2008-09 Catalog

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Program Description

Undergraduate Research in Scientific Inquiry

Revised Last Updated: 05/16/2008

Fall, Winter and Spring quarters

Faculty: Clyde Barlow chemistry, Dharshi Bopegedera chemistry, Andrew Brabban biology, Elizabeth Kutter microbiology, Judy Cushing computer science, Clarissa Dirks biology, James Neitzel biochemistry, David McAvity (FW) mathematics, physics, Lydia McKinstry organic chemistry, Donald Morisato biology, Neal Nelson computer science, Paula Schofield chemistry, Rebecca Sunderman chemistry, EJ Zita physics, Sheryl Shulman computer science, Richard Weiss computer science, mathematics

Faculty Signature Required: Students must contact individual faculty sponsors to make arrangements.

Major areas of study include lab biology and chemistry, computer science, health sciences, teaching, environmental sciences, applied mathematics, physics and astronomy. Upper division credit awarded for upper division work.

Class Standing: Sophomores or above; transfer students welcome.

Prerequisites: Negotiated individually with faculty sponsor.

A number of faculty members in this planning group are engaged in research projects that offer collaborative research opportunities for students. These provide an important aspect of work in the sciences that takes advantage of faculty expertise and Evergreen's flexible structure and excellent equipment. In general, students begin by working in apprenticeship with faculty and laboratory staff and gradually take on more independent projects within the context of the specific program.

Clyde Barlow (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.

Dharshi Bopegedera (chemistry) would like to engage students in three projects. (1) FTIR spectroscopy of free radicals. This project is for advanced chemistry students who are interested in using infrared spectroscopy to understand molecular properties of free radicals synthesized in situ in a microwave discharge. (2) An interdisciplinary study of drinking water in the South Puget Sound. Students who have completed general chemistry with laboratory can carry out this project. (3) Science and education. We will work with local teachers to develop lab activities that will 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.

Andrew Brabban (biotechnology) and Elizabeth Kutter (molecular biology) study microbiology and biotechnology, focusing particularly on bacteriophages–key model organisms in molecular genetics that play major roles in controlling microbial ecology worldwide. Their research involves approximately 12 students each year who explore bacterial metabolism and the infection process under a variety of environmental conditions, phage ecology and genomics and the application of phages as antibacterial agents in systems such as E. coli in infant diarrhea or the guts of livestock, Pseudomonas in human and dog-ear infections and Aeromonas salmonicida in furunculosis in local hatchery fish. Students are requested to commit at least a full year to the research project and to enroll for 6 to 16 credits each quarter.

Judith Bayard Cushing (computer science) studies how scientists might better use information technology in their research. 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, such as object-oriented systems and new database technologies, can be harnessed to improve the individual and collaborative work of scientists.

Clarissa Dirks (biology) aims to better understand the evolutionary principles that underlie the emergence, spread, and containment of infectious disease by studying the co-evolution 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.

Jim Neitzel (biochemistry) studies Bacteriophage T4, which has been a key model organism in molecular genetics for more than 50 years. Its infection of E. coli leads to rapid cessation of host DNA, RNA and protein synthesis. He is working to clone and over-express the many host-lethal genes that purify and characterize their protein products. The intent of this research is to determine specific functions, look at ways in which genes can be used to better understand bacterial metabolism, and examine the infection process under a variety of environmental conditions. Evergreen is the center for genomic analysis and database development for these phages, and work with phage ecology and their potential uses as antibiotics.

David McAvity (mathematics) is interested in problems in mathematical biology associated with population and evolutionary dynamics. Students working with him would 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.

Lydia McKinstry (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 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.

Donald Morisato (biology) is interested in the developmental biology of the Drosophila 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.

Rebecca Sunderman (inorganic/materials chemistry and 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.

Richard Weiss (computer science, mathematics) studies problems in computer vision and computer architecture. Computer vision is concerned with the processing of images and image sequences to automatically extract information that can be used for many tasks including robotic navigation and assembly, quantitative analysis of medical images, and the creation of geometric models of the environment for simulation and virtual reality. His research interests include object recognition, surface reconstruction, motion estimation, camera calibration, perceptual organization, recognition of handwritten characters, and machine learning.

E. J. Zita (physics) studies the Sun and other magnetized plasmas. Solar changes may affect Earth over decades (as in Solar Max) to millennia (as in climate change). Why does the Sun shine more brightly when it is more magnetically active? Why does the Sun's magnetic field flip every 11 years? We investigate solar mysteries by modeling the magnetic dynamics of the Sun. Students can study solar physics, plasma physics, and magneto hydrodynamics; use simple optical and radio telescopes and tools to observe the Sun from Olympia; and analyze data from satellites and supercomputers. Strong research students may be invited to join our summer research team in Olympia and/or Boulder.

Neal Nelson (computer science) and Sheryl Shulman (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.

Paula Schofield (polymer chemistry, organic chemistry) is interested in the interdisciplinary fields of biomedical polymers and biodegradable plastics. Specific projects within biomedical polymers involve the synthesis of poly (lactic acid) copolymers that have potential for use in tissue engineering. Also, research in the field of biodegradable plastics is becoming increasingly important, as bacterial polyesters show great promise in replacing current petroleum-derived plastics and in reducing the environmental impact of plastic wastes. Students with a background in chemistry and biology will gain experience in the synthesis and characterization of these novel polymer materials, and in biological procedures used to monitor biodegradation and biocompatibility. Students will also present their work at American Chemical Society (ACS) conferences.

Credits: 4, 8, 12 or 16 per quarter

Enrollment: 25

Books: www.tescbookstore.com

Program is preparatory for careers and future studies in chemistry, biology, computer science, environmental sciences, physics, astronomy, applied mathematics and education.

Planning Units: Scientific Inquiry

Program Revisions

Date Revision
May 16th, 2008 Richard Weiss has joined the group of faculty members sponsoring students wishing to do undergraduate research in science.