2014–15 Academic Catalog

2014-15 Undergraduate Index A-Z

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Computer Science [clear]

Title		Offering	Standing	Credits	Credits	When	F	W	S	Su	Description	Preparatory	Faculty	Days	Multiple Standings	Start Quarters	Open Quarters
Computability and Language Theory Sheryl Shulman, Richard Weiss and Neal Nelson computer science mathematics Signature Required: Winter		Program	SO–SRSophomore–Senior	16	16	Day	F 14 Fall	W 15Winter			This program will explore what computers can do, how we get them to do it and what they can't do. It is designed for advanced computer science students and students with an interest in both mathematics and computer science. The program covers topics in formal computer languages, systems of formal logic, computability theory and programming language design and implementation. Students will also study a functional programming language, Haskell, 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.These topics are offered in four distinct threads. The Formal Languages thread will cover the theoretical basis of language definitions, concluding with a study of what is computable. The Logic thread will cover traditional logic systems and their applications to programming languages and computer science. The Functional Language thread covers advanced programming techniques using the programming language Haskell. The Programming Language thread covers both the theoretical basis and practical implementation of programming languages by comparing the design and implementation of the four distinct programming language paradigms. Students will have a project opportunity to implement an interpreter for a small programming language.		Sheryl Shulman Richard Weiss Neal Nelson		Sophomore SO Junior JR Senior SR	Fall	Fall Winter
Computer Applications for the Fiber Arts: Pathways to Innovative Design Gail Tremblay and Richard Weiss art history computer science visual arts		Program	SO–SRSophomore–Senior	16	16	Day			S 15Spring		This interdisciplinary program links computational thinking with fiber arts. It is an opportunity for upper division students with expertise in either one of these fields to learn how to integrate that understanding with the other field. Students in this program will master a variety of techniques used by Fiber Artists to design both fine art and fine craftwork in the field. Everyone will design a warp, warp a loom, and draft and design treadling and weave patterns using a four-quadrant system to create color drafts on the computer. All students will weave a sampler, and learn a variety of off loom processes including felting, and a variety needle arts techniques in which they can use programmable Arduino LilyPad threads that will allow them to design art pieces which have elements that light up, make sound, or do other functions. Students will learn color theory, as it relates to design, and the history of Fiber Arts, in order to understand the evolution of the field over the past seventy-five years. Everyone will be required to design one major individual project and one major group project that they will exhibit at the end of the quarter. To create their projects students will be required to either use computer-aided design for drafting, apply computer science to a design problem, or use programmable threads as part of their projects. In the process, students will learn about the history of computer-aided design (CAD) in industrial and fine art production of fiber arts and robotics and automation. Students will investigate standard CAD tools, as well as theories needed to design programs to create original fiber arts designs. This history will start with the Jacquard loom first introduced in 1801 to allow weavers to automatically program brocade patterns by using a series of cards and end with modern computer driven looms that allow weavers to create complex multi-harness designs. Students will study computational thinking, which is the basis for all programming.Based on their prior experience with programming students will either learn the fundamentals of programming and algorithmic thinking, or for students who would like to do advanced work in computer science, there will be a weekly workshop on Machine Learning and Statistics. The work will include problem sets and programming.The program will include guest lectures by noted artists in the field and at least one field trip, All students will do a research paper and presentation on a fiber artist whose work combines computer applications for the development of fiber designs, and a short PowerPoint Presentation on their work to the class.;		Gail Tremblay Richard Weiss		Sophomore SO Junior JR Senior SR	Spring	Spring
Computer Science Foundations revised Sheryl Shulman, Rik Smoody, Richard Weiss and Neal Nelson computer science mathematics Signature Required: Winter		Program	FR–SRFreshmen–Senior	16	16	Day	F 14 Fall	W 15Winter			In this program, students will have the opportunity to learn the intellectual concepts and skills that are essential for advanced work in computer science and beneficial for computing work in support of other disciplines. Students will achieve a deeper understanding of increasingly complex computing systems by acquiring knowledge and skills in mathematical abstraction, problem solving and the organization and analysis of hardware and software systems. The program covers material such as algorithms, data structures, computer organization and architecture, logic, discrete mathematics and programming in the context of the liberal arts and compatible with the model curriculum developed by the Association for Computing Machinery's Liberal Arts Computer Science Consortium.The program content will be organized around four interwoven themes. The computational organization theme covers concepts and structures of computing systems from digital logic to the computer architecture supporting high level languages and operating systems. The programming theme concentrates on learning how to design and code programs to solve problems. The mathematical theme helps develop mathematical reasoning, theoretical abstractions and problem-solving skills needed for computer scientists. A technology and society theme explores social, historical or philosophical topics related to science and technology.		Sheryl Shulman Rik Smoody Richard Weiss Neal Nelson	Mon Tue Wed Thu	Freshmen FR Sophomore SO Junior JR Senior SR	Fall	Fall Winter
Computers and Cognition revised Ab Van Etten computer science consciousness studies		Program	FR–SRFreshmen–Senior	8	08	Evening			S 15Spring		What types of problems can be solved by computers? How do humans and computers differ in the types of problems they can solve? What is the future of computing, and will computers evolve an intelligence that includes what we would define as human thought? Can computers learn or create on their own? This program will explore the basics of computer science, how computers work, and their possibilities and limits. The program will include basic programming in Javascript, Web development, introductory computer electronics, and other computer science topics. We will contrast this with human cognition. We will then look at how computers will likely affect the way we live, work, and relate in the future. In seminar we will explore the issues surrounding machine vs human consciousness and strong artificial intelligence.		Ab Van Etten	Mon Wed	Freshmen FR Sophomore SO Junior JR Senior SR	Spring	Spring
Making Meaning Matter: The Ornament of Materiality Sarah Williams and Arlen Speights computer science consciousness studies cultural studies education gender and women's studies media studies somatic studies sustainability studies writing		Program	FR–SRFreshmen–Senior	16	16	Day and Evening	F 14 Fall				What do wampum, bitcoin, quantum computing, 3D printing, community, and forgetting have in common? What does the education of women have to do with reproduction and population growth? How do these "things" differ in connecting the ethereal with the physical? Non-verbal experiences evolve into expressible thoughts and ideas, which can be crafted and manufactured into material existence, all of which may carry value. What are the stakes of each step of reification, given their carbon footprint in an ecozoic anthropocene? What are alternative, sustainable processes for learning, computation, and currency?This program investigates this connection between meaning, making, and matter using scholarly as well as contemplative inquiry, experimental writing, moving images, and 3D printing. We’ll experiment with the role of optimism both in connecting mind and body and in debugging mental habits. Students will use 3D printing to bring an idea, developed through their writing, reading, and film experience into physical being. We'll analyze the relationships between an object’s material and non-material natures and values. Students will begin this program with a meditation retreat to become more familiar with bodily, felt experiences as the materiality of, and for, thought processes.The program is designed to be self-bootstrapping and evolving using innovative pedagogy, through which all students actively participating in activity planning and community building. Possible texts include by James Marcus-Bach, by Lambros Malafouris, by Nassim Taleb, by Neal Stephenson, by Martin Seligman, by Mark Frauenfelder, by David Loy, and by Ruth Ozeki. The program will continue as a studio component of the program “The Nature of Ornament” in the winter and spring quarters.		Sarah Williams Arlen Speights		Freshmen FR Sophomore SO Junior JR Senior SR	Fall	Fall
The Nature of Ornament: Chaos, Code, Cosmos Robert Leverich, Arlen Speights and Sarah Williams architecture art history computer science consciousness studies cultural studies gender and women's studies visual arts writing		Program	FR–SRFreshmen–Senior	16	16	Day		W 15Winter	S 15Spring		Ornament struggles to serve its ancient purpose, which is to bring order and produce cosmos out of chaos. --Bloomer, Why do we like some objects plain and others ornamented? Does ornament arise out of the making of the thing or is it applied afterward? What are the personal, political, and technological dimensions of ornament within different historical and cultural contexts? Are our possessions—from clothes and cars to laptops and smartphones—a form of ornament? Is thinking always mediated by, alongside,and through objects? How is our relationship to ornament changed by our ability to automate and cheaply create through new technology? From an evolutionary perspective might the neurological be ornamental and reason mere embellishment? Are the abstract, technical artifacts of mathematics and science devoid of ornament or can physical embodiment become mere ornament? We will consider how things—plain or adorned—shape and are shaped by our mental as well as our physical landscapes. Possible sites for our investigation of the cognitive life of vibrant matter are many and diverse: beads (abacus to jewelry), classic Greek running patterns, Islamic interlaces, cursive writing and digital typography, computer-generated art, the design and representation of web pages, 3D-printed objects, pattern creation using cellular automata, Native American figure/ground relationships, Bach’s well-ordered table of musical ornaments, the poetics of Gertrude Stein Louis Sullivan’s Rudolf Steiner’s sequenced instruction in form drawing (and its relationship to projective geometry), or Henry Goodyear’s Each student will choose to do program creative work in two of three interrelated studios each quarter: one focused on materials, tools, and making in wood, metals, clay and plaster; one focused on computer programming using the Processing language and 3D printing; and a third focused on ornament as a creative, gendered, evolutionary and projective process for adding value to materials, tools, making, programming, and printing. Although individual studio work will diverge in addressing how forms and patterns of ornamentation arise from nature, abstract systems, and cultural imperatives, our primary assessment and evaluation practices will focus on small group projects requiring the cultivation and ornamentation of individual work by students from each of the studios each quarter. Winter projects will center on the idea of – permeable surfaces and membranes that frame and modulate movements and flows. Spring projects will address the idea of – multi-dimensional forms and modules that address boundaries between inside and outside. Studio work and small group projects will lead to opportunities for substantive research and creative projects, including a week-long field study winter and a two-week field study or studio intensive spring quarter. Through all-program lectures/workshops, peer presentations, seminars and field trips, as well as studio projects, students will develop abilities in drawing and design, tools and materials (both low-tech and high-tech), and experimental forms of expressive, expository, and reflective thinking, speaking and writing. Book possibilities include: (Pallasmaa), (Trilling), (Pasztory), (Adoo), (Ingold), (Rasula and McCaffery), (Malafouris and Renfrew), (Teyssot), (France), (Stephenson), Ornament: The Politics of Architecture and Subjectivity (Picon), (Berssenbrugge), and (Tufte).		Robert Leverich Arlen Speights Sarah Williams	Mon Tue Wed Thu	Freshmen FR Sophomore SO Junior JR Senior SR	Winter	Winter Spring
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 D. McAvity David McAvity biology computer science mathematics 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. 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. (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.	theoretical biology, computer science, mathematics.	David McAvity		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring
Undergraduate Research in Scientific Inquiry with J. Cushing Judith Cushing computer science 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. (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.		Judith Cushing		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring
Undergraduate Research in Scientific Inquiry with N. Nelson Neal Nelson computer science 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. (computer science) is interested in working with advanced computer topics and current problems in the application of computing to the sciences. His 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.		Neal Nelson		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring
Undergraduate Research in Scientific Inquiry with S. Shulman Sheryl Shulman computer science 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. (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.		Sheryl Shulman		Sophomore SO Junior JR Senior SR	Fall	Fall Winter Spring