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2012-13 Undergraduate Index A-Z
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Upper Division Science
These offerings may include upper division science credit. See individual listings for details.
| Title | Offering | Standing | Credits | Credits | When | F | W | S | Su | Description | Preparatory | Faculty | Days | Multiple Standings | Start Quarters | Open Quarters |
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Bret Weinstein
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | Bret Weinstein | Sophomore SO Junior JR Senior SR | Fall | Fall Winter | |||||
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Abir Biswas and Clarissa Dirks
Signature Required:
Spring
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Program | JR–SRJunior - Senior | 16 | 16 | Day | S 13Spring | This program is designed for students who have a strong background in biology or geology and would like to do advanced work around either topic as it applies to arid ecosystems in the Southwestern U.S. or Eastern Washington State, though there may be opportunities for students to contrast arid systems with more temperate forest ecosystems in Western Washington State. There will be an emphasis on student- and faculty-derived research projects throughout and students will meet regularly with faculty to discuss progress and receive feedback. Students with prior backgrounds or analytical experience in biology and/or geology, seeking to join the program in the spring to conduct field- and/or lab-based research projects are encouraged to contact the faculty early. Students will need to develop their research proposals in the first 2 weeks of the quarter while studying the primary literature. Students will then be conducting their proposed field work and/or laboratory work in weeks 3-6. Students will spend the rest of the quarter completing their analyses in preparation for presenting their work at the end of the program. The expectations and workload will be based on advanced work for upper division credit. In part, the content and themes of this program will be merged with another ongoing program offered by the faculty. Students continuing from that program will have developed group research proposals that will be the basis of their spring research project component. The work of those students is not advanced and the expectations are different. These two groups will meet together only for certain lectures or other activities whereby both will learn more about the faculty research projects and arid/southwest ecosystems. Advanced research students could potentially join the Grand Canyon river trip to conduct research studying Southwestern ecosystems but would need to contact the faculty as soon as possible (prior to Spring quarter registration). Students could also conduct comparative field work in arid or temperate ecosystems in Washington State that will be the basis of their quarter-long research project. | Abir Biswas Clarissa Dirks | Junior JR Senior SR | Spring | Spring | |||||
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Alison Styring
Signature Required:
Summer
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Program | JR–SRJunior - Senior | V | V | Day, Evening and Weekend | Su 13Summer Full | Alison Styring | Junior JR Senior SR | Summer | Summer | ||||||
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Alison Styring
Signature Required:
Summer
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Research | JR–SRJunior - Senior | V | V | Day, Evening and Weekend | Su 13Summer Full | Alison Styring | Junior JR Senior SR | Summer | Summer | ||||||
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Cindy Beck
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Program | SO–SRSophomore - Senior | 8 | 08 | Evening and Weekend | F 12 Fall | W 13Winter | Students will study the anatomy and physiology of the human body using a systems approach. Students will also explore the interrelationship of health and disease in the human body by studying common pathological conditions. Each system will be covered utilizing a traditional lecture and laboratory format. At the conclusion of each system, students will demonstrate their knowledge through exams and research projects.Credits in this class meet some requirements for the MiT program as well as prerequisites for many graduate programs in health sciences. | wellness, health, and health-related fields | Cindy Beck | Mon Wed | Sophomore SO Junior JR Senior SR | Fall | Fall Winter | ||
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Erik Thuesen
Signature Required:
Fall
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Program | JR–SRJunior - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | In the 19th century, well-known European scientists such as Darwin, d'Orbigny and Bonpland traveled in Argentina and brought their knowledge of the flora and fauna back to Europe. The marine, desert and alpine environments of the Southern Cone harbor flora and fauna very different from similar environments in North America. In this two-quarter program, we carry out intensive natural history studies of the unique organisms and ecosystems of Argentina, focusing on those of Patagonia.After an introductory week in Olympia at the start of fall quarter, the study abroad portion of the program will commence with a 4-week intensive study of Spanish language in Buenos Aires to prepare us for our travels and studies in Argentina during fall and winter quarters. We will begin to study the flora and fauna of the Southern Cone through preliminary readings, lectures and class work in Buenos Aires. We will take a short trip to the sub-tropical province of Misiones during October, then move to the coastal and mountain regions of Patagonia in November. We will study the natural history of Patagonia, beginning with field studies on the Atlantic coast and then moving to the Andean Lakes District, taking advantage of the progressively warmer weather of the austral spring.Students will conduct formal field exercises and keep field notebooks detailing their work and observations. We will read primary literature articles related to the biodiversity of Argentina and augment our field studies with seminars.During winter quarter (summer in the southern hemisphere), students will reinforce their language skills with two weeks of intensive Spanish studies in Patagonia, examine montane and steppe habitats, then work in small groups on focused projects examining biodiversity topics. It will be possible to conduct more focused studies on specific ecosystems or organisms, including those in more southern parts of Patagonia, at this time of the year. Clear project goals, reading lists, timelines, etc., will be developed during fall quarter in order to insure successful projects in winter quarter. Examples of individual/small-group projects include: comparisons of plant/animal biodiversity between coastal, desert and alpine zones; comparative studies of the impacts of ecotourism activities on biodiversity; or examining community composition of intertidal habitats along a gradient from north to south, among others. | Erik Thuesen | Junior JR Senior SR | Fall | Fall | ||||
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Jennifer Calkins
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Program | FR–SRFreshmen - Senior | 8 | 08 | Evening and Weekend | S 13Spring | What are the structures of biological systems from cells to populations? How do biological systems store, replicate, and share information? The theory of evolution provides the best framework through which we can answer questions such as these regarding the diversity of biological systems. In this program, we will use evolutionary theory to help us explore biological patterns ranging from the structure of a cell to the organization of populations to patterns of evolutoin over time and processes ranging from the replication of genetic information to the generation of energy. In the context of our study we will investigate the diversity of biological systems, its origin, and its current threats. More specifically, we will study aspects of the structure and information of biological systems and will ask how the theory of evolution can explain the patterns and processes at these levels. This course will prepare students for further study in biology and will provide them with the biological literacy necessary to engage complex issues from cloning to conservation with knowledge and understanding. The course will include lectures and small-group seminar discussions as well as lab, computational, and field-based projects. Readings will include portions of a basic biology text, peer-reviewed research papers, and readings from popular science. Students will be responsible for keeping a journal, doing the readings, participating in group discussions and projects, and completing weekly assignments. Students will be evaluated on their participation, their assignments, and their performance on two exams. | Jennifer Calkins | Sat | Freshmen FR Sophomore SO Junior JR Senior SR | Spring | Spring | ||||
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Frederica Bowcutt
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Program | FR–SRFreshmen - Senior | 16 | 16 | Day | W 13Winter | This program investigates people's relationships with plants for food, fiber, medicine and aesthetics. We will examine economic botany including agriculture, forestry, herbology and horticulture. We will also work through a botany textbook learning about plant anatomy, morphology and systematics. Lectures based on the textbook readings will be supplemented with laboratory work. Students will explore how present form and function informs us about the evolution of major groups of plants such as mosses, ferns, conifers and flowering plants. Students will get hands-on experience studying plants under microscopes and in the field. To support their work in the field and lab, students will learn how to maintain a detailed and illustrated nature journal. Students will write a major research paper on a plant of their choosing. Through a series of workshops, they will learn to search the scientific literature, manage bibliographic data, and interpret and synthesize information, including primary sources. | Frederica Bowcutt | Freshmen FR Sophomore SO Junior JR Senior SR | Winter | Winter | |||||
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Paula Schofield and Lydia McKinstry
Signature Required:
Fall Winter
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | This upper-division chemistry program will develop and interrelate concepts in experimental (laboratory) organic chemistry and biochemistry. It will cover the chemistry material that is usually offered in Molecule to Organism. Throughout both quarters we will integrate topics in both subjects to gain an understanding of the structure-property relationship of synthetic and natural organic compounds. We will also examine the key chemical reactions of industrial processes as well as those reactions that are important to the metabolic processes of living systems.There will be a significant laboratory component--students can expect to spend at least a full day in lab each week, maintain laboratory notebooks, write formal laboratory reports and give formal presentations of their work. Students will work collaboratively on laboratory and library research projects incorporating the theories and techniques of chemical synthesis and instrumental methods of chemical analysis. All laboratory work and approximately one half of the non-lecture time will be spent working in collaborative problem-solving groups. We also hope to attend a chemistry conference.This is an intensive program. The subjects are complex, and the sophisticated understanding we expect to develop will require devoted attention and many hours of scheduled lab work each week. Each student will be expected to develop a sufficient basis of advanced conceptual knowledge and practical skills necessary for pursuing work in a chemistry-based discipline. | chemistry, biochemistry, industrial or pharmaceutical research, medicine, dentistry, veterinary medicine, naturopathy, optometry and pharmacy. | Paula Schofield Lydia McKinstry | Sophomore SO Junior JR Senior SR | Fall | Fall Winter | |||
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Rob Cole
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | W 13Winter | We will explore the causes of global climate change and study the many actions and social behaviors that we can take to minimize human contributions to it. We will examine the scientific evidence for global warming and the efforts to discredit that evidence. We will study the role of multinational corporations in global climate change and how they influence governmental policies and public opinion. We will focus on how to respond to global warming in a fashion that works toward sustainability and equity in the ecosystems that support life on the planet. We will pay particular attention to issues of justice between humans, and how humans interact with other species.In order to understand actions we can take, this program will explore sustainable lifestyle strategies as well as how to resist corporate influence on consumer consumption. We will study the approaches of biomimicry, sustainable architecture, equitable distribution of food and shelter, minimal-impact industrial processes, local food production, less toxic methods of producing, and a variety of low-impact lifestyles. We will examine the methods advocated by visionary groups like Second Nature, Climate Solutions, and Cradle-to-Cradle. We will study current federal energy policy and it connection to climate change, as well as the more proactive policies adopted by hundreds of cities. Students will complete a series of audits of their personal consumption and carbon-generation patterns. We will study methods of computing carbon dioxide budgets including carbon sequestration methods, the intricacies of carbon capping and offsetting strategies, and opportunities to reduce net carbon dioxide production. Students can expect to do research on emerging technologies and strategies that move us to carbon neutrality while fostering sustainability and justice.In addition to exploring how we can all lessen our impact on global climate change and move toward equity, students can expect to sharpen their critical reasoning, writing and speaking skills, as well as their ability to work with quantitative methods and to interpret quantitative data from a variety of sources.Students will be expected to make at least two small-group presentations on a climate solution of their own choosing, and complete a term research paper on a topic of their choice. | Rob Cole | Mon Wed Thu | Sophomore SO Junior JR Senior SR | Winter | Winter | ||||
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Sheryl Shulman, Aaron Skomra and Neal Nelson
Signature Required:
Winter
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | Computers are such an omnipresent and useful tool that it might seem like they can do anything. Through studying topics in advanced computer science, this program will explore what computers can do, how we get them to do it, and what computers can't do. It is designed for advanced computer science students and students with an interest in both mathematics and computer science. Topics covered will include formal computer languages, systems of formal logic, computability theory, and programming language design and implementation. Students will also study a functional programming language, , learn the theoretical basis of programming languages and do an in-depth comparison of the properties and capabilities of languages in the four primary programming paradigms: functional, logic, imperative and object-oriented. Program seminars will explore selected advanced topics in logic, language theory and computability. Topics will be organized around three interwoven themes. The theme will cover the theoretical basis of language definitions, concluding with a study of what is computable. The theme will cover traditional logic systems and their limits, concluding with some non-traditional logic systems and their applications to computer science. In the theme we will study both the theoretical basis and practical implementation of programming language definitions by comparing the implementations of the four programming language paradigms. Students will have an opportunity to conclude the program with a major project, such as a definition and implementation of a small programming language. | Sheryl Shulman Aaron Skomra Neal Nelson | Sophomore SO Junior JR Senior SR | Fall | Fall Winter | ||||
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Richard Weiss, Aaron Skomra and Judith Cushing
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | S 13Spring | This project-oriented program for intermediate and advanced computer science students will weave together the theory and practice of two cross-cutting topics in computer science, pattern analysis and modeling, in the context of eScience. The overriding question of the program is how pattern analysis and modeling, broadly defined, might advance the natural and physical sciences, particularly in the areas of environmental science and climate change studies. The program will meet four days a week for lectures, seminar, workshops, and labs. Particularly in seminar, students will share responsibility for presenting and discussing concepts from the readings and lectures. One seminar group will focus on applying computation, visualization, data mining, and statistics to problems faced by scientists. Another group will apply statistics to machine learning and network analysis, and a third will focus on another area, to be determined by faculty and student expertise and interest. This program will include a guest lecture series that focuses on (how computers are used in) modeling environmental systems. In addition to seminar, the program has two disciplinary components and a project. The disciplinary foci will be 1) the theory and practice of statistics, and 2) data mining, machine learning and pattern recognition. Students will also be expected to apply the computing discipline of their choice to a research paper, or a programming or statistics project, and present their work. To facilitate projects, faculty will organize small research groups that meet twice weekly (once with a faculty advisor) to discuss progress. Projects will begin with a proposal and bibliography, and should be either small enough in scope to be completed in one quarter or a self-contained part of a larger project. Possible CS subdisciplines in which faculty will encourage project work include data mining, machine learning, database systems, data visualization (especially visual analytics), networking, security, algorithmic complexity, and formal languages. This program aims to give students from , , and opportunities to continue work begun in those programs. Students who have taken will be expected to complete more advanced work. | Richard Weiss Aaron Skomra Judith Cushing | Mon Tue Wed Thu Thu | Sophomore SO Junior JR Senior SR | Spring | Spring | ||||
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Dennis Hibbert
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Course | SO–SRSophomore - Senior | 4 | 04 | Weekend | F 12 Fall | Ice, air, water, land, and green growing things—these interact to shape our world's climates. We will study these interactions and how they have changed over time as we follow flows of energy, carbon, and water through the climate system. We will address present changes in climate related to our own activities, the consequences of these changes that we now cannot avoid, and our options for modifying them and for adapting to the world we are bringing about. | Dennis Hibbert | Sat | Sophomore SO Junior JR Senior SR | Fall | Fall | ||||
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Michael Paros
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Program | FR–SRFreshmen - Senior | 16 | 16 | Day | S 13Spring | This academically rigorous field-based course will provide students with the fundamental tools to manage livestock and grasslands by exploring the ecological relationships between ruminants and the land. We will begin the quarter learning about the physiology of grasses and their response to grazing and fire. Practical forage identification, morphology and production will be taught. Ruminant nutrition, foraging behavior, and digestive physiology will be covered as a precursor to learning about the practical aspects of establishing, assessing and managing livestock rotational grazing operations. We will divide our time equally between intensive grazing and extensive rangeland systems. Classroom lectures, workshops and guest speakers will be paired with weekly field trips to dairy, beef, sheep and goat grazing farms. There will be an overnight trip to Eastern Washington where students can practice their skills in rangeland monitoring. Other special topics that will be covered in the program include: co-evolutionary relationships between ruminants and grasses, targeted and multi-species grazing, prairie ecology and restoration, controversies in public land grazing, and perennial grain development. | animal agriculture, ecology, conservation, rangeland management, animal physiology and behavior. | Michael Paros | Freshmen FR Sophomore SO Junior JR Senior SR | Spring | Spring | ||||
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Andrew Brabban, Clyde Barlow and Kenneth Tabbutt
Signature Required:
Winter Spring
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | S 13Spring | "Beauty is in the eye of the beholder." For scientists, beauty may be at the scale of the landscape, the organism, or the atomic level. In order to describe a system, scientists are required to collect quantitative data. This is a rigorous program that will focus on investigations in geology and biology supported with analytical chemistry. Instrumental techniques and chemical analysis skills will be developed in an advanced laboratory. The expectation is that students will learn how to conduct accurate chemical, ecological and hydrogeological measurements in order to define baseline assessments of natural ecosystems and determine environmental function and/or contamination. Quantitative analysis, quality control procedures, research design and technical writing will be emphasized.During fall and winter quarters, topics in physical geology, geochemistry, microbiology, molecular biology, freshwater ecology, genetics, biochemistry, analytical chemistry, GIS, and instrumental methods of chemical analysis will be addressed. Students will participate in group projects studying aqueous chemistry, hydrology, and the roles of biological organisms in the nutrient cycling processes of local watersheds. Analytical procedures based on EPA, USGS and other guidelines will be utilized to measure major and trace anion and cation concentrations. Molecular methods and biochemical assays will complement more classical procedures in determining biodiversity and the role of specific organisms within an ecosystem. Computers and statistical methods will be used extensively for data analysis and simulation and GIS will be used as a tool to assess spatial data. The program will start with a two-week field trip to Yellowstone National Park that will introduce students to regional geology of the Columbia River Plateau, Snake River, Rocky Mountains and the Yellowstone Hotspot. Issues of water quality, hydrothermal systems, extremophilic organisms and ecosystem diversity will also be studied during the trip.Spring quarter will be devoted to extensive project work continuing from fall and winter. There will be a 5-day field trip to eastern Washington. Presentation of project results in both oral and written form will conclude the year. | geology, hydrology, chemistry, microbiology, molecular biology, biochemistry, ecology, chemical instrumentation, environmental analysis and environmental fieldwork. | Andrew Brabban Clyde Barlow Kenneth Tabbutt | Sophomore SO Junior JR Senior SR | Fall | Fall Winter Spring | ||
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Dylan Fischer and Alison Styring
Signature Required:
Spring
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Program | JR–SRJunior - Senior | 16 | 16 | Day | S 13Spring | This program will focus on intensive group and individual field research on current topics in ecological science. These topics will include forest structure, ecosystem ecology, effects of forest management, ecological restoration, riparian ecology, fire history, bird abundance and monitoring, insect-plant interactions, and disturbance ecology. Students will be expected to intensively use the primary literature and student-driven field research to address observations about ecological composition, structure and function. Multiple independent and group research projects will form the core of our work in local forests of the south Puget lowlands, national forests, national parks, state forests and other relevant natural settings. Students are expected to "hit the ground running" and should develop research projects for the entire quarter within the first several weeks of the program.Through a series of short, intensive field exercises, students will hone their skills in observation, developing testable hypotheses, and designing ways to test those hypotheses. We will also explore field techniques and approaches in ecology, and especially approaches related to measuring plant and avian biodiversity. Students will have the option to participate in field trips to sites in the Pacific Northwest and the Southwest (U.S.). Research projects will be formally presented by groups and individuals at the end of the quarter. Finally, student research manuscripts will be created throughout the quarter utilizing a series of intensive multi-day paper-writing workshops. We will emphasize identification of original field research problems in forest habitats, experimentation, data analyses, oral presentation of findings, and writing in scientific journal format. | Dylan Fischer Alison Styring | Junior JR Senior SR | Spring | Spring | |||||
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Noelle Machnicki and Lalita Calabria
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Program | JR–SRJunior - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | Fungi. What are they? Where are they and what roles do they play in terrestrial ecosystems? How do they get their energy? How do they grow? What do they taste like? How do they interact with other organisms? During this two-quarter long program we will answer these and other questions about fungi. Fall quarter will cover the fundamentals of fungal and lichen biology, fungal and lichen diversity, physiology, and systematics. Students will learn to describe and identify fungi and lichens using chemical and microscopic techniques, along with a wide variety of taxonomic keys. Students will participate in a quarter-long project to curate their own collections of herbarium-quality lichen and mushroom specimens. Several multi-day field trips and day trips will provide students with an opportunity for collecting specimens and studying the natural history of western Washington. During winter quarter, we will explore fungi and lichens through the lens of forest ecology. Forest ecosystems rest on a foundation of fungi, and students will learn about the pivotal roles fungi and lichen play as mutualists to plants and animals, as nutrient cyclers, disease-causing agents, and indicators of environmental quality. Lab work will focus on advanced methods and examining taxonomically-challenging groups of lichens and fungi. Students will also learn about museum curation by organizing and accessioning the class lichen and mushroom collection for submission into the Evergreen herbarium. Students will engage in a two-quarter-long group research project relating to fungi. Research topics may include ecology or taxonomy-focused lab and field studies, cultivation or herbarium research. During fall quarter, students will participate in research and writing seminars and quantitative skills workshops to inform their research. Each group will prepare a concise research proposal including a thorough literature review and a pilot study exploring the most appropriate data collection and analysis methods for answering their research questions. During winter quarter, students will conduct research experiments in the field and/or lab, analyze their data and write a research paper outlining their results. | Noelle Machnicki Lalita Calabria | Mon Mon Tue Thu Thu | Junior JR Senior SR | Fall | Fall | |||
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Cindy Beck
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Program | FR–SRFreshmen - Senior | 6, 12 | 06 12 | Evening | Su 13Summer Full | Students will study the anatomy and physiology of the human body using a systems approach while exploring the interrelationship of health and disease in the human body. Each body system will be covered utilizing a traditional lecture and laboratory format. This course meets prerequisites for nursing and graduate programs in health sciences. | health and medicine | Cindy Beck | Tue Wed Thu | Freshmen FR Sophomore SO Junior JR Senior SR | Summer | Summer | |||
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Jennifer Calkins
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Program | JR–SRJunior - Senior | 16 | 16 | Day | W 13Winter | Ecology, evolutionary biology | Jennifer Calkins | Mon Tue Thu | Junior JR Senior SR | Winter | Winter | ||||
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Peter Impara
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | S 13Spring | At what scale should we manage or study an ecosystem or landscape? What is a natural landscape, and how do (or can) we manage it? Geographers and ecologists have pondered the question of scale in ecosystems, and how to apply scale issues to conservation and research. Many ecosystem and related studies have been conducted at fine spatial scales, yet many of the problems and issues of resource management and conservation are best approached at broader, landscape-level spatial scales. This program will investigate broader scale approaches to on-going conservation and management activities in important ecosystems and approaches of scientists regarding the issues of scale and the ecological patterns and processes used to define "natural systems."Scale, landscape analysis and pattern-process interactions will be addressed using computer labs in GIS and spatial analysis. Students will learn about landscape ecology concepts through lectures, field trips to nearby natural areas to observe pattern-process interactions, and through the design and implementation of a landscape ecology research project. Through class and field work students will learn about important ecological principles such as disturbance regimes, biotic diversity and species flow, nutrient and energy flows, and landscape change over time. Seminar readings will tie landscape ecology principles to on-going ecosystem management activities.Students will develop skills in ecological pattern and spatial analysis, natural history and field interpretation, and the generation of multiple research hypotheses and methods to address those hypotheses. | Peter Impara | Sophomore SO Junior JR Senior SR | Spring | Spring | |||||
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Brian Walter, Gary Howell and John Schaub
Signature Required:
Winter Spring
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | S 13Spring | Close observation of the natural world reveals a high degree of underlying order. One of the ways scientists understand and explain this order is using the language of mathematics. Indeed, the degree to which the universe lends itself to a mathematical description is remarkable. The goal of this advanced program is to introduce the mathematical language and methods we use to describe and create physical models of our world. To that end, we will examine a number of key physical theories and systematically develop the mathematical tools that we need to understand them.We will begin, in fall quarter, with a detailed study of classical mechanics--the mathematical description of the clockwork universe envisioned by Newton and others who followed him. We will focus initially on linear approximations for which analytical solutions are possible. The mathematical methods we will learn for this purpose include differential equations, vector calculus and linear algebra. In winter quarter we will move beyond linear approximations and study non-linear systems and chaos and the implications of these ideas for the determinism implied by classical mechanics. We will also consider electrodynamics, the theory that governs the interactions between charged particles, and extend our study to the realm of the very fast by considering Einstein's theories of special and general relativity. We will continue our study of vector calculus and partial differential equations to develop these ideas. In spring quarter we will explore modern physics and quantum theory, which describe physics at the atomic scale. In support of this work we will continue to study boundary value problems and partial differential equations.The work in this program will consist of lectures, tutorials, group workshops, student presentations, computer labs and seminars on the philosophy and history of mathematics and physics, current topics in physics, and mathematics and physics in literature and writing. | mathematics, physics, chemistry and education. | Brian Walter Gary Howell John Schaub | Mon Tue Wed Thu | Sophomore SO Junior JR Senior SR | Fall | Fall Winter Spring | |
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Carolyn Prouty and James Neitzel
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Program | SO–SRSophomore - Senior | 16 | 16 | Day | S 13Spring | This program will explore the molecular events that determine the biological activity and toxicity of selected xenobiotic molecules--chemicals not normally produced by the body. These molecules include natural products, drugs and chemicals released in the environment by human activity. We will focus on specific molecules, which might include drugs like ethanyl estrodiol (birth control pill), natural carcinogens like aflatoxin, and other toxicants like BPA (bisphenol A). For each molecule, we will examine in detail the molecular mechanisms by which they act on cellular or physiological processes. How do chemicals treat a disease or cause cancer? Are all people (or species) equally sensitive to these therapeutic and/or toxic effects? How are chemicals metabolized and what molecular targets does a xenobiotic molecule alter? How are genes affected by chemicals and how do the genes affect the way the chemicals act or their fate in the body? Can we use molecular structures to predict which molecules may bioaccumulate and cause cancer, while other molecules can be easily detoxified and excreted?To help understand the actions of these molecules, this program will examine biochemical pathways used in the transformations of these molecules. We will examine cellular signal pathways in detail, as the biological actions of these molecules are often due to perturbations of these normal signal processes. We will also use tools from modern genetics and bioinformatics to examine how genetic differences can influence the effects of these chemicals. This will include current research in epigenetics that proposes mechanisms that explain how prior environmental exposures can influence an organism's current health.We will emphasize data analysis and interpretation obtained from primary literature reports or agency databases. Quantitative reasoning will be a major component of class examples, workshop and homework assignments. Embedded in these activities are principles of cell biology and biochemistry, organic chemistry, genetics, physiology and epidemiology. Students who take this program and Chemistry of Living Systems in fall and winter will cover all of the major subject areas usually covered in Molecule to Organism. | Carolyn Prouty James Neitzel | Tue Wed Thu | Sophomore SO Junior JR Senior SR | Spring | Spring | ||||
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Arun Chandra and Richard Weiss
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Program | FR–SOFreshmen - Sophomore | 16 | 16 | Day | F 12 Fall | W 13Winter | Systems are not only of things but the relations between them.Mathematics offers an elegant language for the creation and analysis of relations and patterns, in and out of time. In its essence it is about order, continuity and difference.Music (when not merely reproduction) comes into being when a composer desires, specifies and implements sounds in a system of relations. ("Style" being a short-hand for a particular system of sounds and their relations.)Thus, music realizes the offer of mathematics when an implementation of desire involves systems of thought: what you want is what you get---but you have to want something! and articulate it! in a language! of things! and relations!---which is cybernetics."Cybernetics is a way of thinking about ways of thinking, of which it is one." --Larry Richards.This program interleaves the composition of computer music with the mathematics and analysis of sound. We will explore how it relates to scientific methodology, creative insight and contemporary technology. We will address "things" such as music and sound, rhythms and pulses, harmonics and resonances, the physical, geometrical, and psycho-physical bases of sound, acoustics, and their differing sets of relations by which they become "systems".A composer/musician and a computer scientist/mathematician will collaborate to offer a creative and practical, accessible and deeply engaging introduction to these subjects for interested non-specialists. Our math will be at a pre-calculus level, though students may do research projects at a more advanced level if they choose. Interdisciplinary projects could include creating music algorithmically with computers, or analyzing sound mathematically.Cybernetics offers both a philosophy underlying systems of thought, as well as frameworks with which one can both analyze and create. This program is designed for those who find their art in numbers, their science in notes, their thoughts on the ground, and their feet in the stars. By combining music, mathematics and computer science, this program contributes to a liberal arts education, and appeals to the creativity of both buttocks of the brain. | Arun Chandra Richard Weiss | Mon Mon Tue Tue Thu Thu | Freshmen FR Sophomore SO | Fall | Fall Winter | |||
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Lydia McKinstry
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Program | SO–SRSophomore - Senior | 12 | 12 | Day | Su 13Summer Full | This program is designed to be the equivalent of a year-long college level course in organic chemistry. It will be fast-paced and rigorous with an emphasis on the relationship between the structure and chemical behavior of organic molecules. Specific topics will include electronic structure, chemical bonding, acid-base properties of organic molecules, stereochemistry, nomenclature, electron delocalization, conjugation, and resonance. The reactions and mechanisms of nucleophilic substitution, elimination, electrophilic addition in olefinic and aromatic systems, nucleophilic addition and addition-elimination in carbonyl compounds and aromatic compounds, enol/enolate alkylation and acylation, and radical chemistry will be studied in detail. The fundamental theories of mass spectrometry (GC-MS), infrared (FT-IR) and nuclear magnetic resonance (FT-NMR) spectroscopies will be presented and the method of spectral interpretation will be used to elucidate the structures of organic molecules. Simple organometallic chemistry and asymmetric catalysis may also be introduced, if time permits. Course activities will include lectures, small-group problem solving workshops, homework, quizzes and examinations. Well prepared students should expect to spend a minimum of 32 hours each week outside of class meetings, reading, studying and practicing the material. | Lydia McKinstry | Tue Wed | Sophomore SO Junior JR Senior SR | Summer | Summer | ||||
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Alison Styring and Dina Roberts
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Program | FR–SRFreshmen - Senior | 16 | 16 | Day | F 12 Fall | Birds are the most diverse vertebrates found on the earth. We will explore the causes of this incredible diversity through a well-rounded investigation of general bird biology, the evolution of flight (and its implications), and the complex ecological interactions of birds with their environments. This program has considerable field and lab components and students will be expected to develop strong bird identification skills, including Latin names, and extensive knowledge of avian anatomy and physiology. We will learn a variety of field and analytical techniques currently used in bird monitoring and research. We will take several day trips to field sites in the Puget Sound region throughout the quarter to hone our bird-watching skills and practice field-monitoring techniques. Students will keep field journals documenting their skill development in species identification and proficiency in a variety of field methodologies. Learning will also be assessed through exams, quizzes, field assignments, group work and participation. | Alison Styring Dina Roberts | Tue Wed Thu Fri | Freshmen FR Sophomore SO Junior JR Senior SR | Fall | Fall | ||||
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Trisha Towanda
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Program | JR–SRJunior - Senior | 16 | 16 | Day | S 13Spring | Studying climate change processes in the ocean frequently requires approaches that are unique to the marine environment. In this program, we will study the instruments and methods that allow us to conduct science beneath the sea. Lectures will cover marine topics in climate change and regional ecosystems of the Pacific Northwest.We will explore various marine ecosystems of the Pacific Northwest through a series of formal field exercises, including a multi-day field trip on the Olympic Coast. Students will maintain detailed field notebooks with observations, questions and hypotheses that will be the foundation of subsequent literature research. Working in groups, students will write formal scientific reports on each site to address effects of climate change. Students will also conduct a poster session on oceanographic instruments used to study various physical, geological, chemical and biological phenomena in the ocean. Weekly seminar sessions will allow each student opportunities to facilitate seminars on primary scientific literature. In addition, students will interpret scientific literature regarding effects of rapid global climate change on marine systems for non-scientist audiences though various media forms. Through final group presentations, students will convey the scientific research behind efforts to address the impacts of global climate change on marine environments. | Trisha Towanda | Junior JR Senior SR | Spring | Spring | |||||
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Dennis Hibbert
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Course | SO–SRSophomore - Senior | 4 | 04 | Weekend | S 13Spring | Science comes from someone becoming curious about something in the natural world and working out a way to learn about it. We will see this in action as we read (Darwin), (Tinbergen) and (Ruddiman). The course is based in book seminar; you will write a seminar paper each week as preparation.The course evaluation will be based on participation in seminar and in class, and on any other assignments. All assigned work must be done in order to earn credit for the course. | Dennis Hibbert | Sat | Sophomore SO Junior JR Senior SR | Spring | Spring | ||||
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Alvin Josephy
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Course | FR–SRFreshmen - Senior | 4 | 04 | Evening | W 13Winter | In this class we will explore the concepts of inferential statistics. This class assumes that the student has a prior background in descriptive statistics. The class will discuss probability, especially in terms of probability distributions, and move on to hypothesis testing. In this context, the class will work with several distributions, such as t, chi square, F as well as the normal distribution, and work with ANOVA and multiple regression. The class will finish with an introduction to non-parametric statistics. In addition, the students will consider journal articles and research concepts, and will prepare a small presentation using the concepts from the class. | Alvin Josephy | Tue | Freshmen FR Sophomore SO Junior JR Senior SR | Winter | Winter | ||||
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Alvin Josephy
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Course | FR–SRFreshmen - Senior | 4 | 04 | Evening | S 13Spring | In this class we will explore the concepts of inferential statistics. This class assumes that the student has a prior background in descriptive statistics. The class will discuss probability, especially in terms of probability distributions, and move on to hypothesis testing. In this context, the class will work with several distributions, such as t, chi square, F as well as the normal distribution, and work with ANOVA and multiple regression. The class will finish with an introduction to non-parametric statistics. In addition, the students will consider journal articles and research concepts, and will prepare a small presentation using the concepts from the class. | Alvin Josephy | Wed | Freshmen FR Sophomore SO Junior JR Senior SR | Spring | Spring | ||||
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Steven G. Herman
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Program | FR–SRFreshmen - Senior | 8 | 08 | Day, Evening and Weekend | Su 13Summer Session II | Summer Ornithology is a three week bird-banding course taught entirely in the field. We leave campus on the first day, travel through some of the best birding country in Oregon, then over the next few days find and set up camp in a place where we can net, process, and band a sufficient number of birds to provide all students with appropriate experience. We spend the next two weeks netting, processing, banding, and releasing several hundred birds of about 25 species. We focus on aspects of banding protocol, including net placement, removing birds from nets, identification, sexing, ageing, and record-keeping. We balance the in-hand work with field identification and behavioral observations, and during the last week we tour Steens Mountain and the Malheur area. This course has been taught for over 30 years, and more than 24,000 birds have been banded during that time. Lower or upper-division credit is awarded depending of the level of academic achievement demonstrated. A photo essay on this program is available through and a slide show is available through . | Steven G. Herman | Mon Tue Wed Thu Fri Sat Sun | Freshmen FR Sophomore SO Junior JR Senior SR | Summer | Summer | ||||
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Heather Heying and Jennifer Calkins
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Program | JR–SRJunior - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | S 13Spring | Evolution provides an explanation for the extraordinary biological diversity on this planet. In this program, we will focus on macroevolutionary processes, specifically speciation and the evidence it leaves behind. In doing so, we will address several philosophical questions, including: How do we make claims of knowledge in an historical science such as evolution? We will investigate questions that may seem simple at first--What is a species?--but turn out to have myriad, conflicting answers. This complexity, and our attempts to discern the pattern in that complexity, will be our focus.We will use the vertebrates as our model with which to study evolution, reviewing the morphological and genomic history and diversity of this clade. Innovations have marked the history of vertebrates, including the origins of cartilage, bone, brains, endothermy, and the amniotic egg, which allowed for the invasion of terrestrial habitats. The transformation of existing structures to take on new functions has been another notable feature of vertebrate evolution: from swim bladder into lungs, hands into wings, and scales into both feathers and hair. This vertebrate diversification involved genomic innovation, particularly that involving the variation in the regulation of gene expression and regular bouts of gene duplication and diversification.Classroom work will include workshops and lectures in which active participation by all students will facilitate an enriching learning community. The labs will involve studying the focal traits of the primary two approaches to studying vertebrate evolution: morphological and molecular.In the wet lab, we will study the comparative anatomy of vertebrate skulls and skeletons, and dissect cats and sharks. We will also sequence genes and portions of the genome of various vertebrates. In the computer lab, we will use analyze our genomic data. We will combine our morphological and molecular investigations using software designed for systematic character analysis and for testing the pattern of selection across traits. Using this software, students will generate and analyze molecular and morphological datasets. There will be two multi-day field trips. Students will present short lectures on topics in genomics, molecular evolution, anatomy or physiology (e.g. circulatory system, musclephysiology). Students will also conduct extensive research on a current unresolved topic in vertebrate evolution, and will present that research in both a paper and a talk. | Heather Heying Jennifer Calkins | Junior JR Senior SR | Fall | Fall | |||
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Paul Pickett
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Course | SO–SRSophomore - Senior | 4 | 04 | Evening | Su 13Summer Session II | Water has been described as the "Oil of the 21st Century." The world’s limited supply of water faces huge challenges of human demand and contamination. This course explores the many dimensions of water resources and the critical problems of managing water for humans and the environment. An integrating focus for the course will be watersheds, where many dimensions of environmental function and human activity overlap. | Paul Pickett | Mon Wed | Sophomore SO Junior JR Senior SR | Summer | Summer |
