We propose to use grant funds to develop five new courses in computational science to support a new minor in ComputationalMethods and to create three, year-long integrative biology courses. 

            To integrate computational approaches to problem solving throughout the science curriculum, the Computer Science Program is giving leadership to the development of a minor in Computational Methods.  The minor is designed to enable students majoring in the sciences and mathematics to learn computational methods and their applications in their major area of study.  Students minoring in Computational Methods will take six courses, including three computer science courses -- Introduction to Computing, Data Structures, and Discrete Mathematics; one intermediate-level computer science course; and two computationally-intensive electives offered by the Computer Science Program or other science departments.  

            To augment the offerings of the Computational Methods minor, we propose to develop five new courses (Bioinformatics, Ecological Modeling, Emergent Systems, Visualization: Art and Science, and Geographic Information Systems and Science) that will count as electives in the minor. 

• Bioinformatics.  This course will provide an overview of the computational tools used in the identification and characterization of genes and proteins.  It will cover topics, including gene prediction, multiple sequence alignment, structural analysis, and gene and protein classification and include work with national sequence databases.  The format will include both lectures and in-class computer work.  Bioinformatics will be taught by Deepak Kumar (Associate Professor of Computer Science; relevant expertise in data structures) and Tamara Davis (Assistant Professor of Biology; relevant expertise in genetics/molecular biology). 

• Ecological Modeling.  In this course, students will translate their knowledge of biological processes and computer programming into computational explorations of ecological theory, and into decision-support tools for environmental management.  In the first third of the course, students will study, analyze, and discuss the major types of ecological models, such as compartment models of hydrologic, nutrient, and energy flows in ecosystems.  In the latter two-thirds of the course, students will build a computational model of an ecological process.  The course will be taught by Theodore Wong (Assistant Professor of Biology; relevant expertise in computational science and ecology) and Neal Williams (Assistant Professor of Biology; relevant expertise in ecology).

• Emergent Systems.  This course will be a multidisciplinary exploration of the interactions underlying both real and simulated systems, such as ant colonies, brains, earthquakes, biological evolution, artificial evolution, and computers.  These emergent systems are often characterized by simple, local interactions that collectively produce global phenomena not apparent in the local interactions.  The course is intended to provide an introduction to computer models of phenomena that emerge from simple interactions.  Students will be introduced to models using the NetLogo platform and progress to more sophisticated modeling environments.  The course will involve significant computer work.  Specific topics will include diffusion, pattern generation, neural function, and simple social organization.  Emergent Systems will be taught by Paul Grobstein (Professor of Biology; relevant expertise in computer models and biological systems), Alfonso Albano (Professor of Physics; relevant expertise in dynamical systems), and Douglas Blank (Assistant Professor of Computer Science; relevant expertise in cognitive science).

• Visualization: Art and Science.  This course, which will be developed by Douglas Blank, is designed to provide an understanding of the visualization of complex data through computer manipulation.  It will explore the tools necessary to allow the human mind to make sense of the vast amounts of data now collected by computers.  For example, patterns in geologic formations can become apparent if viewed in an appropriate 3D representation.  Students will explore available software tools for the processing, analysis, and visualization of numerical data and will be taught a simple scripting language to develop their own tools.  Topics include 2D and 3D representation, programming skills, data conversion principles, color representation, issues in cognitive perception, and an introduction to virtual reality.

• Geographic Information Systems and Science.  This lecture and laboratory course, taught by Maria Luisa Crawford (Professor of Geology; relevant expertise in GIS), will provide understanding of spatial data, its entry, analysis and display using ArcGIS and other GIS software.  Instruction will include cartographic principles of map production and interpretation, including map making, symbology, layout aesthetics, geographic coordinates and projections, and map scales.  Through practical applications, students will use GIS methods of inquiry to address problems through queries and analysis.  Students will analyze tabular and spatial data for geographic trends, patterns, and relationships and learn spatial statistical methods.

            In order to implement the new computational science courses, we will upgrade the computing equipment and software in the advanced computing laboratory created with funds from our 1996 HHMI grant.   To accommodate more sophisticated uses of this teaching laboratory, we plan to outfit the facility with upgraded desktop workstations (networked to a central backbone server via a high speed link) and peripherals. 

The biology curriculum has not undergone a substantial revision for more than a decade.  It has a hierarchical organization in which undergraduates choose among a variety of subject-specific, one-semester courses after completing an introductory sequence.  The weaknesses of the current curriculum are: 1) It does not reflect connections among the sub-disciplines of biology or levels of biological organization.  2) There is redundancy in material covered.  3) One semester is insufficient to provide students with a realistic inquiry-based laboratory experience.

The biology faculty will replace nine, semester-long, upper level courses with three, year-long courses, while continuing to teach 12 other existing upper-level courses without modification  The two-semester format provides the time and flexibility needed to integrate concepts and underlying principles across sub-disciplines and to allow lecture, discussion, and laboratory components to be more effectively united.  Biology majors will be required to take two of the new courses.

            Each new year-long course will be team taught by three biology faculty members and will focus on one level of biological organization.  Each course will address the same set of biological themes -- diversity, evolution, and common mechanisms in plants and animals -- and will incorporate elements from faculty research projects into the laboratory component.  All eight tenure-line faculty and one faculty member on continuing appointment will be involved in developing and teaching the courses.

            Integrative Molecular and Cellular Biology.   This new year-long course will focus on subcellular molecular mechanisms.  It will be taught by Tamara Davis (Assistant Professor; teaching expertise in genetics and molecular biology), Karen Greif (Professor; teaching expertise in cell biology and neurodevelopment), and David Prescott (Associate Professor; teaching expertise in biochemistry).  The course will discuss how molecules function individually and how they work together to affect cellular processes such as metabolism, transmission of information, and the regulation of gene expression.  It will be organized to emphasize the interconnectedness of the molecular disciplines of biology, particularly in experimental design.  For example, the complexity of development and disease can be investigated using a variety of genetic and molecular techniques to identify the genes and biochemical pathways involved.

            An investigative laboratory component, which will integrate biochemistry, genetics, and molecular biology techniques, will have small groups of students analyze characteristics of a protein they express and purify.  For example, students will work together in small groups to identify a putative DNA binding protein based on its similarity to a protein containing a known DNA binding motif.  This laboratory module can be easily integrated with Dr. Davis’ research program on imprinted genes.

To successfully implement Integrative Cellular and Molecular Biology, we will renovate an out-dated teaching laboratory space and equip it with computers and peripherals.  This teaching laboratory has undergone no major renovations beyond physical plant upgrades since its construction in the late 1950s.  To facilitate the cooperative, inquiry-based nature of the proposed exercises, the laboratory environment needs to be redesigned to enable small groups of students to work on a project and readily interact with one another and the faculty.  We propose to replace the existing four traditional low benches with four hexagonal workbenches, each of which will accommodate six students for a total of 24 students per lab period.  Pairs of workbenches will be connected by a low bench equipped with two laptop computers.  The facility will be equipped with a projection system; be wired for Internet access; and have wireless capability.  The proposed renovation is estimated to cost $650,000.  We are requesting $500,000 from HHMI toward the project, as the College has committed to providing the remaining $150,000 from other sources. 

            Integrative Cellular and Organismal Biology.  This course focuses on questions related to how organisms cope with environmental challenges by investigating the structure and function of cells and organ systems.  The first semester will begin with a discussion of the requirements of life at the level of individual cells and multi-cellular organisms, the structure of cell membranes and their role in the functioning of cells and organisms, and a comparative examination of single-cell organisms.  It will culminate with a systematic examination of how multi-cellularity was achieved.  The second semester will focus on challenges faced by all multi-cellular organisms by examining anatomy and physiology of organ systems and variations in these systems which allow animals to live in unique environments.  Four challenges to life will be addressed in multi-week, laboratory modules: locomotion and integration of information, respiration and metabolism, circulation, and ionic balance.  The course will be taught by Margaret Hollyday (Professor; teaching expertise in evolution and development), Stephen Gardiner (Senior Laboratory Lecturer; teaching expertise in morphology/anatomy, biological oceanography, and evolution), and Peter Brodfuehrer (Professor; teaching expertise in physiology and neurobiology). 

The laboratory exercises will contain investigative components that require students to be actively engaged with developing the hypotheses and making observations.  For example, in the module on locomotion and integration of information students will determine the function of sensory feedback in generating insect flight rhythm and leech swimming rhythm.  This will introduce students to the concept of central pattern generators, which are a focus of Dr. Brodfuehrer's research, and extracellular recording techniques from muscle and nerve.  Integrated Cellular and Organismal Biology will be taught in a multi-purpose teaching laboratory renovated with funds from our 1993 HHMI grant. 

Integrative Ecology, Evolution, and Behavior.  This course will be organized by spatiotemporal scale.  It will begin by exploring the biochemical, biophysical, and genetic processes that have direct ecological and evolutionary consequences and proceed in a sequence of increasing scale.  In this way, it will consider the physiological basis of behavior; the behavioral basis of population dynamics and community structure; the population-biological basis of ecosystem function; and the biogeochemical and anthropogenic drivers of global change.  Classroom experiences will emphasize application of concepts to complex natural systems.  Each concept will be introduced and examined in the context of either the eastern mixed deciduous forest or human modifications to the biosphere.

Laboratory and field experiences will build on the foundations of students’ previous investigations.  For example, students will undertake field studies to investigate the dynamics of old field and forest succession, the degree to which processes might be driven by variation and competition, and how these processes change across seasons.

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Last updated: 10/16/07