Reed College Catalog

Derek A. Applewhite

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

Kara L. Cerveny

Developmental biology, growth control, neurogenesis, and the visual system.

David A. Dalton

Plant physiology and ecophysiology, biological nitrogen fixation. On sabbatical 2016–17.

Keith Karoly

Plant evolution, evolution of plant mating systems.

Jay L. Mellies

Bacterial pathogenesis, gene regulation.

Suzy C.P. Renn

Comparative functional genomics of behavior.

Anna Ritz

Computational biology, genome structural variation, signaling pathways.

Sarah Schaack

Genetics/genomics, transposable elements, mutation.

Janis Shampay

Molecular biology, telomere structure and function.

Erik Zornik

Neurobiology, neural basis of behavior.

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, 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 and the biochemistry and molecular biology major are described elsewhere in this catalog.

Requirements for the Major

  1. Biology 101/102, 470.
  2. Three semester lecture-laboratory courses in biology, one from each of three clusters: (1) Genes, Genetics and Genomes, Genetics and Gene Regulation; (2) Animal Physiology, Cellular Biology, Developmental Biology, Microbiology, Plant Physiology; (3) Animal Behavior, Evolution, Population Ecology and Evolution, Vascular Plant Diversity.
  3. Two additional units in biology, at least one of which must be a full lecture-laboratory course; the other may be an additional full lecture-laboratory course or two half-course combinations. At least one-half unit should be at the 300 or 400 level. Advanced courses may be taken in any sequence as long as course prerequisites have been met.
  4. Mathematics 111 and either 112, 121, or 141.
  5. Chemistry 101/102 and 201/202.

Physics is recommended.

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. Three semester lecture-laboratory courses in biology, one from each cluster as described for the biology major.
  3. One additional full lecture-laboratory course from the above clusters.
  4. Chemistry 101/102.
  5. Mathematics 111 taken with either 112, 121, or 141.
  6. Six to eight semester courses in the nonscience concentration.

Organic chemistry and physics are recommended.

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. 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. Prerequisite: Biology 101 or consent of the instructor. 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.

Biology 246 - Molecular Evolution

One-half course for one semester. We will cover genome structure, basic bioinformatics methods for characterizing patterns of genome variation, and population genetic models used to characterize the demographic and selective forces shaping genomes. We will also cover molecular phylogenetics, the use of amino acid and nucleic acid sequences to characterize historical familial relationships between species. Finally, we will cover the evolution of sex and sex chromosomes, the origins of novel genes, and mechanisms of speciation. Prerequisite: Biology 101/102 or equivalent. Lecture-conference.

Not offered 2016—17.

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 2016—17.

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 2016—17.

Biology 263 - Molecular Ecology

One-half course for one semester. Survey of how molecular genetic tools are used to investigate ecological processes in natural populations of plant and animal species. Specific topics will include methods for studying genetic variation at the protein and DNA levels, quantitative predictions from ecological and evolutionary theory, and application of molecular genetic markers to research questions related to selection, patterns of migration, population bottlenecks and founder events, and plant and animal mating systems. Conferences will be student led and based on the primary literature. Prerequisites: Biology 101/102. Lecture-conference.

Not offered 2016—17.

Biology 315 - Evolution

Full course for one semester. This course will cover the history and current status of major research areas in evolutionary biology, including mechanisms of evolutionary change, adaptation, and the history of life. Independent laboratory projects will hone skills in experimental design and statistical analysis. Prerequisite: Biology 101/102. Lecture-laboratory.

Not offered 2016—17.

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.

Not offered 2016—17.

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 Mathematics 121 or consent of the instructor. Lecture-laboratory.

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.  An 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 to 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 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 - Animal Physiology

Full course for one semester. An examination of functional mechanisms as they relate to the unique challenges faced by animals. The nervous and endocrine systems will be emphasized as they play a crucial role in integrating distinct but interdependent processes. Readings from the primary literature will be chosen to demonstrate the multidisciplinary approaches used by researchers to understand physiological mechanisms, and to illustrate the questions being currently addressed by modern physiologists. The laboratory will provide hands-on training in modern techniques that students will use to investigate their own questions in physiology. Prerequisite: Biology 101/102 and Chemistry 101/102. Chemistry 201/202 recommended. Lecture-laboratory.

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.

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.

Human Evolution and Ecology. Exploration of human evolution, genetics, behavior, disease, and other current topics. Primary literature will be used to address such questions as: Which features of anatomy and lifestyle set us apart from our closest primate relatives? Is the concept of human races useful? Are the brains of men and women different? Are behavioral traits like alcoholism, intelligence, and sexual orientation heritable?

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.

Mobile DNA. The course will focus on reading, discussing, and presenting papers from the primary literature on mobile genetic elements and viruses, including recent discoveries about transposition mechanisms, horizontal transfer, silencing, and domestication.

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.

Origins of Evolutionary Immune Systems. We will discuss primary literature that explores why organisms haven’t evolved optimum immune responses. Major factors to consider include the constant adaptation of parasite virulence strategies, as well as ecological and evolutionary trade-offs between immunity and other components of host fitness.

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.

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, 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.