Biology Department

BIOL 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 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 113 - Lichens of the Pacific Northwest

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.

BIOL 123 - Lichens of the Pacific Northwest (with Lab)

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 with lecture and lab activities. 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 and the collecting, analyzing, and interpretation of data. Students who have taken BIOL 113 may not take this course.

BIOL 131 - Introduction to Computational Biology

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.

BIOL 133 - Introduction to Conservation Biology

This course will survey key biological concepts and research methods that are used to understand and address the loss of biological diversity. Topics will include ecological and genetic processes that play a role in biodiversity loss and that threaten the survival of rare and endangered species, factors that contribute to habitat loss and the loss of biological communities, and applied methods that can be used for the protection and restoration of species, communities, and ecosystems. The course will offer a combination of lectures and conferences, allowing students to develop an understanding of important biological concepts that structure our understanding of biodiversity loss and apply these concepts to specific case studies from the conservation biology research literature.

BIOL 152 - Introduction to Gene Expression

Gene expression produces the RNA and proteins that interact with each other and the environment to generate traits. This course will introduce the key steps in gene expression (transcription-the synthesis of RNA from a DNA template; and translation-the synthesis of proteins from an RNA template) and explore the many mechanisms that regulate these processes. Topics will include the structure of genes and their regulatory sequences; key examples of transcriptional, post- transcriptional, translational, and post-translational regulation; and the ways in which these regulatory mechanisms combine to enable fine-tuned control of expression. Students will also learn about methods for quantifying gene expression and gene regulation. Lectures will provide foundational knowledge that will then be used to delve into readings from the primary literature.

BIOL 172 - Cells and Society

This course explores the role cells play in society and will simultaneously build 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.

BIOL 181 - Introduction to Neurobiology

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.

BIOL 191 - Introduction to Neurobiology (with Lab)

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, as well as hands-on collecting, analyzing, and interpreting data. Students who have taken BIOL 181 may not take this course.

BIOL 211 - Introduction to Scientific Literature and Discourse

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.

BIOL 273 - Evolution

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).

BIOL 301 - Ecology

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.

BIOL 303 - Leaves to Landscapes

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.

BIOL 313 - Forest Canopy Ecophysiology

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

BIOL 331 - Computational Systems Biology

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.

BIOL 332 - Vascular Plant Diversity

Website

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.

BIOL 333 - Systems Neurobiology

An examination of the neural basis of behavior with a focus on understanding how the brain perceives and processes sensory information from the environment to produce complex behaviors, and how these processes can be modulated. The course will cover the structure of invertebrate and vertebrate nervous systems and neurons, neuronal communication, sensory systems, movement and regulatory systems, sexual behavior, learning and neuronal plasticity, and complex higher-level neuronal processing. We will explore and use a variety of approaches used to understand the brain, including genetic and molecular methods, neuronal recording and silencing, optogenetics, neuroanatomy, and behavior. 

BIOL 342 - Animal Behavior

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.

BIOL 351 - Developmental Biology

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.

BIOL 352 - Bioinformatics

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.

BIOL 358 - Microbiology

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.

BIOL 363 - Genes, Genetics, and Genomes

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.

BIOL 372 - Cellular Biology

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.

BIOL 381 - Neurobiology and Physiology

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.

BIOL 411 - Scientific Inquiry, Methods, and Analysis

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.

BIOL 431 - Seminar in Biology: Contemporary Topics

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. Not all topics offered every year.

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.

Animal Communication
This class explores the diverse ways animals communicate, from vocalizations and body language to chemical signals and electrical impulses. We will examine the mechanisms, evolution, and ecological significance of communication across species, considering how animals convey information for mating, social bonding, warning signals, and territorial defense. Through an interdisciplinary approach, we will integrate concepts from ethology, neurobiology, and evolutionary biology to understand the role of communication in survival and reproduction. Additionally, we will discuss the similarities and differences between animal communication systems and human language, including the limits of nonhuman cognition and expression. By the end of the course, students will have a comprehensive understanding of the adaptive significance and complexity of communication in the animal kingdom.

Bacterial Pathogenesis
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.

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.

Development of Sensory Systems
An exploration of how sensory systems develop across the tree of life, focusing on animals. We will interrogate review articles, contemporary science writing, and primary literature to build a shared understanding of animal sensory system biology. In this course, our reading, writing, and discussions will be guided by questions about developmental lineages, spatial organization, transcriptional profiles, and neural circuit formation. Previous cell and/or developmental biology coursework is highly recommended. Familiarity with genetics, molecular biology, and/or evolution may be beneficial.

Developmental Neurobiology
An exploration of our current understanding of how brains and eyes form. Our investigations will focus on patterning, size determination, morphogenesis, neuronal connectivity, regeneration, stem cells, and developmental/degenerative diseases. This course is designed to help students break down barriers between scientists and nonscientists, providing a forum to develop neurobiology-informed community engagement projects.

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.

Evolution's Rainbow
This discussion section will tackle Joan Roughgarden's Evolution's Rainbow on its tenth anniversary. In this book, Dr. Roughgarden discusses the science behind the diversity of sex and gender across the animal kingdom, in humans, and in human culture through a feminist, gay, and transgender critique. During this class we will read chapters from this popular science book, investigate selected scientific references, and look at how Roughgarden's and others' critiques have or have not shaped research in these subjects. In addition to participating in and leading discussion, students will prepare a presentation on methods used in the process of making discoveries in this field and complete short and medium-length written assignments synthesizing concepts and evidence they have learned about in discussion and from reading. 

Genome Evolution
A growing body of knowledge about the size, shape, content, and dynamics of genome evolution has accrued since the first genomes were sequenced almost 30 years ago. This course will focus on reading, discussing, and presenting papers from the primary literature on genome evolution, including research on the evolution of sex chromosomes, the evolution of chromosome number and size, horizontal transfer, organellar genome evolution, chromosome and genome organization, inheritance, and dynamics. Students will use reviews and perspective pieces from the secondary literature as background, in order to inform both asking and answering questions during discussion of recent research papers. In addition to participating and leading discussion, students will prepare a presentation on methods used in the process of making discoveries in this field and complete short and medium-length written assignments synthesizing concepts and evidence they have learned about in discussion and from reading. 

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.

BIOL 453 - Advanced Evolution

This lecture/conference course will focus on exploring the central, unifying tenet of biology-evolution through readings and discussion. Despite its centrality, evolution is often misunderstood. Learning objectives include 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 theories and debates, 5) read papers from the primary literature on evolution, 6) explore human origins and evolution, 7) confront the problematic and racist roots of evolutionary biology as a field, 8) examine current-day issues related to the acceptance of evolution in society, 9) consider frontiers in evolutionary biology research (e.g., synthetic biology and de-extinction) and 10) discuss the relevance of evolution in applied contexts. Students who have taken BIOL 273 may not take this course.

BIOL 463 - Immunology

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.

BIOL 470 - Thesis

BIOL 481 - Special Topics

Independent laboratory or library research on a topic chosen in consultation with the instructor. A final written report is required.