One-unit semester course. A survey of network models used to gain a systems-level understanding of biological processes. Topics include computational models of gene regulation, signal transduction pathways, protein-protein interactions, and metabolic pathways. Laboratory exercises will involve building a collection of biological networks from public data, implementing a graph library and foundational algorithms, and interpreting computational results. A programming-based independent project will answer biological questions by applying graph algorithms to experimental data. Prerequisite: BIOL 101 and 102, and either BIOL 131, or CSCI 121, or consent of the instructor. Lecture-laboratory.
Not offered 2023–24.
Biology 332 - Vascular Plant Diversity
One-unit semester course. A survey of vascular plants using evolutionary and ecological principles to interpret patterns of diversity in vascular plant form and function. Topics include plant species, methods of phylogenetic reconstruction, paleobotany, plant reproductive biology, and plant ecological interactions. Laboratory work will include a survey of flowering plant families with an emphasis on learning elements of the flora of the Pacific Northwest. Laboratory projects will demonstrate methods used for establishing evolutionary relationships, assessing genetic structure in natural populations, and identifying adaptive features of plant form and function, and will include independent research in the laboratory or field. Prerequisite: BIOL 101 and 102. Lecture-laboratory.
Biology 342 - Animal Behavior
One-unit semester course. An integrated approach to the study of behavior—the phenotype through which an organism interacts with, and also modifies, its environment. We will study how behavioral phenotypes are shaped by the social and physical environment and analyze how they are implemented through development by neural physiology, gene networks, and individual genes. Conversely, we will study how behaviors modify the environment and thus impact the physiology and genetics of organisms as well as the evolution of species. Examples will be drawn from both laboratory and field studies using comparative molecular and behavioral approaches to identify patterns and recurring themes, which will be discussed in the context of existing theories about animal behavior. The laboratory will cover both bench skills and field techniques that will then be applied in independent student projects. Prerequisite: BIOL 101 and 102. Lecture-laboratory.
Not offered 2023–24.
Biology 351 - Developmental Biology
One-unit semester course. Analysis of one of the most remarkable events in biology—the formation of a complex, multicellular organism from a single cell. With an emphasis on principles common among many species, this course explores how cellular, molecular, and genetic events contribute to distinct stages of embryogenesis. How are body patterns generated? What are the morphogenetic processes that give rise to specific organ systems? How is cell fate decided? What are the processes that guide tissue growth, regeneration, and differentiation? We will address these and other fundamental questions, discussing primary literature, recreating classic experiments, and performing new investigations. Students will apply the techniques and skills gained during the first part of the course to carry out an independent laboratory project. Prerequisites: BIOL 101 and 102, CHEM 101 and 102. A course in genetics or cell biology is strongly recommended. Lecture-laboratory.
Biology 352 - Bioinformatics
One-unit semester course. This course will explore the range of biological questions being addressed with genomic approaches, the specific genomic methods employed to address these questions, and the kinds of bioinformatic challenges and solutions that exist for working with genomic data. The primary objectives of this course are 1) to understand the biological principles that underpin and are illuminated by specific genomic techniques and 2) to be able to evaluate and utilize existing bioinformatics tools to work with genomic datasets. Lectures will focus on contemporary studies from the primary literature that utilize genomic approaches. These will provide case studies to critically assess the utility of these approaches for addressing specific biological questions, as well as to examine the kinds of data that are produced and the challenges presented in analyzing them. Computer-based laboratories will provide opportunities to develop and implement bioinformatics pipelines to analyze genomic datasets. Prerequisites: BIOL 101 and 102. Lecture-laboratory.
Biology 358 - Microbiology
One-unit semester course. The biology of microorganisms, including structure and function of the prokaryotic cell, metabolism, genetics interactions with host organisms, and cell-to-cell communication. Course will emphasize current areas of active research using the primary literature to illustrate key concepts discussed in lecture. Laboratory exercises emphasize interactions of bacteria with their environment and with host organisms, using classical and molecular genetic techniques to address biological problems. An advanced independent research project is required. Prerequisites: BIOL 101 and 102, CHEM 101 and 102. Lecture-laboratory.
Biology 363 - Genes, Genetics, and Genomes
One-unit semester course. Overview and exploration of fundamental concepts and processes in genetics including heredity, mitosis, meiosis, DNA replication, transcription, translation, segregation, linkage, recombination, epistasis, selection, migration, drift, and evolution. Topics will also include DNA and RNA structure, coding and noncoding DNA, chromosomes, genome architecture, mechanisms of mutation, horizontal transfer, and genomics. Laboratories will provide the opportunity to investigate genetic questions and concepts using molecular and bioinformatic tools. Prerequisites: BIOL 101 and 102, CHEM 101 and 102. Lecture-laboratory.
Biology 372 - Cellular Biology
One-unit semester course. An in-depth study of the structure-function relationships within eukaryotic cells. The course emphasizes macromolecular organization and compartmentation of cellular activities. Lecture topics include evolution of cells, cellular reproduction, motility, signal transduction, cell-cell interactions, energy transduction, functional specialization, cell death, and cancer. Laboratories investigate models of cellular regulation and incorporate methods that integrate morphological and biochemical techniques. Prerequisites: BIOL 101 and 102, CHEM 101 and 102. CHEM 201 and 202 are recommended. Lecture-laboratory.
Biology 381 - Neurobiology and Physiology
One-unit semester course. An examination of the nervous and endocrine systems, especially as they relate to the unique physiological challenges faced by animals. The course begins with fundamental concepts and mechanisms of nervous system function, followed by an exploration of the role that endocrine systems play in integrating a range of interdependent physiological processes. Readings from the primary literature will be chosen to demonstrate the multidisciplinary approaches used by researchers to investigate neurobiological and physiological processes. The laboratory will provide hands-on training in neurophysiological techniques that students will use to investigate their own questions. Prerequisites: BIOL 101 and 102, CHEM 101 and 102. CHEM 201 and 202 are recommended. Lecture-laboratory.
Biology 411 - Scientific Inquiry, Methods, and Analysis
One-half-unit semester course. In parallel with the biology department seminar series, this course explores current methods of evidence collection and analysis in biology through reading and discussion of primary literature, attending seminars, and interacting with visiting seminar speakers. In this course designed to deepen understanding of the many forms of biological inquiry, students will learn about collecting data, designing experiments, testing predictions, assessing evidence, analyzing data, and making inferences by reading, listening, and talking with scientists about their work. The focus will be on question development, methods, and analysis, but many other related topics (e.g., ethics, collaboration, and innovation) will also be discussed. Prerequisite: BIOL 101 or 102 and junior or senior standing, or instructor permission. Conference.
Biology 431 - Seminar in Biology: Contemporary Topics
One-half-unit semester course. An examination of current topics and areas in biology with an emphasis on primary literature. Participants will lead group discussions and/or make oral presentations. Prerequisites: BIOL 101 and 102, two additional units of biology with laboratory, and junior or senior standing. Conference. Not all topics offered every year. May be repeated for credit.
Advances in Forest Canopy Research. Most research to understand the forest ecosystem has taken place from the forest floor. Yet many of the ecological and physiological processes that drive forest ecosystem function take place far above the ground in the complex intersection of branches that forms the forest canopy environment. This class will explore the history of, common techniques in, and recent advances for studying this unique and important environment through study of the academic literature and hands-on investigation of canopy access techniques, including tree climbing and canopy sampling using drone-based technology.
Bacterial Pathogenesis. - Website. An examination of how bacterial pathogens interact with host organisms in order to cause disease. Topics include adhesion, colonization, invasion, toxins, subversion of host cell signaling events, immune evasion, and bacteria-to-bacteria communication as they pertain to pathogenesis.
Behavioral Genomics. - Website. An exploration of current research that pairs genomic techniques and bioinformatics approaches with classic questions in animal behavior.
Computational Cancer Biology. - Website. Investigation of computational methods to analyze high-throughput biological measurements collected from hundreds to thousands of cancer samples. Biological topics include tumor classification, tumor heterogeneity, and dysregulated signaling pathways. Computational topics include algorithms and models to synthesize, integrate, and manage large-scale cancer datasets.
Conservation Genetics. - Website. An exploration of issues of current controversy and active research in conservation biology, highlighting places where molecular genetic techniques and data are providing new insights for classical problems in the management and conservation of rare and threatened species.
Cytoskeletal Dynamics. An exploration of our current understanding of the cytoskeleton and its role in cell migration, morphogenesis, and disease. We will explore the primary literature and discuss how the cytoskeleton (actin, microtubules, and intermediate filaments) is regulated and how the molecular motors (kinesin, dynein, and myosin) contribute to cellular function.
Developmental Neurobiology. An exploration of our current understanding of how brains and eyes form, focusing on the visual system. Our investigations will focus on patterning, size determination, morphogenesis, neuronal connectivity, regeneration, stem cells, and cancer. Examples of developmental diseases will provide context. This course includes a collaborative writing component.
Ecology and Evolution of Plant-Human Interactions. - Website. Ecological and evolutionary contexts of interactions between plants and humans. Potential topics include agricultural ecology, grazing, plant-resource extraction, crop evolution and their diseases/pests, plant breeding, transgenic species, and invasive plants.
Global Change Ecology. In light of ongoing environmental change, how are the Earth’s ecological systems likely to respond? We will discuss and present primary literature related to advanced basic and applied concepts in ecology to 1) explore the theories and tools for understanding the ecological response to environmental change and 2) identify sources of uncertainty for accurately understanding such issues.
Mobile DNA. The course will focus on reading, discussing, and presenting papers from the primary literature on mobile genetic elements and viruses, including research about transposition, horizontal transfer, silencing, accumulation, and domestication.
Neuroethology. Exploration of modern and classic research aimed at understanding the neural basis of behavior. Neuroethologists investigate how the brains of diverse species generate natural behaviors, with the goal of elucidating fundamental principles of brain function. Topics may include animal communication, learning and memory, locomotion, prey capture, and escape behavior.
Novel Ecosystems. As anthropogenic influences continue to shape our natural world, we are witnessing the emergence of historically unprecedented, “novel” ecosystems composed of both native and nonnative species. Some biologists argue that these ecosystems should be embraced and even curated, as they can fill important ecological niches that would otherwise be lost. Others view this concept as an acceptance of environmental destruction. In this course, we will read excerpts from foundational texts, take a tour of novel ecosystems across the globe, and study the ecological dynamics that shape them. Through this course, students will be encouraged to formulate their own personal “land ethic” and to articulate opposing viewpoints on how to approach novel ecosystems.
Biology 463 - Immunology
One-unit semester course. A discussion of the properties of innate and adaptive immunity, the cells of the immune system, antibody structure and function, antigen recognition, lymphocyte activation, and immunity to microbes. Topics also covered will include immunodeficiency and AIDS, and transplantation. An inquiry-based laboratory exercise will be required. Prerequisite: BIOL 101 and 102, and one of BIOL 351, 358, or 372, or consent of the instructor. Lecture-laboratory.
Not offered 2023–24.
Biology 470 - Thesis
Two-unit yearlong course; one unit per semester.
Biology 481 - Special Topics
One-half-unit semester course. Independent laboratory or library research on a topic chosen in consultation with the instructor. A final written report is required. Prerequisites: standing as a junior or senior biology major, or approval of instructor. Independent study requires approval by the instructor, the department, and the division.