Creation of a Computer Modeling Course for Undergraduate Earth Science Students Kirsten M. Menking Department of Geology and Geography, Vassar College, Poughkeepsie, NY 12604, [email protected] ABSTRACT Entire fields within the Earth sciences now exist in which computer modeling has become the primary work of the discipline. Undergraduate geology/Earth science programs have been slow to adapt to this change, and computer science offerings frequently do not meet geology students' needs. To address these problems, a course in Computer Modeling in the Earth Sciences has been developed at Vassar College. The course uses the STELLA (Structural Thinking Experimental Learning Laboratory with Animation) iconographical box modeling software to teach the fundamentals of dynamical systems modeling and then builds on the knowledge students have gained with STELLA to teach introductory programming. Modeling topics include U-Pb concordia/discordia dating techniques, the impact of climate change on a chain of lakes in eastern California, heat flow in permafrost, and flow of ice in glaciers by plastic deformation. The course has been received enthusiastically by students, who reported not only that they enjoyed learning the process of modeling, but also that they had a newfound appreciation for the role of mathematics in geology. Fully documented and debugged STELLA and Fortran models along with reading lists, answer keys, and course notes are available to anyone interested in teaching a course such as this. INTRODUCTION In recent years computer modeling has gained importance in geological and environmental research as a means to generate and test hypotheses and to allow simulation of processes in places inaccessible to humans (e.g., outer core fluid dynamics, see Olsen and others, 1999), too slow to permit observation (e.g., erosionally-induced uplift of topography, see Small and Anderson, 1995), or too large to facilitate construction of physical models (e.g., faulting on the San Andreas, see Ward and Goes, 1993). Fields within the Earth Sciences now exist in which computer modeling has become the core work of the discipline. Examples include simulations of past climates, seismic hazards, and hydrogeology. The increasing importance of computer modeling has led to an apparent disconnection between the direction in which geological research is moving and the curriculum in many undergraduate programs. Examination of course offerings at several highly selective undergraduate institutions reveals that none offer a course in computer modeling in geology. Thus, as students begin their graduate research careers, they may enter the world of modeling with little or no preparation. While undergraduate Earth science students should, in theory, be able to take courses in computer science to address their future computational needs, in practice, finding suitable courses can be difficult. For example, with the exception of one independent study course, the Vassar College Computer Science department does not 464 offer courses in individual programming languages. Instead, they teach courses such as Software Development Methodology, Computer Organization, Algorithmics, and Artificial Intelligence. While these courses are appropriate for students majoring in computer science, they do not serve geology students' needs. It is for these reasons that I decided to create a course that would address the mechanics of computer modeling within the context of geologic and environmental problems. Students would learn how to glean relevant information from the primary literature, how to break down complex geological and environmental problems into their component parts and relationships, how to represent those parts symbolically, and how to relate them to one another mathematically. In creating a course in Computer Modeling in the Earth Sciences, my goal was also to motivate students to enhance their mathematical abilities. While I have found geology students to be quite capable in mathematics, many express anxiety over perceived inadequacies and are reticent to enroll in math courses that would prove useful to them in their future careers. Furthermore, while many students are readily able to manipulate and solve equations, they don't know where to begin when asked to solve real problems. In creating the Computer Modeling in the Earth Sciences course, I hoped to develop students' abilities in solving real world problems and to build their confidence such that they might be inspired to acquire further training in mathematics. I have taught the course three times now, and the sections that follow describe the pedagogical tools that I have used, the course structure, student responses, problems I have encountered, and availability of course materials. In addition, the broader impacts of the course on the undergraduate curriculum and on students' post-graduation careers are considered. SOFTWARE Building on the work of DeWet (1994), Moore and Derry (1995), Levy and Mayer (1999), and Bice (2001), I chose the STELLA (Structural Thinking Experimental Learning Laboratory with Animation) icon-based dynamical systems modeling software developed by High Performance Systems, Inc. (now Isee Systems) for this course. STELLA is a finite difference modeling tool designed to facilitate understanding of complex systems composed of multiple interacting components. It has been used to research such widely ranging topics as hydrological processes (Lee, 1993), impact of eutrophication on dinoflagellate populations (Costanza and Gottlieb, 1998), crude oil exploration and depletion (Ruth and Cleveland, 1993), and the inorganic carbon cycle in a near-shore coastal area (Norro and Frankignoulle, 1996). STELLA, although applicable to complex basic research, is also easy to use and therefore accessible to students. The software allows visual representation of reservoirs and fluxes as boxes connected by flow arrows Journal of Geoscience Education, v. 54, n. 4, September, 2006, p. 464-470 Figure 1. STELLA model graphic of a course exercise designed to explore the impact of climate change on the Owens River chain of lakes in eastern California. (a) Runoff from the Sierra Nevada mountains fills the box representing Owens Lake, whose volume is then used to determine the lake surface area. This surface area is multiplied by an evaporation rate to determine the volume of water removed from the lake ("evap from Owens" outflow arrow). If the amount of water remaining in the lake after the evaporation step exceeds the maximum volume the lake can hold, excess water is transferred to the next lake in the chain ("overflow to China" arrow). Additional converters (circles) hold volume/depth relationships, and maximum area (O max a) and depth (O max d) boundary conditions. (b) Location map of the Owens chain of lakes. c) Chart showing cyclic (sine curve) changes in runoff from Sierra Nevada and subsequent effect on Owens River chain of lakes. (figure 1). Dependencies of variables are represented with linking arrows, and circles, called converters, hold values of constants and equations. A few clicks of the mouse allow the user to set initial conditions, model time step, mathematical relationships between variables, and simulation length. An internal graphing program allows the modeler to watch the progress of up to five different variables at a time. While students can construct their models entirely within the iconographic interface, they can also view the equations the computer must solve by going to the equation level of the software (figure 2). This equation level serves as a convenient bridge to programming, and as students grow in competence and confidence in their STELLA modeling, I introduce them to Fortran, one of the most widely used programming languages in the Earth Sciences today. The process of coding requires students to learn how the computer handles real versus integer numbers, how the computer keeps track of variable values from timestep to timestep by means of dimensioned arrays, how "do loops" are constructed, and how logical statements work. To facilitate the Fortran programming I use Compaq's Visual Fortran software, which includes a helpful color-coding system for different program components, and which also has a compiler that makes debugging of program errors straightforward. COURSE FORMAT The Computer Modeling in the Earth Sciences course is a senior seminar-level course taken primarily by juniors and seniors. The format of the course has been as follows: each week, a different pair of students was responsible for presenting readings taken from the geological literature that formed the basis for that week's modeling Menking - Creation of a Computer Modeling Course for Undergraduate Earth Science Students 465 Figure 2. Equation level in STELLA for the model shown in figure 1. Only equations for the Owens Lake reservoir are shown. First line shows the basic differential equation the computer solves to update the Owens Lake volume reservoir each timestep. Second line shows initial condition for Owens Lake reservoir. For OUTFLOWS, the amount of water evaporating from Owens Lake in each time step is determined by multiplying lake surface area by 1.34 m/yr vertical evaporation rate. Overflow to China lake occurs if lake volume continues to exceed the maximum volume of the lake at its spill threshold after the evaporation step. Owens Lake’s depth and area are determined based on the volume in the reservoir. If the volume in the reservoir is less than or equal to zero, depth and area are set to zero. If the volume in the reservoir is at the maximum spill threshold, depth and area are set to their maximum values. project. Students then carried out an exercise designed to assist them in creating their models. In developing each exercise, I tried to minimize "cookbooking," and instead aimed to have the students generate their models largely independently, with my role being to facilitate their conceptualization of each problem and to offer hints when they got stuck. In each succeeding week, I gave the students fewer clues as to how to construct their models, such that by the end of the semester, they were on their own. Once the students completed their models, I gave them a series of experiments to perform to develop an understanding of system dynamics. As with model construction, students were initially given more assistance and then were gradually expected to develop their own experiments to foster their abilities to create and test hypotheses. An independent modeling project toward the end of the semester allowed each student to explore individual interests and culminated in a substantial paper and presentation to the class. Grades were based on the weekly modeling assignments, weekly presentations, and the various components of the independent modeling project. The class met one day a week in a four-hour block. I decided to teach the course in this format based largely on my own experience with modeling. I have found that I need a long block of uninterrupted time to create a model, either in STELLA or in Fortran. If I am forced to take my attention away from the model for a period of days, I need between a half hour and a day (depending 466 on the complexity of the model) to refresh my memory of where I was in the process. Colleagues who model have expressed similar needs for long, uninterrupted time blocks, and student evaluations of the course indicate that the format was highly effective. Modeling concepts covered in the course included open vs. closed systems; behavior of systems, including steady state, oscillation, linear growth and decay, and exponential growth and decay; positive and negative feedback loops; response and residence times; initial and boundary conditions; if-then-else logical statements; different integration methods, such as Euler and Runge-Kutta; how to choose a time step; how to determine the appropriate level of model complexity; and the limitations of models. Modeling topics included the global phosphorus cycle, U-Pb concordia/discordia dating techniques, heat flow in permafrost, Earth's energy balance and temperature, James Lovelock's Daisyworld, the impact of climate change on a chain of lakes in eastern California, and scarp diffusion. Students were enthusiastic about their independent projects, and used them to explore both geological processes and phenomena from other disciplines in which they were double-majoring. Their projects included biological controls on purple loosestrife, an invasive plant; eutrophication of Lake George in upstate NY; flow of water in the Hudson and Yangtze Rivers; isostatic uplift and glacial rebound; the Wage-Fund Doctrine economic model; a model of traffic flow incorporating a stop light; flow of groundwater via Journal of Geoscience Education, v. 54, n. 4, September, 2006, p. 464-470 Darcy's Law; predator-prey relationships; and the flow of ice in glaciers by plastic deformation (since developed into a modeling exercise). Because many of these topics were beyond my abilities to assist them in the limited time available, students were evaluated not on the success or failure of their models to replicate observed behavior but on the quality of the project, presentation, and final paper. For those whose models did not yet work by the end of the semester, I was particularly interested in their abilities to critically analyze their work and to explain what they thought might need to be changed in order to get their models to replicate observed behavior. I taught an initial version of the Computer Modeling in the Earth Sciences course to ten students in the spring of 2001, using only the STELLA software. In June of that year, I received National Science Foundation funding that allowed me to incorporate Fortran programming and formal evaluation of the course the next two times it was taught, in spring 2003 (six students) and spring 2005 (four students). The apparent decline in enrollment for the course each time it was offered was related not to the course itself but to fluctuations in the number of students opting to major in geology over that time interval. Typical enrollments for Vassar geology senior seminar courses are around 5 +/- 2 students, and the class of 2001 was unusually large, having 12 total members, eight of whom decided to take the modeling course. STUDENT RESPONSES TO THE COURSE For the most part, I was amazed by my students' enthusiasm for the class. In all three offerings, they thoroughly enjoyed working with STELLA, particularly when it came time for them to do their independent projects. Some students expressed frustration with modeling throughout the course, but their frustration generally gave way to "high-fives" and shouts of "we are so cool!" when they successfully debugged their models and got them to work. I had anticipated that students would need a lot of encouragement in developing their modeling skills, and I found myself in the role of coach/cheer leader as much as in the role of teacher. At the same time, the students really took ownership of the course, and I often found them working on their weekly modeling projects and presentations late on Friday evenings, a testament to how seriously they took the class and to how much they enjoyed it. I was impressed with my students' ability to pick up Fortran in the 2003 and 2005 semesters. They wrote their first program after only three weeks of class, and required much less help in debugging their codes than anticipated. Students were able to use the equations from their STELLA models in their Fortran codes and then focus on the looping structure, declaration and dimensioning of variables, and input and output commands that Fortran requires. In the 2003 and 2005 offerings of the course, I administered formal questionnaires at the beginning and end of the semester to gauge my students' levels of preparedness for the course, attitudes towards mathematics, and feelings about how the course impacted their knowledge and abilities. These questionnaires and summaries of students' narrative responses can be obtained from the authors. In the end of class questionnaire, students reported that they felt the course was highly effective in teaching the basics of system dynamics and how systems could be modeled, that they found the iconographic structure of STELLA very useful in learning modeling, and that the STELLA modeling prepared them well for the work in Fortran. Responses to the question 'how would you describe the impact of this course on your general understanding of system dynamics and of how systems can be modeled?' included: ''Before I took this course I had no idea how people knew what they knew about systems with large scales and long timescales. Now I see how useful a computer model can be to understanding this. I also learned that the models can be simple but still give a lot of information. This class has been so useful in making geologic problems realistic." "This class had a tremendous impact on my general understanding of modeling and system dynamics. It has helped me to realize how valuable modeling can be in geology and how to go about modeling a problem." "I have learned much particularly in regards to troubleshooting and assessing the limitations of models, running experiments with models and both simplifying and adding complexity to modeled systems." "Highly effective, I now understand what modeling a system consists of and can think about such relations mathematically much better than I could six months ago." Like Moore and Derry (1995), I found that my students developed feelings of competence and empowerment from their new skills and that they enjoyed the creative aspects of modeling. Due to time and budgetary constraints, high school science classes often present science as a catalog of facts to be learned, rather than as a creative process. As a consequence, undergraduate students often do not understand how to construct hypotheses from observational data or how to test those hypotheses (PKAL, 2000). By its very nature, computer modeling fosters experimentation, and students in my course came to see that geology is a dynamic science to which they can contribute, not just a body of knowledge to be memorized. MATHEMATICAL SKILLS AND ATTITUDES I administered an initial quiz/questionnaire, in which students were asked to solve a number of problems and were also asked what level of math they had attained to that point and their comfort level with math. The questionnaire component can be obtained from the authors. Of the ten students taking the course in the 2003 and 2005 semesters, three were double-majoring in physics or math and had taken courses in linear algebra, ordinary differential equations, and multivariable calculus; two more had advanced beyond calculus to linear algebra; three had taken 1-2 semesters of college calculus; and two had not taken math beyond high school calculus. Two out of ten students found math difficult, frustrating, and not particularly relevant. Another five expressed neutral attitudes, stating that they sometimes enjoyed math, but often found it difficult and frustrating. Not surprisingly, the three physics and math double majors said they loved math. Menking - Creation of a Computer Modeling Course for Undergraduate Earth Science Students 467 Figure 3. Improvement in quiz scores over the semester as a function of mathematical preparation and attitudes towards math. Students with weaker math backgrounds and with more negative attitudes towards math showed the greatest improvement in their quiz scores over the semester (% change = percentage of correct answers on end of semester quiz minus percentage of correct answers on beginning of semester quiz). The basic quiz that I administered, covering algebraic operations, trigonometry, exponentials, unit conversions, story problems, and asking students to link mathematical concepts to geological phenomena (such as exponential decay and radioactive decay of isotopes or oscillatory behavior and diurnal cycles) revealed, not surprisingly, more difficulty among those students who had weaker preparation and those who found math difficult than among those who enjoyed math and had taken courses beyond calculus. The course appears to have had a large impact on the students with weaker math backgrounds. A quiz administered at the end of the semester revealed a substantial improvement in their mathematical abilities (figure 3), which was matched by a change in attitude toward math. In response to the question 'Did the course have any impact on your understanding of the usefulness of math in geology?' students said: "Yes, this is one of the only courses which has done so." "Yes, it had a huge impact. This class showed me that calculus is very important in the study of geology. Because of this class I'm planning on taking calculus." "DEFINITELY!! I am going to try and improve my math skills and fix any holes and deficiencies I have." "I already had faith in the importance/usefulness of math in geology and this course has helped confirm these feelings." 468 "Yea - now I wish I'd taken more math. I may take some next year but haven't had any since freshman year. For the practical applications such as this you have to be able to truly understand it, not just do it." These comments reveal that students no longer regarded math as a subject beyond their abilities, but rather as a body of knowledge and method for solving problems that they were entitled to learn. Indeed, three of the five students who had taken only high school or college calculus, when asked this question, replied that the course had profoundly influenced them and that they planned to enroll in more math in the near future. Two of these students did in fact do so. STUDENT DIFFICULTIES While the Computer Modeling in the Earth Sciences course has proven to be highly effective in meeting its goals, I also encountered a number of difficulties. First, some students had difficulty analyzing their model results critically and finding mistakes in their models. These students often tried to explain their results by invoking relationships between variables that were not explicitly incorporated into their models or by attributing their results to factors that they did not include in their models. For example, a student might call upon changes in temperature during the late Pleistocene to explain the faulty behavior of a model designed to assess the impact of changes in runoff on lake levels, despite the fact that the model did not incorporate any kind of temperature dependence. Typically the student miscast an equation somewhere or neglected to specify a boundary condition that led the Journal of Geoscience Education, v. 54, n. 4, September, 2006, p. 464-470 model to behave incorrectly. Some students had great difficulty understanding that results were not automatically valid and correct, and therefore used convoluted reasoning to try to explain their results. While most students eventually learned to critically analyze their results and to trust their intuitions when confronted with results that didn't make sense, there occasionally were one or two who didn't by the time the semester ended. Another problem is that the majority of students had difficulty with casting equations such that the order of operations was carried out correctly. They often misplaced parentheses and seemed quite stymied by how to represent long, complicated equations in the parenthetical form required by the computer. Due to the nature of the course, with students developing their own models and codes, it took a lot of time to debug problems, and I found myself spending 20 minutes at a time with an individual student trying to find the one misplaced parenthesis before being able to move on to the next student. This meant that students were often waiting for help, a situation that could be rectified by use of a teaching assistant. BROADER IMPACTS OF THE COURSE Figure 4. Use of numerical modeling by Earth/Environmental Science graduate students. Students have used models in their own thesis and dissertation research (Research) or in courses such as Hydrogeology (Coursework). Fully half of students have had to evaluate model outputs reported in the geologic literature (Evaluation). A minority reported no involvement with modeling (Not used). The Computer Modeling in the Earth Sciences course has impacted other areas of the curriculum in the Geology and Environmental Studies programs at Vassar College. STELLA models are now part of the introductory environmental geology course, a senior seminar in Paleoclimatology, and the Essentials of Environmental Science, taught in the Environmental Studies program. In addition, students who took the modeling course have been able to conduct senior thesis research incorporating numerical modeling. In 2000-2001, two students used the U.S. Department of Agriculture Soil and Water Assessment Tool (SWAT) rainfall/runoff model (Arnold et al., 1996) to assess the impact of global climate change on the water supply for Portland, Oregon. Another student used the SWAT model in 2003-2004 to simulate flow of the Casperkill stream that runs through the Vassar College campus. Part of this student's work involved writing Fortran programs to compute total daily rainfall and to select daily maximum and minimum air temperatures from 20-minute measurements of these variables made at our campus meteorological station. Another student created a STELLA model for her senior thesis on the impacts of deforestation in Nepal. To assess the extent to which students were engaging in modeling after graduating from Vassar, I administered an alumni survey in the spring of 2005. I was able to get in touch with 32 of the 53 students who graduated between 1998 and 2004, and designed two surveys, one for those students who had taken my modeling course and one for those who hadn't. Questions for both groups included whether they were still involved in the Earth Sciences, either in graduate school or in a job, whether they were involved in any numerical modeling work, and if so, what computer languages they used. Those who hadn't taken my course were asked to provide information on where they acquired their modeling skills and whether having had an introduction to modeling at Vassar would have been helpful. The group that took the Vassar modeling course was asked whether the course had prepared them for the work they were now doing. While several students were no longer involved in Earth Science/geology, nearly three quarters were in graduate school in some aspect of Earth or Environmental Science or were employed in geologic consulting. Of the fourteen students in Earth or Environmental Science graduate programs, 43% were involved in modeling as part of their own research, and fully half had to evaluate modeling projects and results published in the geological literature (figure 4). Seventy percent of students engaged in modeling acquired their skills entirely in graduate school, but only 30% of these students had the benefit of being able to take a course in modeling. The remaining 40% were either on their own or had some assistance from a graduate advisor or fellow students. About a third of the students now engaged in modeling had taken the Vassar Computer Modeling in Earth Sciences Course, but these students also reported having to acquire additional knowledge on their own. One student who is currently finishing a dissertation in computational astrogeophysics, and who had no experience with modeling prior to attending graduate school, reported that she is modeling "24-7" and using Fortran, C++, Matlab, and a host of other languages. She stated that she "acquired [her] modeling skills during grad school, through research hours and informal channels. In other words, in the gutter," and stated that having an introductory class in college, particularly in Fortran, would have helped her enormously. Another student who didn't have the Vassar course and is now working on a Ph.D. in biogeochemistry stated "I never got to take your modeling course, but I would have added it to my course list if I knew what I now know," and yet another doing a Ph.D. in stable isotope ecology responded "I feel like modeling has become the core of Earth Science and I don't know what's going on most of the time." This same student, when asked whether she needs to incorporate others' modeling results into her work said, "Yes, this happens frequently." Another student who needs to rely on modeling results reported by others spoke of the difficulty she has in evaluating those results given that she never had a modeling course: "I have enough knowledge to Menking - Creation of a Computer Modeling Course for Undergraduate Earth Science Students 469 understand how models are used but I don't think I have enough knowledge to really evaluate how good/accurate a model is." Conversely, a student who took the Vassar modeling course and is now in graduate school in volcanology said that while he is not currently modeling himself, "the conceptual understanding of how models work and the practical knowledge of how they are constructed have been invaluable skills that have allowed [him] to intelligently evaluate and assess the merits of modeling work conducted by [his] colleagues." Another, who completed a master's in hydrological modeling, reported that the Vassar course "helped [him] understand the theoretical approach behind modeling various systems." This student also spoke of the importance of exposure to Fortran and Matlab. It is quite clear that students understand the importance of acquiring modeling skills, and that wider training of geology/Earth science students in these skills is necessary. Furthermore, the fact that so many students are still left to acquire their modeling skills on their own suggests that we as educators should be stepping in to fill this need. AVAILABLE COURSE MATERIALS For anyone interested in teaching a course such as Computer Modeling in the Earth Sciences, I have created a website on which I have posted the syllabus for the course, a reading list, documented STELLA and Fortran models, copies of exercises and answer keys, and course notes. I have also posted supplementary information that explains the motivations behind each exercise, background mathematics and concepts needed to understand the exercise, and typical problems encountered by students. The course materials can be accessed by going to http://blackboard.vassar.edu, selecting the Login button, and then using the word "geoguest" for both the login name and the password. Once logged into Blackboard, select the ADMIN-GEOL-GRANT link in the "My courses" box to view the content on the site. ACKNOWLEDGEMENTS I gratefully acknowledge the support of the National Science Foundation, which funded this work through the Course Curriculum and Laboratory Improvement Adaptation and Implementation track (Grant #0087996). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author and do not necessarily reflect the views of the National Science Foundation. I also thank Roger Y. Anderson and Jeffrey R. Walker for their comments on the manuscript, and Emily M. Geraghty and Robert C. Thomas for their constructive reviews. Inspiration for developing this course came from my graduate advisor, Robert S. Anderson (University of Colorado, Boulder), who teaches a similar course for graduate students, from the late Rolfe Stanley, who taught a STELLA modeling course at the University of Vermont for many years, and from Andrew DeWet at Franklin and Marshall College, who first introduced me to STELLA. I would also like to thank Joel Dashnaw, Vassar College class of 2005, for his hard work on the Blackboard site. 470 REFERENCES Arnold, J.G., Williams, J.R., Srinivasan, R., and King, K.W., 1996, SWAT: Soil and Water Assessment Tool. USDA, Agricultural Research Service, Grassland, Soil and Water Research Laboratory, 808 E. Blackland Road, Temple, TX 76502. Bice, D.M., 2001, Using STELLA models to explore the dynamics of earth systems: experimenting with Earth's climate system using a simple computer model, Journal of Geoscience Education, v. 49, p. 170-181. Costanza, R., and Gottlieb, S., 1998, Modelling ecological and economic systems with STELLA: Part II, Ecological Modelling, v. 112, p. 81-84. DeWet, A.P., 1994, Integrating field observations with physical and computer models in an introductory environmental-geology course, Journal of Geological Education, v.42, p. 264-271. Lee, J., 1993, A formal approach to hydrological model conceptualization, Hydrological Sciences Journal, v. 38, p. 391-401. Levy, J., and Mayer, L., 1999, Systems modeling of nonequilibrium chemical reactions using STELLA, Journal of Geoscience Education, v. 47, p. 413-419. Moore, A., and Derry, L., 1995, Understanding natural systems through simple dynamical systems modeling, Journal of Geological Education, v. 43, p. 152-157. 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