Reed College Catalog

Derek A. Applewhite

Cellular biology, cytoskeletal dynamics, cell motility, and morphogenesis.

Kara L. Cerveny

Developmental biology, neurogenesis, signaling pathway interplay, and the visual system.

Jeremy Coate

Plant genomics and physiology, whole genome duplication.

David A. Dalton

Plant physiology and ecophysiology, biological nitrogen fixation.

Samuel Fey

Species interactions, population ecology, global change ecology.

Keith Karoly

Plant evolution, evolution of plant mating systems.

Jay L. Mellies

Bacterial pathogenesis, gene regulation.

Aaron Ramirez

Translational ecology, fire and drought, socio-ecological systems.

Suzy C.P. Renn

Comparative functional genomics of behavior.

Anna Ritz

Computational biology, genome structural variation, signaling pathways. On sabbatical and leave 2018–19.

Sarah Schaack

Genetics/genomics, transposable elements, mutation. On sabbatical spring 2019.

Janis Shampay

Molecular biology, telomere structure and function.

Erik Zornik

Neurobiology, neural basis of behavior. On sabbatical 2018–19.

The biology major emphasizes developing the student’s capacity to use and contribute scientific knowledge. The curriculum includes both conceptual and experimental approaches to studying biology at the molecular, cellular, organismic, population, and species levels. Courses provide students with opportunities to develop an intellectual framework and learn the techniques necessary for answering questions that interest them. Faculty members, through active professional research programs of their own, offer opportunities for student involvement in biological research. A regular research seminar series adds to the unique research-oriented experience of the Reed biology undergraduate. The synergism between the interests and motivations of Reed students and the rigorous nature of our program, including a research-intensive thesis, enables students to pursue their individual interests and primes them for careers in the life sciences. Reed routinely ranks near the top in the percentage of graduates who earn PhDs, and many other biology graduates advance to successful careers in medicine, biotechnology, education, law, and advocacy.

The Lewis Kleinholz Biological Laboratories are well-equipped and permit students to engage in mentored and independent research projects during their course of study. Coursework and summer opportunities in both laboratory and field biology are designed to prepare students for the senior thesis. Upper-division courses include independent research components to foster the development of hypothesis generation, experimental design, and results analysis and interpretation skills. Reed students may also broaden their research experience by arrangement with the faculties of the Oregon Health & Science University, the Oregon Graduate Institute of Science and Engineering, the Oregon National Primate Research Center, or other area institutions. In addition, Reed has formal relationships with Malheur Field Station in Oregon’s Great Basin, the Organization for Tropical Studies, the School for Field Studies, the Sea Education Association, and the University of Costa Rica. Students may take courses for credit through these programs or at other field or marine stations.

Through the alternate biology program (described below) the biology department provides students with the flexibility of combining biology with other areas of inquiry, including but not limited to economics, political science, and anthropology. Faculty advisers help students plan programs based on their motivations and interests. Alternate and ad hoc joint degree programs can be arranged between the biology department and most other Reed departments. The environmental studies program, the neuroscience major, and the biochemistry and molecular biology major are described elsewhere in this catalog.

Requirements for the Major

  1. Biology 101/102, 470.
  2. Four semester lecture-laboratory courses in biology, one from each of four clusters:
    1. Biology 363: Genes, Genetics and Genomes; Biology 356: Gene Regulation; Biology 331: Computational Systems Biology; Biology 352: Bioinformatics.
    2. Biology 372: Cellular Biology; Biology 358: Microbiology; Biology 351: Developmental Biology.
    3. Biology 381: Neurobiology and Physiology; Biology 322: Plant Physiology; Biology 342: Animal Behavior.
    4. Biology 301: Ecology; Biology 303: Leaves to Landscapes; Biology 332: Vascular Plant Diversity.
  3. One additional unit in biology or biochemistry. This unit may be an additional full lecture-laboratory course, or two one-half unit courses, or Chemistry 391 or 392. Advanced courses may be taken in any sequence as long as course prerequisites have been met.
  4. Two courses from the mathematics department.
  5. Chemistry 101/102 and 201/202.

Students are strongly encouraged to consult with advisers, as specific courses may be preferred depending upon disciplinary interests or career plans.

The Alternate Program in Biology

The alternate program allows students to integrate a comprehensive grounding in biological science with an understanding of one or more alternate disciplines. Working with their advisers, students can tailor their educational program to prepare them for careers or for graduate and professional programs in environmental studies and conservation, public health, urban planning, environmental law, government, social work, precollege teaching, medical illustration, science journalism, and other fields. The primary academic adviser will be a member of the biology staff, and the student will choose a consulting adviser from the appropriate alternate field. After discussion with both advisers, the student must submit a formal petition to the department with a rationale for the integrated course of study. Except in unusual cases, this petition should be made no later than the end of the sophomore year. After the petition is approved by the department, the alternate biology major may then be declared.

Requirements for the Alternate Biology Major

  1. Biology 101/102, 470.
  2. Four semester lecture-laboratory courses in biology from at least three different clusters, the rationale for which is articulated in the petition.
  3. Chemistry 101/102.
  4. Two courses from the mathematics department.
  5. Six to eight semester courses in the nonscience concentration.

Students are strongly encouraged to consult with advisers, as specific courses may be preferred depending upon disciplinary interests or career plans.

Biology 101 - Topics in Biology I

Full course for one semester, 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

Full course for one semester, 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

Full course for one semester. 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 consent of the instructor. Lecture-laboratory.

Not offered 2018–19.

Biology 211 - Introduction to Scientific Literature and Discourse

One-half course for one semester. 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 course for one semester. 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 101/102 or equivalent. Lecture-conference.

Not offered 2018–19.

Biology 256 - Human Genetics

One-half course for one semester. 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 molecular genetic approaches and concepts. Consent of instructor is required for students who have completed Biology 356 or 363. Prerequisite: Biology 101/102. Lecture-conference.

Not offered 2018–19.

Biology 301 - Ecology

Full course for one semester. 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

Full course for one semester. This course examines how the underlying structure, function, diversity, and ecology of plants determine environmental patterns. Lecture topics to be covered include plant water and carbon relations, plant life-history and resource-use strategies, resilience of plants and ecosystems to disturbance, and plant responses to global change. Lab exercises will focus on building skills for measuring and modeling these patterns and processes at multiple spatial and temporal scales. In addition, this course will explore how these patterns and processes operate in complex socio-ecological systems: specifically, how research in this area can be used to inform environmental decision making by natural resource managers and policy makers. These topics will be taught through a variety of activities in lecture, lab, and field settings and through active participation in all aspects of the scientific process. Prerequisite: Biology 101 and 102. Lecture-laboratory.

 

Biology 322 - Plant Physiology

Full course for one semester. An analysis of cell biology, biochemistry, metabolism, ecophysiology, and development of plants. Lecture topics include water relations, respiration, photosynthesis, nitrogen fixation, mineral nutrition, plant hormones, plant molecular biology, genetic engineering, the role of environmental signals in plant development, and the environmental physiology of Pacific Northwest forests. Lectures will be supplemented with readings in research journals. Laboratory exercises are designed to demonstrate basic research techniques as well as the principles covered in lectures. Students are required to conduct an advanced, independent project. Prerequisites: Biology 101/102 and Chemistry 101/102. Chemistry 201/202 is recommended. Lecture-laboratory.

Biology 331 - Computational Systems Biology

Full course for one semester. 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 2018–19.

Biology 332 - Vascular Plant Diversity

Full course for one semester. 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 101/102. Lecture-laboratory.

Biology 342 - Animal Behavior

Full course for one semester. 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 101/102. Lecture-laboratory.

Biology 351 - Developmental Biology

Full course for one semester.  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. Prerequisite: Biology 101/102 and Chemistry 101/102. A course in genetics or cell biology is strongly recommended. Lecture-laboratory.

Biology 352 - Bioinformatics

Full course for one semester. 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

Full course for one semester. 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 101/102 and Chemistry 101/102. Chemistry 201/202 is recommended. Lecture-laboratory.

Biology 358 - Microbiology

Full course for one semester. 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 101/102, Chemistry 101/102. Lecture-laboratory.

Biology 363 - Genes, Genetics, and Genomes

Full course for one semester. 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 101/102, and Chemistry 101/102. Lecture-laboratory.

Biology 372 - Cellular Biology

Full course for one semester. 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 101/102 and Chemistry 101/102. Chemistry 201/202 is recommended. Lecture-laboratory.

Biology 381 - Neurobiology and Physiology

Full course for one semester. 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 and Chemistry 101 and 102. Chemistry 201 and 202 are recommended. Lecture-laboratory.

Not offered 2018–19.

Biology 431 - Seminar in Biology: Contemporary Topics

One-half course for one semester. 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 101/102, two additional units of biology with laboratory, and junior or senior standing. Conference. Not all topics offered every year.


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. 

Behavioral Genomics. An exploration of current research that pairs genomic techniques and bioinformatics approaches with classic questions in animal behavior.

Climate Change Biology. An examination of the causes and biological consequences of global climate change. Consideration will be given to underlying physiological processes involved in responding to environmental challenges such as drought, pollution, ultraviolet radiation, and temperature extremes, particularly with respect to agricultural and natural systems in the Pacific Northwest.

Cell and Developmental Biology of Neural Progenitor Cells. This course offers an interactive environment in which students and faculty will work together to explore and interrogate current literature about the regulation of neural progenitor cell behaviors, including proliferation control, migration, differentiation, and the concept of a neural stem cell niche.

Chromosome Structure and Function. 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.

Computational Cancer Biology. 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.

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. 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.

Evolutionary Genetics. The course will focus on reading, discussing, and presenting papers from the primary literature. Topics may include a variety of phenomena and ideas in genetics and evolution. For example, we may focus on papers related to mechanisms of non-Mendelian inheritance, genetic conflict, levels of selection, codon bias, vertical versus horizontal transmission genetics, gene drive, genetic engineering, the evolution of chromosome number, organellar evolution, complex trait evolution, and/or the evolution of sex determination systems.

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.

The Human Microbiome. Microbes comprise over 90% of the cells of the human body, and form distinctive communities in different regions of our bodies. The microbiome is a complex and dynamic community of microbes having major impact on human health. Using the primary literature, we will investigate how the microbiome intersects with organ development, the immune system, gut health and nutrient acquisition, acute and chronic disease, dysbiosis, and behavior.

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.

Microbiomes and Behavior. The microbiome is a complex and dynamic community of microbes having major impact on human and animal health. Using the primary literature, we will investigate how the microbiome intersects with immunity and behavior, addressing questions in humans and multiple animal model systems.

Molecular Genetic Analysis of Plant Evolution. 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.

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.

Socio-ecology of Wildfire 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. 

 

Biology 463 - Immunology

One-half course for one semester. 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 358 or 372. Lecture-laboratory-conference.

Biology 470 - Thesis

Full course for one year.

Biology 481 - Special Topics

One-half course for one semester. 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, and approval of instructor, department, and division.