Biology

Courses

Biology 101 - Topics in Biology I

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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. Biology 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

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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. Biology 101 and 102 comprise a full year of introductory biology, and may be taken in either order. Lecture-laboratory.

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: Biology 101 or 102, or consent of the instructor. Lecture-laboratory.

Not offered 2022–23.

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: Biology 101 and 102 and sophomore standing, or consent of the instructor. Credit/no credit only. Conference.

Biology 251 - Plant Communities of the Pacific Northwest

One-half-unit semester course. An exploration of the principles underlying the distribution and abundance of plants in the Pacific Northwest. Topics include the structure and basic ecological features of communities, adaptation of organisms to their abiotic and biotic environments, symbiotic relationships, success, endemism, and biogeography. These concepts will be developed to address current environmental problems such as resource extraction, climate change, invasive species, pollution, and loss of biodiversity. The course will include field trips. Suitable for nonmajors. Prerequisite: Biology 101 and 102 or equivalent. Lecture-conference.

Not offered 2022–23.

Biology 256 - Human Genetics

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One-unit semester course. The nature and function of genes and genomes, using human case studies. Readings will include classic and modern examples from the primary literature to illustrate fundamental genetic approaches and concepts. How do genes influence human phenotypes, and how does the study of human phenotypes illuminate the working of genes? What are the applications of DNA variation, and the implications of a postgenomics world? Consent of the instructor is required for students who have completed related 300-level coursework. Prerequisite: Biology 101 or consent of the instructor. Lecture-conference.

Not offered 2022–23.

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: Biology 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: Biology 101 and 102, or consent of the instructor. Lecture-laboratory.

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: Biology 101 and 102. Lecture-laboratory.

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 tradeoffs, 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: Biology 101 and 102. Lecture-laboratory.

Not offered 2022–23.

Biology 324 - Molecular Plant Development

One-unit semester course. An exploration of molecular and cellular programs that underlie plant development and physiology. Course will emphasize evolutionary innovations and broader implications of climate change. Lecture topics include plant genetics and genomics, molecular and cell biology, water relations and mineral nutrition, biochemistry and metabolism, growth and development, and responses to environmental cues. Laboratories will investigate models of plant development and incorporate functional genomics, molecular genetics, and cell biology approaches. Prerequisite: Biology 101 and 102, Chemistry 101 and 102. Chemistry 201 and 202 are recommended. 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: Biology 101 and 102, and either Biology 131, or Computer Science 121, or consent of the instructor. Lecture-laboratory.

Not offered 2022–23.

Biology 332 - Vascular Plant Diversity

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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: Biology 101 and 102. Lecture-laboratory.

Not offered 2022–23.

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: Biology 101 and 102. Lecture-laboratory.

Biology 351 - Developmental Biology

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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: Biology 101 and 102, Chemistry 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: Biology 101 and 102. Lecture-laboratory.

Biology 356 - Gene Regulation

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One-unit semester course. The molecular biology of eukaryotes, particularly as it relates to the control of gene expression. Genome organization, packaging and perpetuation, and mechanisms of gene regulation will be treated in depth, with the focus on experimental approaches and what they reveal about the conversion of genotype to phenotype. The laboratory will emphasize molecular approaches to analysis of genomes and gene expression, which will then be used in independent projects. Prerequisites: Biology 101 and 102, Chemistry 101 and 102. Chemistry 201 and 202 are recommended. Lecture-laboratory.

Biology 358 - Microbiology

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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: Biology 101 and 102, Chemistry 101 and 102. Lecture-laboratory.

Not offered 2022–23.

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: Biology 101 and 102, Chemistry 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: Biology 101 and 102, Chemistry 101 and 102. Chemistry 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: Biology 101 and 102, Chemistry 101 and 102. Chemistry 201 and 202 are recommended. Lecture-laboratory.

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: Biology 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.

The Genetics and Cell Biology of Cancer. In this course, students and faculty will work together to explore and interrogate current literature about how the genetics of cancer dictates the behavior of tumor cells. We will be exploring this relationship through the eyes of computational biology, genetics, and cell biology.

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.

Integrative Animal Behavior Animal behavior is the product of intrinsic properties (physiology, genetics, etc.) and extrinsic properties (environmental interactions, ecology, etc.) that have been shaped by evolutionary forces including both natural selection and sexual selection. This course will seek out research that integrates mechanistic studies with an ecological and evolutionary approach.

Integrative Neuroethology. Neuroethology is an integrative approach to understanding the neural basis of behavior. While the discipline has historically been dominated by physiological approaches, neuroethologists today increasingly rely on genomic and bioinformatic tools to address their questions. We will explore modern research that integrates physiological and genomic approaches to understanding how evolution has shaped behaviors and the neural circuits that generate them.

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.

Molecular Genetic Analysis of Plant Evolution. - Website. An exploration of issues of current controversy and active research in plant evolution, highlighting places where molecular techniques and data are providing new insights for classical problems in plant evolution.

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.

New Views on Sexual Selection. All fields of biology are constantly updated with current knowledge and new thinking, sexual selection is no exception. From Darwin’s view of female passivity to Bateman’s and Trivers’s male-centric description of sexual selection, the field has suffered from a restricted viewpoint. The course will read works that have successfully altered these views as well as other works that seek to expand upon and/or challenge current thinking. Discussions will focus on what concepts the authors claim need improvement or abandonment and how the proposed alternatives can be tested and lead to new insights into sexual selection.

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.

Plant Biotechnology. An exploration of emerging technologies, especially genetic engineering, that are revolutionizing agriculture and allowing for the production of plants with enhanced qualities. Emphasis will be placed on the molecular and physiological principles involved as well as the ecological risks and benefits.

Plant Cell Collectives. Dynamic cell identities and transitions underlie flexible developmental events and thereby orchestrate plant responses to changing climates. In this course, we will examine fundamental principles that define coordinated cell collectives by leveraging emerging insights from functional genomics, molecular genetics, and cell biology.

Socio-ecology of Fire and Drought. The impact of wildfires and droughts is increasing in many regions. Addressing these risks requires an understanding of how fires and droughts operate as natural ecosystem processes, as well as how they affect and are affected by human society. We will explore these complex socio-ecological issues through study of the academic literature and discuss the science and management of fire- and drought-impacted systems in the twenty-first century.

Telomeres and Telomerase. Investigation of elements needed for chromosome stability, using contemporary studies of telomere metabolism, regulation of telomere length, and the role telomeres play in cellular senescence and cancer. Prior coursework in genetics or cell biology is required.

Biology 463 - Immunology

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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: Biology 101 and 102, and one of Biology 351, 358 or 372, or consent of the instructor. Lecture-laboratory.

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.