Keck-phase-2

1) Cover Page

• Enter prose or upload finished MS Word (tm) document here.

2) Project Abstract

• 150 word limit.

Earlham College requests $358,877 to develop multidisciplinary science curriculum modules and student/faculty research projects focusing on a common core problem: metals in the environment. This project will emphasize collaboration among our natural science departments, including biology, chemistry, computer science, geosciences, mathematics, and environmental science. Scientific research is becoming increasingly multidisciplinary, collaborative, and computational. Therefore, it is essential to train our students to develop multi-faceted approaches to problem solving that use both traditional laboratory techniques and computational methods. This project will introduce an important scientific problem (metals in the environment), ask students to collect and analyze data, and to make interpretations using different disciplinary perspectives. This idea of collaborative multidisciplinary learning will transform our undergraduate curriculum in the sciences and provide a model for programs among the sciences at other liberal arts colleges.

3) Project Narrative

• Maximum of 25 pages conforming to the following requirements:
• 8.5" by 11" paper
• Single spaced with all margins measuring at least 1"
• At least 12 point font in Times New Roman
• No more than 6 lines of type within a vertical space of 1"
• Proposals that do not comply with these requirements will not be accepted

• Question: 25 pages for the project narrative section or the whole application?
• Define module - thematic unit with specific learning objectives

1)Statement of the work to be undertaken and expected significance.

One important objective of scientific research applied to the environment is to determine the extent, the magnitude and the timing of adverse human impacts upon natural systems. In the past decades, major research efforts have addressed such problems and have led to both enhanced media attention as well as a groundswell of students who are interested in solving environmental problems. Science courses at the undergraduate level can capture student interest by explicity focusing on environmental problems.

One of the traditional difficulties in science education is teaching scientific content in a way that builds a strong understanding of the mechanisms of scientific inquiry. A large proportion of existing survey courses, often targeted at fulfilling institutional science requirements, introduce a large amount of content and require low levels of critical thought. Upper level courses more commonly focus on higher orders of problem-solving but are almost always discipline-specific and lack clear multidisciplinary links.

In this proposal, we reformulate the model of undergraduate science. In lower-division classes, we emphasize the mechanisms by which scientific knowledge is acquired in an environmental context, thus reinforcing student interest in environmental problems and teaching them the methods of authentic scientific inquiry. In upper-division courses, we will focus on the multidisciplinary aspect of modern science, by exposing students to the many different disciplinary lenses through which to view scientific problems.

2)Objectives/goals for the proposed work.

Major goals for this proposed work include:

• Bridging the gap for students between scientific research and science education by incorporating research modules into several lower and upper division courses
• Increasing student and faculty understanding of multidisciplinary use of field, laboratory, and computational methods to solve a particular problem
• Conducting an extensive study of the fate, transport and toxicity of metals in our local watershed
• Encouraging student interest in the sciences
• Expanding Earlham’s Environmental Sciences program by incorporating the study of environmental issues into the core courses of several disciplines
• Developing a workshop to teach faculty at other liberal arts colleges how to incorporate multidisciplinary research modules into their science courses

3)Project timeline keyed to the objectives/goals.

The implementation of this project begins with the development of the instrumentation and computer interfacing necessary to monitor field sites as well as the development of the first sets of curriculum modules to be integrated into both lower and upper division science courses. It continues with the development and implementation of the remainder of the proposed curricular modules and ends with plans to conduct a faculty development workshop to disseminate the process and content of developing integrated multidisciplinary research modules with a computational modeling component as well as the evaluation of the project.

Add David's notes to the timeline

2007:

Spring:

• Development of instrumentation and interfacing for field monitoring equipment
• Development of General Chemistry module

Summer:

• Development of Equilibrium and Analysis (Analytical Chemistry), Physical Geology, Cell Physiology and Ecological Biology course modules
• Deployment of field monitoring equipment

Fall:

• Implementation of General Chemistry, Ecological Biology, and Physical Geology course modules
• Development of Parallel and Distributed Computing and Hydrogeology course modules

2008:

Spring:

• Implementation of Equilibrium and Analysis, Hydrogeology, and Parallel and Distributed Computing course modules

Summer:

• Formative Evaluation
• Development of course modules for Environmental Chemistry, Geochemistry, Geophysics, In Silico (computational modeling course geared toward first year students), and Cell Physiology
• Refinement of existing course modules

Fall:

• Implementation of In Silico and Cell Physiology course modules

2009:

Spring:

• Implementation of Environmental Chemistry, Geochemistry, and Geophysics course modules

Summer:

• Dissemination (workshop presentation)
• Evaluation

Fall:

• Evaluation and writing of the final report

QUESTIONS: 1. WHERE DOES STATISTICS AND ENVIRONMENTAL MODELING GO? Mic 2. WHEN WILL THE POSTER SESSION AND THE COURSE/LECTURE/SEMINAR/COLLOQUIUM WHICH IS FACULTY/STUDENT LED BE IMPLEMENTED 3. WE ASSIGNED PROBABLE IMPLEMENTATION AND EVALUATION DATES FOR THE BIO COURSES WITHOUT INPUT FROM BIOLOGY. DO THOSE ABOVE MAKE SENSE?

4)Relation of the objectives to:

• the present state of knowledge in the field
  • Multi-disciplinary, computational, science pedagogy
  • Text from 3 page version (Mike and others)

Inquiry-based, multidisciplinary science education that involves computational technology is transforming the landscape of undergraduate learning in the natural sciences. Courses that are shaped around the practice and process of science rather than the rote mastery of facts and theories have been known to significantly enhance the learning of science in undergraduate courses (NRC, 1996; McConnaughay et al., 1999; Uno, 1999). In addition, the importance of computational science in answering disciplinary research questions requires rethinking standard science curricula at the undergraduate level. Currently, several national mandates call for this type of curriculum restructuring (NRC, 2003; PITAC, 2005).

Many institutions have recognized the need for innovative approaches to science education at the undergraduate level. Carleton College has established an Interdisciplinary Science and Math Initiative (CISMI) aimed at integrating the physical sciences and mathematics in undergraduate courses and research projects. Additionally, Carleton College is currently working on ways to integrate computational modeling across their curriculum to enhance learning. Carleton is also emphasizing computational science at all levels of the curriculum, which is similar in scope to our proposed project. Trinity University is also focused on interdisciplinary faculty and student research as well as interdisciplinary curricular development with their recently funded Keck Center for Macromolecular Studies; however, Trinity’s program has a major focus on the integration of biology and chemistry, while our proposed program uses biology, chemistry, geosciences, mathematical, and computational science methods to explore environmental problems. Shippensburg University of Pennsylvania has implemented an Interdisciplinary Watershed Research Laboratory for field-based environmental laboratories. This project is similar in scope to our proposed project, but primarily integrates biology and geography/earth science, while we are proposing to involve more disciplinary perspectives.

• work in progress by the project personnel under other support

There has been a long tradition of Earlham science faculty involvement in multidisciplinary and computational student/faculty research. In the last 20 years, faculty members in biology, geology and chemistry have been engaged in studies ranging from atmospheric measurements of mercury and aquatic ecosystem studies at the college's Dewar Lake Biological Research Station to determination of metal contamination in lake sediments. Across our science curriculum, a strong emphasis is placed on quantitative, analytical and research-based projects. Many of our research projects engage our student/faculty teams in multidisciplinary efforts; currently, our computer science faculty and students work with both biologists and chemists on computational projects. e.g. computational phylogenetic reconstruction and molecular dynamics simulations. For many years, our biology and chemistry departments have collaborated on a variety of research and curriculum projects, e.g. determination of atrazine concentration from agricultural runoff in local water sources and its effect on the physiological development of aquatic species.

Additionally, many of our science faculty have worked with state, municipal and public representatives to provide expert witness on local environmental issues. Examples of collaborative input to local issues include:

• Expert witness testimony relative to proposed plans to develop an industrial park - including a chromated copper arsenate (CCA) pressure treated lumber plant - over a pristine unconfined aquifer system within Richmond, Indiana city limits.

• Expert witness testimony concerning proposed plans for commercial development of recharge areas for highly-susceptible Public Community Water Supply (PCWS) sources.

What specifically can we reference here?

Ron and Springwood Lake data

• Charlie and NCSI workshops
• Charlie and Folding@Home?

• EPA metal requirements and research directions (Ron)

5)Concise description of methods and procedures for implementation and experimentation.

• Overview goes here

Curriculum modules will be incorporated into 6 introductory courses and at least 7 upper level courses in biology, chemistry, computer science, geosciences and mathematics. During the academic year, students taking courses that include these modules will be strongly encouraged to participate in a weekly, faculty facilitated seminar in which they will discuss their course experiences. At the end of each semester, students participating in courses that have these modules will be required to attend and present their group projects at a locally hosted poster session. Initially, the summer research component will involve developing and testing curriculum modules. In summers two and three, students will have the opportunity to conduct more advanced research related to metals in the environment including analyses of metals in a variety of environmental matrices, descriptions and quantifications of food chains and computational modeling of rates of biomagnification of metals at higher trophic levels, performance of whole-soil hydraulic conductivity tests and determination of soil mineral reactivities, and computer modeling of biochemical and groundwater processes. All students participating in summer research will have two opportunities each week to discuss the multidisciplinary perspectives related to their projects: faculty from all departments will facilitate a weekly seminar and students will discuss their research projects in a student-led seminar.

• Either by department or as a whole describe the summer research activities. Some of this is course module development and some "real" research. Developing local soil models, database (post grant).

• Each courses' plan goes below. We need to show linkages between each of these courses where possible, both intra and inter departmental.

chemistry

Throughout our projects, site-specific data will be collected and models will be used to assess the fate and transport of metal contaminants.

We propose to incorporate a new environmental chemistry module in our general chemistry class (CHEM 111, typical enrollment of 90). This unit will introduce students to fate and transport modeling by measuring the distribution coefficient, Kd, which is a common parameter used to estimate the concentration and movement of metal pollutants in ground water. Kd is a measure of the extent of interactions between a pollutant and the soil matrix and is one of the keys to the understanding of the mobility and persistance of metals in the environment. A distribution coefficient for copper has previously been measured in a standardized soil material (Dunnivant, 2002), and the procedure can be adapted to soils collected from our study sites.

The module will be conducted over two laboratory periods. The first week will consist of a spectroscopy lab, where the students will be introduced to atomic and molecular absorption for the determination of the metal concentration in water, and to infrared spectroscopy for the characterization of the soil. In the second week, students will use atomic spectroscopy to determine Kd of a metal (copper in year 1, and additional metals in subsequent years) in both standard soils, and soils collected from both our field and test sites.

The distribution coefficient for metal contaminants varies greatly with experimental conditions, both of the soil and the aqueous system (pH, ionic strength, concentrations of pollutants, etc.). This variability will be illustrated by looking at the effect of pH on Kd for the soils investigated. The results will be used to discuss such environmental issues as acid rain and metal mobilization. Using the Kd results obtained in the laboratory and some simple assumptions, students will calculate a retardation factor(R) for the movement of the metal through the soil/water system (R = (1 + (pb/ne) * Kd)), where pb is the bulk density of the soil and ne is the soil porosity at saturation) . The effects of the chemical changes on Kd and on retardation factor will be modeled using a spreadsheet based model. The soil Kd results will also be integrated in a database for use in transport modeling, and could be further studied in the student research projects in the Equilibrium and Analysis class (CHEM 331).

The Equilibrium and Analysis course (CHEM 331) is a sophomore level course with an approximate enrollment of 25 students per year. The module for this course will be conducted during a two-week laboratory (four lab meetings) and will use diffusive gradients in thin films (DGT) to determine the speciation of metals (Cu, Ni and Zn) in both simulated laboratory solutions as well as water samples obtained both from the field site and the off-campus site. The speciation results of the DGT study will be compared to the results obtained with the speciation model Visual MINTEQ, a freeware version of the program released by the United States Environmental Protection Agency (USEPA).

This experiment will replace two of our current labs designed to expose students to atomic spectroscopy. It will accomplish the same pedagogical goal of teaching students how to prepare samples and standards for atomic analysis, as well as provide them with hands-on experience with the equipment necessary for spectroscopic analyses. Moreover, students will now also learn about ion exchange, metal speciation, the environmental importance of bioavailability, as well as the power of computational modeling.

In DGT, metals are accumulated on an ion exchange resin imbedded in a hydrogel and covered with a diffusion layer of a different hydrogel and a filter (Zhang and Davison, 1995). In this technique, the transport of metal ions to the resin occurs only by molecular diffusion (ref), resulting in a direct linear relationship between the metal mass accumulated and the time of deployment (see figs 1 and 2 – from Zhang and Davison, 1995))

The advantages of DGT include its simplicity, relative independence from hydrodynamics of the system, multi-elemental capability and its inherent pre-concentration capabilities, which enables the measurement of even extremely small concentrations in solution. With this technique, only the labile forms of the metals in solution (i.e. the inorganic free metal forms and organic labile complexes) will be measured. In addition, since the labile inorganic and the labile organic complexes have different diffusion coefficients in the hydrogels, the concentration of each type of species can be determined by this method. Zhang and Davison (2000, 2001) have shown that by varying the properties of the diffusion hydrogel, both the organic and inorganic metal concentrations can be obtained. In addition, the authors demonstrated that a single DGT device, with a very restrictive pore size, could measure the labile inorganic concentration with only a small correction factor. When using a single DGT device, the total concentration of a metal in the solution must be determined, and the difference between that total value and the DGT value will represent the organically bound metal. Because of their well characterized nature, we will purchase the DGT device components from DGT Research Ltd during the first few years of implementation. As part of the summer research, we intend to characterize the diffusion coefficients of various metals and organic species (humic and fulvic acids) in polymers that we will synthesize. In addition, resins other than the standard Chelex (used to bind many +2 and +3 ions) can be explored for selectivity of other metals or oxidation states that are bound tightly to Chelex.

In practice, these devices are deployed into a well-stirred solution for times ranging from hours to days. After this time, the device is disassembled and the metals are then eluted from the resin using a nitric acid solution and analyzed using either graphite furnace atomic absorption spectroscopy (GFAAS) or inductively coupled plasma atomic emission spectroscopy (ICP-AES).

Three different systems will be tested using this method: a laboratory system with known parameters, a water sample from our field site, and a water sample from our remote site (Springwood Lake). These water samples can be tested both for endogenous metals as well as spiked laboratory samples. The water samples from the field site and remote site will be characterized by the teaching assistants for the additional parameters required for Visual MINTEQ modeling, but not measured directly by the students in the course (such as anions).

Previous literature indicates that DGT can accurately predict speciation under a variety of conditions if the water parameters are well characterized (refs). In particular, it is important to know precisely not just the DOC (Dissolved Organic Carbon), but the percentage of DOC that is humic acid vs. fulvic acid. While both humic acid and fulvic acid complexes diffuse much more slowly than the inorganic form, humic acid complexes diffuse about twice as slowly as fulvic acid complexes. In addition, both acid concentrations have a large impact on the speciation model predictions (Zhang and Davison, 2000). The effect of varying these parameters on the fit of the model to the experimental data will be explored.

This experiment will be done over four lab periods. During the first lab period, the students will set up the water samples with the DGT devices and allow them to incubate until the following laboratory period (48 hours). They will also be introduced to the trace metal analysis equipment (GFAAS and ICP-AES) and will prepare and analyze standards and samples for major cations using ICP-AES. During the second lab period, students will elute the devices and analyze them using the appropriate method. During the third and fourth lab period, the students will utilize the Visual MINTEQ program to calculate the speciation and then compare with the measured results. As part of the laboratory samples, students can explore the effects of pH, dissolved organic content and ionic strength on both the DGT results as well as the agreement between the model calculations and the DGT measurement. Students will also be provided with data from the Principles of Chemistry class on Kd and its variation with the same parameters. The effects both of transport and bioavailability on the ultimate toxicity of a given metal will be discussed.

This experiment will replace two of our current labs designed to expose students to atomic spectroscopy. It will accomplish the same pedagogical goal of teaching students how to prepare samples and standards for atomic analysis, as well as provide them with hands-on experience with the equipment necessary for spectroscopic analyses. Moreover, students will now also learn about ion exchange, metal speciation and the environmental importance of bioavailability.

The environmental chemistry and toxicology course (CHEM 371) is a new course that will be introduced in the spring of 2007. This course will be an upper level chemistry course with a prerequisite of equilibrium and analysis. The expected enrollment will be 10-15 students.

Two modules will be developed for this course. As an extension to the work performed in Equilibrium and Analysis, the first module will involve the in situ deployment of DGT devices at both our field site and our remote site. Data on temperature, pH, dissolved organic carbon, alkalinity, as well as major cations (Ca2+, Mg2+, Na+ and K+), major anions (SO42- and Cl-), and sulfide concentrations will be collected for both sites. In addition, further characterization of the dissolved organic content for each site will be performed in order to accurately quantify the amount of humic acid and fulvic acid present (this data will then be provided to the Equilibrium and Analysis course to help in their calculations). For this model, we will deploy several DGT devices, each of them corresponding to a different diffusion layer hydrogel. The data obtained will provide a direct measure of the metal speciation. Visual MINTEQ will also be used to model each metal speciation.

A second module will involve the use of a model organism, Daphnia magna, to monitor toxicity of a metal in various water samples and the use of the biotic ligand model (BLM) to predict toxicity under the same conditions. Toxicity testing with a specific organism is the most accurate method of determining the toxicity of a metal in the environment, but also the most time consuming. The biotic ligand model, which treats the organism of interest as a ligand which is competing for metal binding with the other ligands in the solution, is of great interest because of its ability to greatly simplify the measurement of potential toxicity.

Well characterized water samples from our two test sites, as well as laboratory samples for various metals will be used in the study. Daphnia magna, also called water fleas, are crustaceans commonly used in environmental toxicity studies. These are easy to handle and grow as well as inexpensive. Using these organisms, students will first construct toxicity curves for known metals (Cu, Cd, Zn) in synthetic water solutions with controlled parameters. These studies will then be repeated using water from the three systems described above. The results will then be compared to those predicted by the BLM (ref) to demonstrate the usefulness of such a model as well as help students understand how they are constructed.

biology

Keck-Eco Bio and field module now up with John I's and Bill B's blessing. Amy & Peter are looking at cell phys module now.

The ecological impact of heavy metal pollution at Springwood Lake will be explored through modules within two field biology classes and through summer research. We propose to develop a module for Biology 111, Ecological Biology. This is an introductory level course, with approximately 100 students annually. Non-science majors typically represent 50 to 65% of the class size. Students will help inventory the biota of the lake in a sampling lab, share data, interpret data, and be introduced to population modeling computation. Learning outcomes include: • Gaining an appreciation for the interrelationships and natural history dynamics of ecological communities. • Understanding the importance of quantitative techniques and reasoning in the description and study of complex ecosystems. • Gaining the ability to critically evaluate sampling protocol efficacy and the quality of quantitative data. In this module, each lab group in EcoBio will make a field trip to Springwood Lake and learn aquatic biota sampling techniques. Plants will be sampled manually; invertebrates by plankton tows, nets, and dredges; and vertebrates by seine or fyke nets. Students will work in groups of four or five and each group will gather higher taxon-specific data such as mensural and meristic measurements, age estimations, population density and biomass calculations. Portions of samples will also be preserved for metal analysis by the chemistry department during summer research. Groups will share data and an accurate biotic inventory of the lake will emerge.

This module would be introduced in the Fall of 2007 and continue, allowing us to track changes in populations which will be vital information for assessing the significance of heavy metal pollution at the lake.

Biotic inventory work and food-chain construction will be continued in a module to be developed for Biology 346, Vertebrate Zoology. This is an upper-level course with a typical enrollment of 20-25 students. Learning outcomes for this module include: • Learning the theoretical concepts as well as the field techniques of population ecology of vertebrates. • Learning about vertebrates in aquatic ecosystems and aquatic toxicology and how geology and chemistry are vital to understanding these fields. • Being exposed to the application of contemporary computational methods used in vertebrate population modeling.

In this module, students will use mark-recapture studies (using injection of passive integrated transponders [PIT tags]) to estimate population sizes and standing crop biomass of macrovertebrates (fish and turtles). Gut content analysis (by dissection for invertebrates, and non-destructive stomach flushing of vertebrates) will be used to determine food chains. Blood and/or tissue samples (non-destructive whenever possible) will be saved for analysis of metals during summer research, and these values will be related to the trophic ecology of individual species. We would also do sampling of tissues of these same organisms in other county lakes as reference values for this general region.

This module will be introduced in the Spring of 2008, and repeated annually, with special emphasis on following tagged animals and investigating evidence for bioaccumulation of metals in these animals.

It is predicted that some students involved in this course work will continue to work on the problem in summer research in 2008 and 2009. The above course work will establish the populations and food-chains involved at Springwood Lake, while summer research will focus on the actual analysis of metals in representative organisms from the lake. In addition to samples saved from the course work discussed above, students will re-sample fish and turtles. Some fish will be sacrificed for analysis of metals in specific tissues, specifically gill, liver, kidney and gonad. Metal analyses will be performed by the Earlham chemistry department. Bioaccumulation and biomagnification at higher trophic levels will be assessed. Tissues will also be processed for microscopy and examined for histopathologic evidence of metal intoxication using routine histologic techniques which are currently being used at Earlham.

Do I need to add chemistry’s exact methodology here?

To study cellular responses to metals, a laboratory module will be developed for Biology 341, Cell Physiology. This is a sophomore level course which typically has an enrollment of approximately eighty students. Over the course of the semester, students will investigate the effects of heavy metals on the expression of heat shock proteins in fish red blood cells, explore the chemical and physical variables that effect toxicity of metals in aqueous environments, work with complex data sets and multivariate statistics, and become introduced to bioinformatics.

Learning outcomes will include: • Students will gain an understanding of how cells and organisms respond to heavy metal intoxication. • Students will understand how bioavailability of heavy metals is a function of water characteristics and see how chemistry and hydrogeology play important roles in toxicology. • Students will gain experience in experimental design, multivariate statistics, spectrophotometry, protein quantification, and Western blot analysis. • Students will be introduced to bioinformatics.

Fish red blood cells are an ideal system for studying cellular responses to heavy metals. Because they are nucleated and capable of transcription, translation, and protein synthesis, fish red blood cells are a valuable model for studying cellular responses to a variety of stresses (Currie and Tufts, 1997). Fish red blood cells reliably respond to heavy metal stress by the expression of heat shock proteins (HSPs), and is some cases do so in a graded, dose-dependent manner (Fulladosa, et al, 2006.)

In weeks 1-3 of this lab module, readings and worksheets will introduce students to the concepts of heat shock proteins, models for studying cell physiology, heavy metals and environmental toxicology, aqueous environments from a chemistry and hydrogeology perspective, and protein analysis. After this introductory material, students will help choose what chemical and physical variables to add to the protocol; choosing variables that most closely approximate those found at Springwood Lake that would affect the bioavailability of metals.

Lab groups will be assigned the parameter that they will be testing: controls, metals as stressors, or metals plus chemical or physical variables affecting bioavailability. During this period they will also construct standard curves for protein quantification on spectrophotometers with bovine serum albumin and the Bradford method.

In weeks 4-7, the wet lab will be conducted. We will purchase juvenile or adult rainbow trout, Oncorhynchus mykiss, from a regional supplier. Ideally, the trout will be kept in Earlham aquaria for an aclimitization period of one month. Trout will be anesthetized in buffered 3-aminobenzoic acid ethyl ester (MS-222, Sigma) and blood drawn from the caudal vein. The red blood cells will be separated by centrifugation and then incubated in Hank’s Balanced Salts Solution prepared with known amounts of CdCl2, PbCl2, or K2Cr2O7, either alone or in combination with chemical or physical variables such as nitrates, sulfates, organic matter, anions, acid or alkaline conditions or variable temperatures. Cells will be incubated at 20oC for 2 hours and samples prepared for protein analysis by lysis, centrifugation and supernatant collection. Total protein will be determined by the Bradford method, and gel electrophoresis and Western blot will be used to detect hsp70 using murine anti-hsp70 antibody (Sigma). Students will be able to semi-quantitatively analyze changes in hsp70 expression among the various groups. Groups will share their data with the entire class.

Weeks 8-12 will involve data interpretation and multivariate statistical analysis, as well as the bioinformatics portion of the module. A member of Earlham’s math department will help with the instruction of the multivariate statistics.

The bioinformatics portion of this module will center around the metallothionein family of proteins. Metallothioneins (MTs) are polypeptides, and like heat shock proteins, they are produced in response to metal intoxication in a number of organisms and models, including fish red blood cells (Bauman, et al, 1993.) MTs are known to help protect cells against cadmium toxicity; they bind a variety of metals with abundant cysteine residues, which are highly conserved across phyla (Klaassen, et al, 1999). Students will use Biology Workbench, SwissProt, and ClustalW to construct gene trees and phylogenies using the MT family of genes. They will also explore MT structure, folding, function and molecular evolution using PDB and ConSurf.

The wet lab portion of this module is a modification of the current Cell Physiology laboratory using similar if not identical methods and equipment. In the current lab, students investigate the expression of hsp70 in hemolymph of the tobacco hornmworn, Manduca sextans, as induced by a variety of stressors. This particular module will be developed in the summer of 2007 with summer research students performing all aspects of the lab, including preparation, writing a lab manual, and trouble-shooting. It will be the first time that multivariate statistics and bioinformatics will be taught in this course.

geology

Introductory-Level Course Module-GEOS211 Physical Geology

Physical Geology at Earlham is an introductory-level course that is taken by both science and non-science majors. Students in this course who are non-science majors generally lack confidence in their ability to “do” science and have had little to no exposure to an inquiry-based science classroom. In this course module, students will apply fundamental geologic methods of analysis to an environmental project. By the end of this module, students will be able to:

Use web-based GIS to display and organize data relevant to the characterization of the project site.

Use field and laboratory observations to describe the geology of the project site.

Organize and analyze geochemical data to display the concentration distribution of heavy metals in lake bottom sediments at the project site.

Establish a chronology of heavy metal loading to the project basin via interpretation of heavy metal stratigraphy.

Create a scientific report synthesizing the results of the project and suggesting areas for further study.

Upon completion of the project, selected students will present results to other introductory-level students participating in courses with applied modules. All students will then be required to write a report describing the different approaches and results each of these courses takes in studying this environmental problem.

This module will use the final four laboratory sessions in Physical Geology. Students will have a basic background in geology and will be able to apply that knowledge to the local area. Each laboratory section has a maximum of twenty-two students, with one professor and one upper-level undergraduate teaching assistant.

Week One: Readings and worksheets will focus on the general problem of metals in the environment with emphasis on lake sediments as pollutant archives. Readings will be keyed to discussions of the hydrologic cycle with an emphasis placed on the connection between groundwater flow and subsurface geology. Students will begin to learn how to use web-based GIS to create displays of the study area.

Week Two: Field trip to the project site. Students will examine the geology and hydrology of the project site (Springwood Lake) and participate in a demonstration of sampling a sediment core from the lake.

Week Three: In teams, students will observe and describe a suite of sediment cores to determine terms of sediment composition, texture, color, sorting, fabric and sedimentological characteristics.

Week Four: Students will be given geochemical data keyed to the cores described in Week Three (geochemical data will have been collected by upper-level geochemistry students or will have been collected as part of a summer research project). Students will be required to plot and analyze this data and make interpretations about the concentrations of heavy metals in Springwood Lake over time as a result of their analysis. Students will then write a full scientific report of this project and share the results with other introductory-level science students working on different aspects of this project.

Upper-Level Course Module: GEOS 362 Hydrogeology

Hydrogeology at Earlham is taught with an emphasis on practical application of theoretical concepts. Two course modules will be developed for hydrogeology; one each for each of the project sites. These course modules will enrich student comprehension of the significance of ground water/surface water interaction in the vicinity of the project sites and will develop student capabilities for collecting, analyzing, displaying and interpreting ground water data.

At the on-campus field site, students will be active participants in designing, installing and managing data collection from ground water monitoring devices. instrumentation instrumenting the

At the conclusion of these modules students will be able to:

• Evaluate data collection requirements (number and spacing of piezometers, monitoring wells)Prepare geologic and hydrostratigraphic unit cross-sections from well-boring data.

• Obtain laboratory measurements of whole soil porosity for each hydrostratigraphic layer at each of the project sites.

• Collect, tabulate and display ground water elevation data and prepare detailed maps of potentiometric surfaces.

• Determine horizontal hydraulic conductivity values for saturaed media at each project area.

• Computationally analyze potentiometric, porosity and permeability data to calculate rates of ground water flow and formulate predictions of ground water flow behavior.

computer science

Develop data model and entry/display interface for the local data will be accumulating.

In parallel and distributed programming do protein folding in the presence of metals (David and Mike).

Links to Green Science and HIP, experience with developing data models and deploying interactive, graphical, interfaces.

mathematics

Math 120, Elementary Statistics, is a general education course taught each semester in which students are introduced to the key notions of statistics: descriptive statistics and inference testing. We would make use of the data sets in teaching students how to do typical tasks of descriptive statistics: measures of central tendency, measures of dispersion, and construction and interpretation of graphical displays of statistical information (univariate and bivariate data). Data sets from Springwood Lake and our back-campus field site would help students grasp the differences in origin and potential uses between observational and experimental data. Probably the greatest advantage of using this data is that it would be real to the students. They would know the sites (and potentially the historical context of those sites) where the data was collected, and the students involved in the collection and experimental designs.

Math 300, Statistics, is a calculus-based introductory course which we teach every other fall semester. We would make similar use of real data sets as for Math 120.

EnPr 242, Environmental Models, is taught each fall and is required for all students who are earning a major or a minor in either environmental science or environmental studies. This course is taught by a mathematics professor and includes coverage of applications involving biology, chemistry, computer science, geology, and mathematics. One of the topics is the chemistry of hazardous materials, and "metals in the environment" data from our local area would be quite. (Mike, I will continue to think about it, but I'm having a hard time seeing the connection with this course -- we don't do any statistics in it. We work on interpolation and analysis of spatial data sets for a little while, as well as considering how pollution spreads in the groundwater (not streams) and in the air. That might be a place to use some of the data. We do some population viability work, but I don't see how the metals data will apply to that.)

6) Technical problems that may be encountered and how they will be addressed.

Two aspects, multi-disciplinary, computational, pedagogy and then all the science. Almost all of the individual pieces have been deployed elsewhere, we are adapting and refining them...

7) Roles of all key project personnel.

Each of us needs to provide our own prose here.

Michael Deibel - As part of this project, Dr. M. Deibel will help develop course modules for environmental chemistry and equilibrium and analysis. In addition, he will conduct independent research with students to analyze water, soil and biological samples for various metals.

Corinne Deibel

John Iverson

Mic Jackson

Dave Matlack

Ron Parker

Charlie Peck

Meg Streepey - Dr. Streepey will develop the course module for introductory geosciences. She will also direct the management and coordination of the multidisciplinary student seminar programs. (unless somebody else wants it :)

Lori Watson - Dr. L. Watson will assist in the development and implementation of course modules for general chemistry. In addition, she will coordinate the program assements during years 2 and 3 of the grant.

8) Organization chart of key project personnel.

Description

.

9) Description of facilities, equipment and resources available for the project.

The science complex at Earlham consists of three interconnected buildings, Dennis Hall (Computer Science, Geology, Physics, and Mathematics), Noyes Hall (Science Library, large computer lab) and Stanley Hall (Biology and Chemistry) with a net square footage of 76,000. .

The laboratory portion of the chemistry modules will utilize two laboratories (one for general chemistry/equilibrium and analysis and a separate lab for environmental chemistry). These labs have a total square footage of 2950 (1719 for gen chem, 1230 for p chem) and a combined total of 11 hoods and each lab has benchspace for approximately 20 students.

Analysis of metals will be conducted on two separate instruments: an inductively coupled atomic emission spectrometer (ICP-AES) and a combination flame/graphite furnace atomic absorption spectrometer (GFAAS). The ICP-AES (Perkin Elmer Optima 4100DV) is a dual view, multielement analyzer capable of analyzing up to 50 elements in under a minute. We have also recently installed an ultrasonic nebulizer (CETAC U-5000-AT), which will increase our sensitivity by a factor of 10. The GFAAS (Perkin Elmer AAnalyst 800) is a state of the art transverse heated graphite tube system with Zeeman background correction. This instrument will be utilized in GFAAS mode to analyze metals when the detection limits of ICP-AES are insufficient for the levels present in our samples. It will be utilized in flame mode when analyzing major elements such as calcium or magnesium. Both instruments are fully automated (allowing the analysis to continue even after the 3 hour lab has ended) and utilize the same software platform (which will simplify student training).

Prior to analysis by the methods listed above, solid samples must be converted into a homogenous aqueous form. Our current microwave digestion system (CEM MDS-2000) has both temperature and pressure control and will be useful in method development for digestion protocols. It is, however, limited in sample throughput to 12 vessels.

Three different biology teaching laboratories will be used for the course modules. Each lab is approximately square feet, with bench space for 24 students. Equipment to be used includes dissecting microscopes, compound micrscopes, spectrophotometers, UV pectrophotometers, mini-Protein gel electrophoresis units, mini trans-blot cells, microcentrifuge, 6 computer stations for statistical analysis, E-gel units, refrigerators, ultra-low freezer, environmental chambers.

10) Equipment requests should:

• Describe comparable equipment already at the institution and explain why it cannot be used.
• Explain if the new equipment will be available to support other efforts and how time will be allocated on it.
• Describe plans for facility operations and maintenance.

Large freeze dryer – There is currently one small freeze-dryer that would be available for this project. Given the large number of soil, plant, and biological samples that will be processed for this project, there is a need for a high capacity freeze dryer. The model we have requested will include bulk drying trays and a large capacity.

Acid digestion system - There is currently one microwave digestion system. Digestion of solid samples will likely be one of the bottlenecks in the analysis of samples by our atomic spectroscopy equipment. The instrument that we propose to purchase will be a CEM MARSxpress system with a high throughput capacity (40 sample tray).

Atomic Absorption Spectrometer (AAnalyst 800) and Spectroscopy supplies. Recently we have purchased an AAnalyst 800 combination graphite furnace and flame atomic absorption spectromter. We will need to purchase additional lamps and other supplies to utilize this instrument for the wide array of metals that we propose to analyze.

Semi-automated Total Organic Content Analyzer - for the more sophistocated fate and transport models as well as the biotic ligand model, it is imperative to know the dissolved organic content. We do not currently have this capability.

Differential GPS

Field monitoring eqpmnt (Temperature, pH (digital), conductivity, redox (reduction oxidation potential), pressure transducer, nitrate selective probe, computer, packaging, and communications)

Field Sampling Kits (Lake sediment cores to 2 m, Shelby soil cores, Monitoring wells (one time install), Drawing equipment)

Biology sampling gear (Nets (ten 50’ fyke nets @ $300 each; Nichols Net and Twine), Containers: Rubbermaid fiberclass stackable tubs (10 @ $30), Passive Integrated Transponder (PIT) tags (250 @$7) and reader (InfoPet))

11) Plans for this project beyond the proposed time period, including financial support.

We request that WMKF, with institutional support from the College, fund this pilot project. The College has committed $167,049 in resources as start-up funding. We are embarking on a capital campaign that includes a goal of building a $3 million endowment for science faculty/student research. We believe that a WMKF investment will serve as a catalyst for major gifts from alumni, friends, corporations and other foundations.

12) Describe how the success of the project will be evaluated in terms of the goals proposed. Include information regarding outside review committees, if appropriate.

• Evaluation Team: We have identified several possible sources of both internal and external evaluation. Internal evaluations will be conducted by one or more members of the project and other faculty and staff within the science division who are not directly involved in developing or using these curricular modules. External evaluators will be drawn from program assessors who have worked previously with Earlham College and/or from organizations which provide consultancy services such as the Council on Undergraduate Research (CUR). CUR can provide program evaluation sensitive to issues at predominantly undergraduate institutions including evaluators with experience in evaluating interdisciplinary and interdepartmental programs.

• Timing: Evaluation of the Keck program will occur both during (formative) and at the end (summative) of the grant period. The formative process evaluations conducted at various points throughout the grant period will assist the faculty and academic departments involved in this interdisciplinary project to refine the project goals and objectives and to make any ongoing modifications or revisions. They will identify what is working during the initial implementation and point to areas needing further development. The summative evaluation will take place at the end of the grant period and will provide a measure of how well the program goals were met as well as provide directions for future growth.

• Goals: The project leaders will meet with the evaluators to clarify, operationalize, and select and development instruments which evaluate the stated and implicit goals of the project (above). The project evaluators will also help to conceptualize key issues or problems that would keep our program from meeting our stated objectives and specify particular criteria for success as well as identify particular data needed to determine how well the components of the program are meeting their objectives.

• Methods: Delineating project goals will assist us in developing both qualitative and quantitative measures for determining how well our goals are being met during both the formative and summative evaluation phase. Qualitative evaluations will include:
  • Open-ended surveys: The evaluator will collect answers without preset response categories to written questions. Surveys with an open-ended component would be given to all students enrolled in courses where a research-based interdisciplinary module was used, faculty who developed and taught such courses, and participants in any workshops in which the faculty involved in the Keck program presented the pedagogy and organization of this project.
  • Semi-structured interviews: The evaluator will conduct semi-structured interviews of key personnel and a representative sample of students to allow the evaluator some first hand experience with the evaluated activities and a chance for in-depth exploration of particular issues.
  • Peer evaluation: Efforts at developing interdisciplinary course modules incorporating computational modeling will be described in peer-reviewed publications providing feedback from the reviewers as well as others who read the articles.

Quantitative evaluations will include:

• • Quantitative surveys: Quantitative pre and post surveys of student or workshop participant attitudes toward and confidence in computational methodology, interdisciplinary collaboration, relevance of environmental studies in particular disciplines, and interest in science and society.
  • Institutional data: Assessment of pre and post grant levels of student participation in undergraduate research, likelihood of taking a secod science class, and number of science majors.
  • Incorporation in curriculum: Measurement of the pre and post grant percentages of incorporation of computational modeling in primarily field or laboratory based courses and field or laboratory modeling in computational courses.
  • Incorporation in co-curriculum: Comparison of the numbers pre and post grant interdisciplinary projects including collaborative research projects and grant writing efforts.

• Results: Final reports summarizing both the quantitative and qualitative data will be produced. They will asses which and to what degree goals have been met for affected students, faculty, and the institution as a whole as well as provide recommendations for further implantation and dissemination.

4) Project Budget Form

• Do we have a spreadsheet template to work from?
• Upload spreadsheet to <here>.

5) Budget Narrative

1. Provide a brief justification of each budget line item.

Personnel – Salary & Fringe Benefits (Total 3 year budget $ 227,613 : $201,777 grant funded, $25,836 institutional funding) 48 Faculty weeks per year(total 144 faculty weeks) @ $600 per week + .0765 FICA and Medicare for summer research and curricula work (e.g. 6 faculty x 8 weeks per year) 96 student weeks per year (total 288 student weeks) @ $400 per week +.0765 FICA and Medicare for collaboration with faculty in research and curricula work (e.g. 12 students x 8 weeks per year) Grant support @ $3,000 + .0765 FICA and Medicare + 10% TIAA/CREF as staff for, reporting, purchasing supplies, budget monitoring, etc. Equipment (Total 3 year budget $100,000 - $80,800 grant funded, $19,200 institutional funding) Large freezer dryer @ $15,000 – drying of biological and soil samples in preparation for digestion and analysis.

Acid digestion system @$17,500 – dissolution of biological and soil samples prior to analysis by GFAAS or ICP-AES

Atomic Absorption Spectrometer – college funded ($19,200) – analysis of low levels of toxic metals such as lead and arsenic

Semi-automated Total Organic Content Analyzer @ $12,000 - for the more sophistocated fate and transport models as well as the biotic ligand model, it is imperative to know the dissolved organic content. We do not currently have this capability.

DGPS @$2250 – will be used to precisely locate sampling sites in our remote sampling location (Springwood Lake)

Field monitoring equipment – 4 sets @ $3,000 will include electronic and computer components necessary for the construction of field monitoring stations that will be used to continuously monitor temperature, pH (digital), conductivity, redox potential, pressure, and nitrate levels at our on-campus field site

Field sampling equipment @ $15,000 – will be used to construct our on-campus and remote field sites including construction of a monitoring well and equipment for obtaining sediment and soil cores.

Biology sampling gear @ 3800 – will include equipment such as nets and electronic identification tags that will be used to capture and/or monitor biological samples such as fish and turtles.

Operations (Total 3 year budget $198,313 - $76,300 grant funded, $122,013 institutional funding

Consumable supplies @ $25,333 per year - will include lab supplies necessary for sample processing and atomic analysis for both academic year and summer, which will impact X students per year (e.g. clean acids, consumables for atomic spectroscopy (graphite tubes, Ar gas), pipet tips)

Travel/symposiums @$11,100 per year – will fund faculty and student travel to regional and national meetings to present the results of this research as well as the costs of poster.

Facilities Overhead – All institutional funded

Evaluation – @$3000 per year – construction and analysis of surveys........

Library Acquisitions @ $2000 per year – will fund purchase of relevant texts as well as interlibrary loans.

2. State the number of students (undergrad/grad/postdoc), research associates or technicians to be supported and number of years of support.

The project will support summer research for approximately 12 students each summer for 3 years.

3. Explain why W. M. Keck Foundation support is essential for this project.

Funding for undergraduate research at small, liberal arts colleges is limited. The WMKF is known and respected throughout the scientific community as a foundation that supports innovative science programs at high-quality undergraduate institutions. WMKF funding would allow Earlham to launch its multidisciplinary science project. Keck support would also raise the visibility of the sciences within the College and with external audiences regionally and nationally.

4. List all current and pending federal and non-federal support, including institutional or departmental funding, related to this project.

Earlham College will provide $167,000 specifically toward this project. There is no other pending funding. However, with the leverage and prestige that a Keck grant will provide, we believe that we will be well-positioned to solicit major gifts (both for current use and for an endowed student/faculty research fund) for continuation and expansion of multidisciplinary science projects, as well as submission of proposals for future funding to NSF and other private foundations.

5. If construction or remodeling is involved, provide a copy of the permits required or an explanation of how and when the permits will be acquired.

There are no construction or remodeling components of this proposal.

6) Recognition Statement

• Describe the manner in which the institution will recognize and acknowledge a W. M. Keck Foundation grant for this project.

Earlham College science faculty and public information staff will work closely with the W.M. Keck Foundation to publicize grant funding. Upon approval of text, Earlham's public information staff will distribute news releases to local, regional and national media, and to educational publications such as the Chronicle on Higher Education to announce receipt of a Keck grant.

NITLE paragraph.

CUR paragraph.

In addition, a feature article for the Spring 2007 Earlhamite, Earlham's alumni magazine, will be prepared and submitted to the Foundation for approval. The Keck award will be highlighted on the Earlham College web page with links to news coverage and the Earlhamite article. Keck will also be acknowledged on our Natural Sciences web page, and on each participating discipline web page.

Faculty and student written and oral presentations on the multidisciplinary curriculum development and/or research projects will acknowledge Keck support. These presentations could include journal articles, and papers and poster sessions at regional and national conferences, as well as in publications in organizations such as the Council for Undergraduate Research (CUR).

7) Project Documents

• 1. Biographical sketches (limit 2 pages for each investigator)
  • Required for key personnel at the applicant institution and collaborators at other institutions.
  • Each sketch should contain name, position title, organization, contact information included e-mail address, degrees, years and field of study for each academic degree, a listing of research and professional positions, awards, and honors, and references to all publications for the past three years along with any earlier publications pertinent to this application.
    • Charlie
    • Corrine
    • Mike
    • Meg
    • Dave
    • John
    • Ron
    • Lori

• 2. Collaborative Arrangements: Provide letters from the collaborators and the director of their institution(s) endorsing this request and the role of each collaborator. Please include contact information including e-mail addresses.
  • We already have some of this in the phase I submittal.
  • NITLE letter - Nancy Millichap (or the director); support for logistics, advertising, and hosting of a dissemination workshop.
  • City of Richmond/Parks Department
  • IDEM

• • Letters should be sent to us for inclusion and addressed to:

Mat Varma, Ph.D.
Program Director
W. M. Keck Foundation
550 S. Hope Street, Suite 2500
Los Angeles, CA 90071

• 3. Bibliography of the literature cited in the project.
  • bibliography