2014–15 Academic Catalog

2014-15 Undergraduate Index A-Z

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Biochemistry [clear]

Title		Offering	Standing	Credits	Credits	When	F	W	S	Su	Description	Preparatory	Faculty	Days	Multiple Standings	Start Quarters	Open Quarters
The Chemistry of Living Systems Lydia McKinstry and Paula Schofield biochemistry chemistry Signature Required: Fall Winter		Program	SO–SRSophomore–Senior	16	16	Day	F 14 Fall	W 15Winter			This upper-division science 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. 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.	Lydia McKinstry Paula Schofield		Sophomore SO Junior JR Senior SR	Fall	Fall Winter
Forensics and Criminal Behavior Rebecca Sunderman, Andrew Brabban and Toska Olson biochemistry biology chemistry communication gender and women's studies mathematics physiology sociology writing		Program	FR–SRFreshmen–Senior	16	16	Day	F 14 Fall	W 15Winter	S 15Spring		How can we think analytically and critically about crime in America? Why is crime such a central focus in modern American society? How is a crime scene analyzed? How are crimes solved? How can we prevent violent crime and murder? This program will integrate sociological and forensic science perspectives to investigate crime and societal responses to it. We will explore how social and cultural factors including race, class and gender are associated with crime and criminal behavior. In addition, we will consider criminological theories and explore how social scientists can help identify offenders through criminal profiling and forensic psychology.Through our forensics investigations, we will examine subjects including biology, chemistry, pathology and physics. We will study evidentiary techniques for crime scene analysis, such as the examination of fingerprints, DNA, blood spatter, fibers, glass fractures and fragments, hairs, ballistics, teeth, bones and body remains. Students will learn hands-on laboratory and field approaches to the scientific methods used in crime scene investigation. Students will also learn to apply analytical, quantitative and qualitative skills to collect and interpret evidence. Students can expect seminars, labs, lectures, guest speakers and workshops, along with both individual and group project work.This is an introductory program about science, critical thinking and the perspectives of sociology, chemistry and biology through the lens of crime analysis. Students interested in developing their skills in scientific inquiry, critical thinking and interdisciplinary studies should consider this program. Students who may not consider themselves to be "science" students are encouraged to enroll.		Rebecca Sunderman Andrew Brabban Toska Olson		Freshmen FR Sophomore SO Junior JR Senior SR	Fall	Fall Winter
Undergraduate Research in Scientific Inquiry Paula Schofield, Richard Weiss, David McAvity, Neil Switz, Brian Walter, Abir Biswas, Michael Paros, Clyde Barlow, Judith Cushing, Dharshi Bopegedera, Rebecca Sunderman, EJ Zita, Donald Morisato, Clarissa Dirks, James Neitzel, Sheryl Shulman, Neal Nelson and Lydia McKinstry biochemistry biology chemistry computer science mathematics physics Signature Required: Fall Winter Spring		Program	SO–SRSophomore–Senior	V	V	Day	F 14 Fall	W 15Winter	S 15Spring		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, with specific information listed in the catalog view. Contact faculty 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. (biotechnology) studies the physiology and biochemistry of prokaryotes of industrial and agricultural importance. Students who commit at least a full year to a research project, enrolling for 4 to 16 credits each quarter, will learn a broad range of microbiology (both aerobic and anaerobic techniques), molecular (DNA analysis and cloning), and biochemical techniques (chemical and pathway analysis, protein isolation). Students will also have opportunities for internships at the USDA and elsewhere, and to present data at national and international conferences. (chemistry) would like to engage students in two projects: (1) There is concern that toxic metals are found in unsafe quantities in children’s toys and cosmetics. I would like to engage a student in the quantitative determination of these metals using the AA and the ICP-MS. Students who are interested in learning to use these instruments and quantitative analysis techniques 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 background. (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. Another major area of interest is plant natural products, screening local plants for the presence of salicylates, which are important plant defense signals and 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) is interested in working with advanced computer topics and current problems in the application of computing to the sciences. His interests 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 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 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. (computer science) is interested 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. (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. (physics) develops optical instruments for use in biophysical and biomedical applications, including low-cost diagnostics. Projects in the lab are suitable for motivated students with quantitative backgrounds in physics, biology, chemistry, mathematics or computer science. (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. (physics), who has expertise in energy physics, modeling and organic farming, is researching sustainability and climate change. Many students have done fine projects on sustainable energy and food production in her academic programs. Zita is working with Judy Cushing to model land use impacts on climate change and with Scott Morgan to plan and facilitate sustainability projects on campus. More information on Zita's research is available at .		Paula Schofield Richard Weiss David McAvity Neil Switz Brian Walter Abir Biswas Michael Paros Clyde Barlow 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
Undergraduate Research in Scientific Inquiry with J. Neitzel James Neitzel biochemistry Signature Required: Fall Winter Spring		Research	SO–SRSophomore–Senior	V	V	Day	F 14 Fall	W 15Winter	S 15Spring		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. (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.	biochemistry, alternative energy, health sciences.	James Neitzel		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring