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2012-13 Undergraduate Index A-Z
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| Title | Offering | Standing | Credits | Credits | When | F | W | S | Su | Description | Preparatory | Faculty | Days | Multiple Standings | Start Quarters | Open Quarters |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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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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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Donald Morisato and Martha Rosemeyer
Signature Required:
Winter Spring
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Program | FR–SRFreshmen - Senior | 16 | 16 | Day | F 12 Fall | W 13Winter | S 13Spring | What should we eat? What is the link between diet and health? How do we define "organic" and "local" food? How are our agricultural practices linked to issues of sustainability?This program will take a primarily scientific approach to food and cooking. The topics will span a broad range of scale, from ecological agriculture to molecular structure, including sustainable production, the coevolution of humans and food, the connection between food and medicine, as well as the transformation of food through the processes of cooking and fermentation. Throughout history, food and cooking have not only been essential for human sustenance, but have played a central role in the economic and cultural life of civilizations. This interdisciplinary exploration of food will take a broad ecological systems approach as it examines the biology and chemistry of food, while also incorporating political, historical and anthropological perspectives.Students will directly apply major concepts learned in lectures to experiments in the laboratory and kitchen. Field trips will provide opportunities for observing food production and processing in the local community. Program themes will be reinforced in problem-solving workshop sessions and seminar discussions focused on topics addressed by such authors as Michael Pollan, Harold McGee, Gary Paul Nabhan, Sidney Mintz and Sandor Katz.In fall quarter, we will introduce the concept of food systems, and analyze conventional and sustainable agricultural practices. We will examine the botany of vegetables, fruits, seed grains and legumes that constitute most of the global food supply. In parallel, we will study the genetic principles of plant and animal breeding, and the role of evolution in the selection of plant and animal species used as food by different human populations. We will consider concepts in molecular biology that will allow us to understand and assess genetically modified crops.In winter quarter, we shift our attention to cooking and nutrition. We will explore the biochemistry of food, beginning with basic chemical concepts, before moving on to the structure of proteins, carbohydrates and fats. We will study meat, milk, eggs, vegetables and cereal doughs, and examine what happens at a biochemical level during the process of cooking and baking. We will explore how our bodies digest and recover nutrients, and consider the physiological roles of vitamins and antioxidants, as well as the complex relationship between diet, disease and genetics. Finally, we will study the physiology of taste and smell, critical for the appreciation of food.In spring quarter, we will examine the relationship between food and microbes, from several different perspectives. We will produce specific fermented foods, while studying the underlying biochemical reactions. We will also consider topics in microbiology as they relate to food safety and food preservation, and focus on specific interactions between particular microbes and the human immune system. | Donald Morisato Martha Rosemeyer | Freshmen FR 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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Paula Schofield, Brian Walter, Richard Weiss, Abir Biswas, Michael Paros, Clyde Barlow, Benjamin Simon, Judith Cushing, Dharshi Bopegedera, Rebecca Sunderman, EJ Zita, Donald Morisato, Clarissa Dirks, James Neitzel, Sheryl Shulman, Neal Nelson and Lydia McKinstry
Signature Required:
Fall Winter Spring
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Program | SO–SRSophomore - Senior | V | V | Day | F 12 Fall | W 13Winter | S 13Spring | Rigorous quantitative and qualitative research is an important component of academic learning in Scientific Inquiry. Research opportunities allow science students to work on specific projects associated with faculty members’ expertise. Students typically begin by working in an apprenticeship model with faculty or laboratory staff and gradually take on more independent projects within the context of the specific research program as they gain experience. Students can develop vital skills in research design, data acquisition and interpretation, modeling and theoretical analysis, written and oral communication, collaboration and critical thinking. These are valuable skills for students pursuing a graduate degree or entering the job market.Faculty offering undergraduate research opportunities are listed below. Contact them directly if you are interested. (chemistry) works with biophysical applications of spectroscopy to study physiological processes at the organ level, with direct applications to health problems. Students with backgrounds in biology, chemistry, physics, mathematics or computer science can obtain practical experience in applying their backgrounds to biomedical research problems in an interdisciplinary laboratory environment. (geology, earth science) studies nutrient and toxic trace metal cycles in terrestrial and coastal ecosystems. Potential projects could include studies of mineral weathering, wildfires and mercury cycling in ecosystems. Students could pursue these interests at the laboratory-scale or through field-scale biogeochemistry studies taking advantage of the Evergreen Ecological Observation Network (EEON), a long-term ecological study area. Students with backgrounds in a combination of geology, biology or chemistry could gain skills in soil, vegetation and water collection and learn methods of sample preparation and analysis for major and trace elements. (chemistry) would like to engage students in two projects. (1) Quantitative determination of metals in the stalactites formed in aging concrete using ICP-MS. Students who are interested in learning about the ICP-MS technique and using it for quantitative analysis will find this project interesting. (2) Science and education. We will work with local teachers to develop lab activities that enhance the science curriculum in local schools. Students who have an interest in teaching science and who have completed general chemistry with laboratory would be ideal for this project. (computer science, ecology informatics) studies how scientists might better use information technology and visualization in their research, particularly in ecology and environmental studies. She would like to work with students who have a background in computer science or one of the sciences (e.g., ecology, biology, chemistry or physics), and who are motivated to explore how new computing paradigms can be harnessed to improve the individual and collaborative work of scientists. Such technologies include visualizations, plugins, object-oriented systems, new database technologies and "newer" languages that scientists themselves use such as python or R. (biology) aims to better understand the evolutionary principles that underlie the emergence, spread and containment of infectious disease by studying the coevolution of retroviruses and their primate hosts. Studying how host characteristics and ecological changes influence virus transmission in lemurs will enable us to address the complex spatial and temporal factors that impact emerging diseases. Students with a background in biology and chemistry will gain experience in molecular biology techniques, including tissue culture and the use of viral vectors. (mathematics) is interested in problems in mathematical biology associated with population and evolutionary dynamics. Students working with him will help create computer simulations using agent-based modeling and cellular automata and analyzing non-linear models for the evolution of cooperative behavior in strategic multiplayer evolutionary games. Students should have a strong mathematics or computer science backgroun. (organic chemistry) is interested in organic synthesis research, including asymmetric synthesis methodology, chemical reaction dynamics and small molecule synthesis. One specific study involves the design and synthesis of enzyme inhibitor molecules to be used as effective laboratory tools with which to study the mechanistic steps of programmed cell death (e.g., in cancer cells). Students with a background in organic chemistry and biology will gain experience with the laboratory techniques of organic synthesis as well as the techniques of spectroscopy. (biology) is interested in the developmental biology of the embryo, a model system for analyzing how patterning occurs. Maternally encoded signaling pathways establish the anterior-posterior and dorsal-ventral axes. Individual student projects will use a combination of genetic, molecular biological and biochemical approaches to investigate the spatial regulation of this complex process. (biochemistry) uses methods from organic and analytical chemistry to study biologically interesting molecules. A major focus of his current work is on fatty acids; in particular, finding spectroscopic and chromatographic methods to identify fatty acids in complex mixtures and to detect changes that occur in fats during processing or storage. This has relevance both for foods and in biodiesel production. The other major area of interest is in plant natural products, such as salicylates. Work is in process screening local plants for the presence of these molecules, which are important plant defense signals. Work is also supported in determining the nutritional value of indigenous plants. Students with a background and interest in organic, analytical or biochemistry could contribute to this work. (computer science) and (computer science) are interested in working with advanced computer topics and current problems in the application of computing to the sciences. Their areas of interest include simulations of advanced architectures for distributed computing, advanced programming languages and compilers, programming languages for concurrent and parallel computing and hardware modeling languages. (biology, veterinary medicine) is interested in animal health and diseases that affect the animal agriculture industry. Currently funded research includes the development of bacteriophage therapy for dairy cattle uterine infections, calf salmonellosis and mastitis. A number of hands-on laboratory projects are available to students interested in pursuing careers in science. (organic, polymer, materials chemistry) is interested in the interdisciplinary fields of biodegradable plastics and biomedical polymers. Research in the field of biodegradable plastics is becoming increasingly important to replace current petroleum-derived materials and to reduce the environmental impact of plastic wastes. Modification of starch through copolymerization and use of bacterial polyesters show promise in this endeavor. Specific projects within biomedical polymers involve the synthesis of poly (lactic acid) copolymers that have potential for use in tissue engineering. Students with a background in chemistry and biology will gain experience in the synthesis and characterization of these novel polymer materials. Students will present their work at American Chemical Society (ACS) conferences. (computer science) isinterested in working with advanced computer topics and current problems in the application of computing to the sciences. Her areas of interest include simulations of advanced architectures for distributed computing, advanced programming languages and compilers, programming languages for concurrent and parallel computing, and hardware modeling languages. (biology) is interested in immunology, bacterial and viral pathogenesis, vaccine development and gene therapy applications. Recent focus has been on developing novel methods for vaccine delivery and immune enhancement in finfish. Specific projects include using attenuated bacteria to deliver either protein-based or nucleic acid vaccines in vivo and investigating bacterial invasion mechanisms. In collaboration with (faculty emerita) other projects include characterization of bacteriophage targeting the fish pathogen and elucidation of phage and host activities in stationary-phase infected with T4 bacteriophage. Students with a background in biology and chemistry will gain experience in laboratory research methods, including microbiological techniques, tissue culture and recombinant DNA technology, and may have opportunities to present data at regional and national conferences. (inorganic/materials chemistry, physical chemistry) is interested in the synthesis and property characterization of new bismuth-containing materials. These compounds have been characterized as electronic conductors, attractive activators for luminescent materials, second harmonic generators and oxidation catalysts for several organic compounds. Traditional solid-state synthesis methods will be utilized to prepare new complex bismuth oxides. Once synthesized, powder x-ray diffraction patterns will be obtained and material properties such as conductivity, melting point, biocidal tendency, coherent light production and magnetic behavior will be examined when appropriate. (mathematics) is interested in problems relating to graphs, combinatorial games and especially combinatorial games played on graphs. He would like to work with students who have a strong background in mathematics and/or computer science and who are interested in applying their skills to open-ended problems relating to graphs and/or games. (computer science, mathematics) has several ongoing projects in computer vision, robotics and security. There are some opportunities for students to develop cybersecurity games for teaching network security concepts and skills. In robotics, he is looking for students to develop laboratory exercises for several different mobile robotic platforms, including Scribbler, LEGO NXT and iRobot Create. This would also involve writing tools for image processing and computer vision using sequences of still images, video streams and 2.5-D images from the Kinect. In addition, he is open to working with students who have their own ideas for projects in these and related areas, such as machine learning, artificial intelligence and analysis of processor performance. (physics) studies the Sun and the Earth. What are the mechanisms of global warming? What can we expect in the future? What can we do about it right now? How do solar changes affect Earth over decades (e.g., Solar Max) to millennia? Why does the Sun shine a bit more brightly when it is more magnetically active, even though sunspots are dark? Why does the Sun's magnetic field flip every 11 years? Why is the temperature of the Sun’s outer atmosphere millions of degrees higher than that of its surface? Students can do research related to global warming in Zita's academic programs and in contracts, and have investigated the Sun by analyzing data from solar observatories and using theory and computer modeling. Serious students are encouraged to form research contracts and may thereafter be invited to join our research team. Please go to the catalog view for specific information about each option. | Paula Schofield Brian Walter Richard Weiss Abir Biswas Michael Paros Clyde Barlow Benjamin Simon Judith Cushing Dharshi Bopegedera Rebecca Sunderman EJ Zita Donald Morisato Clarissa Dirks James Neitzel Sheryl Shulman Neal Nelson Lydia McKinstry | Sophomore SO Junior JR Senior SR | Fall | Fall Winter Spring | |||
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James Neitzel
Signature Required:
Fall Winter Spring
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Research | SO–SRSophomore - Senior | V | V | Day | F 12 Fall | W 13Winter | S 13Spring | Rigorous quantitative and qualitative research is an important component of academic learning in Scientific Inquiry. This independent learning opportunity allows advanced students to delve into real-world research with faculty who are currently engaged in specific projects. Students typically begin by working in apprenticeship with faculty or laboratory staff and gradually take on more independent projects within the context of the specific research program as they gain experience. Students can develop vital skills in research design, data acquisition and interpretation, written and oral communication, collaboration, and critical thinking that are valuable for students pursuing a graduate degree or entering the job market. (biochemistry) uses methods from organic and analytical chemistry to study biologically interesting molecules. A major focus of his current work is on fatty acids; in particular, finding spectroscopic and chromatographic methods to identify fatty acids in complex mixtures and to detect changes that occur in fats during processing or storage. This has relevance both for foods as well as in biodiesel production. The other major area of interest is in plant natural products, such as salicylates. Work is in process screening local plants for the presence of these molecules, which are important plant defense signals. Work is also supported in determining the nutritional value of indigenous plants. Students with a background and interest in organic, analytical, or biochemistry could contribute to this work. | biochemistry, alternative energy, health sciences. | James Neitzel | Sophomore SO Junior JR Senior SR | Fall | Fall Winter Spring |
