Below are the first 10 and last 10 pages of uncorrected machine-read text (when available) of this chapter, followed by the top 30 algorithmically extracted key phrases from the chapter as a whole.
Intended to provide our own search engines and external engines with highly rich, chapter-representative searchable text on the opening pages of each chapter. Because it is UNCORRECTED material, please consider the following text as a useful but insufficient proxy for the authoritative book pages.
Do not use for reproduction, copying, pasting, or reading; exclusively for search engines.
OCR for page 75
Bio 2010: Transforming Undergraduate Education for Future Research Biologists 4 Engaging Students with Interdisciplinary and Project-based Laboratories RECOMMENDATION #4 Laboratory courses should be as interdisciplinary as possible, since laboratory experiments that confront students with real-world observations do not separate well into conventional disciplines. THE ROLE OF LABORATORIES Science courses and the laboratories associated with them should cultivate the ability of students to think independently. They should provide students with exposure to realistic scientific questions and highlight those aspects that are inherently interdisciplinary. They can also provide opportunities for students to learn to work cooperatively in groups. The committee recommends that project-based laboratories with discovery components replace traditional scripted “cookbook” laboratories to develop the capacity of students to tackle increasingly challenging projects with greater independence. Laboratories can illustrate and build on the concepts covered in the classroom. Once students have time to examine the specimens, materials, and equipment described in class, they will be better prepared to carry out experiments. The purpose of restructuring the emphasis of the teaching laboratory is to stimulate student interest and participation. Project-based laboratories are also choice arenas for developing the scientific writing, speaking, and presentation skills of students.
OCR for page 76
Bio 2010: Transforming Undergraduate Education for Future Research Biologists Interdisciplinary laboratories are a promising means of strengthening the physical science and quantitative background of life science majors and of introducing biology to uncommitted students or those majoring in other fields. Harvey Mudd College has developed an introductory laboratory course consisting of three-week interdisciplinary experiments that are openended and highly investigative. The goal of the laboratory course, called ID Lab, is to help students understand the research approach in science and the natural relationship between biology and other scientific disciplines. Case Study #6 illustrates one way to strengthen undergraduate education by making learning a highly active experience from the first day of college. The other case studies (#7 and #8) and examples presented here are project-based laboratories that can engage students and cultivate independent learning. This is not meant to be an exhaustive list, but rather an array of examples that illustrate what can be done, and what is now being done, at institutions nationwide. PROPOSED NEW LABORATORIES Not all schools will find it practical to adopt a completely project-based approach to their physics courses. If the traditional lecture is retained, modifications can still be made to the laboratory component of the course. Two ideas for getting started are included here. The first retains a straight physics approach, while the second incorporates ideas from engineering. A Proposed Physics Laboratory Based on a “Crawl, Walk, Run” Approach The physics laboratory can be used to introduce new concepts, in addition to its traditional use of reinforcing concepts already presented in lecture. Some concepts are best learned through laboratory exploration, such as error analysis, uncertainty, fluctuations, and noise. Furthermore, examples drawn from biology can be introduced in the section on Newtonian and macroscopic mechanics, as well as in other areas. Properties of materials (e.g., bone, tendon, hair), biological fluid flows, and motions of bacteria or bioparticles in water provide excellent opportunities. The laboratory is also a choice arena to teach principles of engineering as they apply to biology. The “crawl, walk, run” approach is one means of developing the capac-
OCR for page 77
Bio 2010: Transforming Undergraduate Education for Future Research Biologists ity of students to tackle increasingly challenging projects with greater independence. This three-step model can gradually teach students to think through a process and carry out experiments on their own in order to acquire a conceptual understanding of the topics. In the “crawl” phase, students are given step-by-step instruction and data sheets to record their observations. In the “walk” phase, they are given guidelines and examples of how experiments might be carried out, but not explicit directions. In the “run” phase, they are given open-ended questions to explore and answer. The duration of laboratory modules would range from one week in the crawl phase to three weeks or even longer in the run phase. Students benefit from the interactions required to perform laboratory work in teams of two or three students. However, it is often necessary to require that writing be done individually, in order to assess learning and to encourage the students to further develop their writing skills. By the run phase, students would be able to hand in a short report explaining the problem studied, the methods used, and their findings, and also give a brief oral report. It may not be feasible to have a physical lab for all the desired laboratory experiences. Physical laboratories are generally preferred, but both physical and virtual labs can be utilized. LabVIEW (http://sine.ni.com/apps/we/nioc.vp?cid=1381&lang=US) and Matlab ( http://www.mathworks.com/products/matlab/) both offer excellent environments for students to learn laboratory skills and concepts. These software packages use mathematical computing to facilitate data acquisition, data analysis, creation of algorithms, and data visualization. Web-based learning is most useful when particular experiments are not available or may be hard to reproduce locally. Ideas for crawl- and walk-phase experiments related to conservation of energy and Newtonian mechanics are listed here; ideas for the run phase follow. The choice of topics for crawl or walk sessions would be determined by the instructor, taking into account the syllabus for any accompanying course, the students’ backgrounds, and available equipment. Conservations of energy: energy input and storage, basal metabolism, measurement of energy expenditure, external and/or internal mechanical work, and energy efficiency. Newtonian mechanics: muscles as force actuators, moments created by muscles, free body diagram analysis within the context of human joint mechanics, ground reaction forces, mechanics of gait-running, and standing balance, calculation of the center of pressure and center of reaction,
OCR for page 78
Bio 2010: Transforming Undergraduate Education for Future Research Biologists CASE STUDY #6 Interdisciplinary Laboratory Harvey Mudd College In Harvey Mudd’s Interdisciplinary Laboratory (ID Lab), all experiments include technique development, instrumental experience, question formation and hypothesis testing, data and error analysis, oral and written reporting, and, most importantly, the opportunity to explore in an open-ended way some of the details of phenomena that are familiar and of interest to students. In several experiments, the students visually study molecular interactions via molecular modeling software that is installed on the laptops they use in the laboratory. Finally, students are paired with a different partner for each module, developing teamwork skills in the process, and they share and discuss their experimental results after each module, gaining a sense for collective work in science. A variety of assessment efforts have been used to evaluate the lab course, including student evaluations after individual modules and at the end of each semester. The student response to the course has been very positive, particularly in regard to the interdisciplinary nature of the experiments. At the end of the 1999-2000 course, an assessment exercise was administered to the ID Lab students and those enrolled in the regular chemistry lab sequence. The ID students were also completing the second semester of the regular chemistry lab course, and the other students were completing the first semester of the physics lab sequence. Thus, both groups had completed three semesters of lab coursework at that point. The result of the exercise, which was evaluated by a faculty member from another college, was that the ID students and the other students performed equally on many measures, but the ID students showed higher-level thinking skills for developing hypotheses, designing creative experiments to test those hypotheses, and identifying sources of experimental error (in-house assessment data). A secondary outgrowth of the development and implementation of this laboratory has been faculty development. If students are to be encouraged in their interdisciplinary thinking, faculty must also
OCR for page 79
Bio 2010: Transforming Undergraduate Education for Future Research Biologists think along these same interdisciplinary lines, an approach to teaching and learning that is not always natural or comfortable for college faculty. The ID Lab has promoted cross-disciplinary understanding by the faculty and, as such, is a positive step toward encouraging students to think about disciplinary connections. Finally, the lab requires that students apply rigorous quantitative approaches to analyzing their experimental work, thus helping them see the importance of studying further mathematics and computer science if they are going to solve important problems in the life sciences. While it is too early to tell whether the lab will lead students in mathematics, computer science, or the physical sciences to pursue careers in the life sciences, or whether those who were planning on studying biology will take a more quantitative path toward their career, it seems possible that such results may occur. Some of the laboratory exercises that ID Lab students conduct include: Thermal properties of an ectothermic animal: Are lizards just cylinders with legs? Molecular weight of macromolecules: Is molecular weight always simple? Mechanical resonance of a high-rise building: Are seismic nightmares avoidable? Carbonate content of biological hard tissue: Of what are shells composed? Using digital logic to time a simple pendulum: What makes a good clock? A structure-activity investigation of photosynthetic electron transport: How does a biological system convert physics into chemistry? Synthesis and characterization of liquid crystals: Or when are liquids not? A genetic map of a bacterial plasmid: Where are the restriction sites? For more information: http://www2.hmc.edu/~karukstis/IDLab/1999_2000/home.htm
OCR for page 80
Bio 2010: Transforming Undergraduate Education for Future Research Biologists CASE STUDY #7 Neurobiology Laboratory Harvard University An inquiry-based approach to neuroscience at Harvard University uses state-of-the-art technology to study the development and function of the nervous system. Each of four faculty members leads a three-week laboratory module centered on a common theme. This one-semester course meets for three hours, twice weekly. Because the experiments are open-ended, students can spend additional time in the laboratory as desired. For each module, students prepare a report describing their experimental results and interpretation. In the following example, the course was centered on the visual system. The themes of the four modules were: Visual processing in the retina. Students examined electrical recording of action potentials from retinal ganglion cells of the salamander. They analyzed the neural code for visual signals, in particular temporal integration and color processing. Methods used included dissection, extracellular recording, pharmacology, and spike train analysis. Cellular electrophysiology. Students performed patch clamp analysis of horizontal cells isolated from the retina. They studied the various electrical conductances of the neuronal membrane, including how they are activated by changes in voltage and binding of ligands. Methods used included current clamp and voltage clamp recording, light microscopy, and pharmacological studies. Development of the visual system in Drosophila. Topics included how molecules direct axon guidance, the mechanisms that determine neural connectivity throughout development. Methods used included microdissection, immunohistochemistry, video microscopy, confocal microscopy, and mutant analysis. Circadian rhythms in the suprachiasmatic nucleus. Students observed neural firing in the brain’s biological clock, how it varies rhythmically with time of day, and how it is entrained by the environmental light cycle. They monitored corresponding changes in gene transcription for molecular components of the clock. Methods used included brain slice dissection, extracellular recording, and PCR amplification. For more information: http://www.mcb.harvard.edu/Education/Undergrad/Biochem/int_and_adv_courses.html
OCR for page 81
Bio 2010: Transforming Undergraduate Education for Future Research Biologists inverse dynamics modeling of a simplified foot to determine ankle reaction forces, moments, and powers; and force control within the context of motor control. Laboratory exercises on the above topics could also include a special emphasis on the numerical and mathematical analysis of experiments. For example, students studying the inverse dynamics model of a mass and spring could use an experimental setup including an accelerometer on the mass, and a spring supported by a load cell. Students would measure the mass location using an encoder or potentiometer. They would take measurements while the system oscillates and use inverse dynamics to calculate the spring force. The calculation can be done using two different methods. One method of calculation would require them to numerically low-pass filter the location data and then numerically differentiate the location data to achieve acceleration as a function of time and calculate the spring force. In the second method, they would calculate the spring force using the acceleration data and an idealized mathematical model of the mass, spring stiffness, and initial conditions. The group could then discuss the similarities and differences between the two descriptions of the spring force. In the run phase, the labs would each last approximately three weeks, to give students an opportunity to consider each area in depth. Topics could include sensors, data acquisition systems, signal processing, or computational analysis of data. The labs would be designed to give students the ability to characterize, specify, analyze, and integrate devices. Labs could be centered on applications relevant to modern biological research or clinical biomedical studies such as these examples: The human eye: optical measurements, structure of the eye, functioning of the eye, the optical system of the eye, the response system of the eye, resolution of the eye, the eye’s response to varying illumination, depth perception, or defects of vision. Biomedical measurement: cell, nerve, and muscle potentials; electrocardiograms (ECG), electromyograms (EMG), body temperature, control of body temperature, heat loss from the body, blood pressure measurement, blood flow and volume measurements, noninvasive blood-gas sensors, optical microscopy, cell adhesion, optical sources and sensors, lung volume, heart sounds, drug delivery devices, surgical instruments, or electroshock protection. Medical imaging: origin of x-rays, the x-ray beam, attenuation and
OCR for page 82
Bio 2010: Transforming Undergraduate Education for Future Research Biologists CASE STUDY #8 Workshop Physics Dickinson College Project-based teaching has completely replaced traditional lecture and laboratory teaching in a physics course entitled Workshop Physics, pioneered at Dickinson College in 1986. Workshop Physics uses guided inquiry workshops featuring computers and specially designed equipment to help students learn by doing. Inquiry-based cooperative learning is combined with the comprehensive use of computer tools for data acquisition, data analysis, and mathematical modeling. Students meet in three two-hour sessions each week. There are no formal lectures. Each section has one instructor, two undergraduate teaching assistants, and up to 24 students. Each pair of students shares the use of a microcomputer and an extensive collection of scientific apparatus and other gadgets. Among other things, students pitch baseballs, whack bowling balls with rubber hammers, pull objects up inclined planes, attempt pirouettes, build electronic circuits, explore electrical unknowns, ignite paper with compressed gas, and devise engine cycles using rubber bands. The Workshop labs are staffed during evening and weekend hours with undergraduate teaching assistants. Kinematics, Newton’s laws of motion, conservation laws, rotational motion, and oscillations are studied in the first semester. The second semester covers thermodynamics, electricity, electronics, and magnetism. The material is divided into units lasting about one week. Students use an activity guide (e.g., Laws, Workshop Physics Activity Guide, 1997), which has expositions, questions, and instructions as well as blank spaces for student data, calculations, and reflections. The guide is keyed to a standard textbook. Microcomputer-based laboratory tools (called MBL tools) are used extensively to collect, analyze, and display data. An MBL station consists of a sensor or probe that is plugged into a microcom absorption of x-rays, x-ray filters, beam size, radiographic image, production of x-rays, computed tomography, ultrasound, MRI, nuclear imaging, single-photon emission computed tomography, or positron emission tomography.
OCR for page 83
Bio 2010: Transforming Undergraduate Education for Future Research Biologists puter via an electronic interface (e.g., www.vernier.com and www.pasco.com). Sensors that have been linked directly to the computer include an ultrasonic motion detector, photogates, temperature sensors, light probes, pressure sensors, currents and voltage probes, magnetic field sensors, rotary motion sensors, and Geiger tubes. With a new generation of MBL software developed at Tufts University, the computer can perform instantaneous calculations and produce real-time graphs. Software features allow users to enter new calculations into the software for the real-time display of derived quantities. For example, position vs. time data acquired using the motion sensor can be used to calculate kinetic energy vs. time data in real time. The software also allows users to perform FFT analysis, do curve fitting and modeling, and find derivatives and integrals for selected portions of the data. Data can also be transferred easily to a spreadsheet for additional analysis. Video analysis tools allow students to capture and digitize two-dimensional motion. About two-thirds of the students who have taken Workshop Physics strongly prefer this method to the lecture approach. Although the conceptual gains of Workshop Physics students are greater than those achieved by students taking conventional physics courses in many topic areas, the gains are not universal, and in certain areas Workshop Physics students perform no better than their traditional peers. Student performance in upper-level physics courses and in solving traditional textbook problems is as good as or better than that of students in the traditional curriculum. Moreover, Workshop Physics students demonstrate a comparatively greater degree of comfort working with computers and other laboratory equipment. For more information: http://physics.dickinson.edu/Workshop_Physics/Workshop_Physics_Home.htm A Proposed Engineering-for-Life-Scientists Laboratory One way to engage students with engineering concepts important to biology is through an “engineering-for-life-scientist” laboratory. This idea is presented here because it was suggested as an alternative to a physics lab by the panel on physics and engineering. It could also be adapted for teaching as an independent course or as the laboratory component of a
OCR for page 84
Bio 2010: Transforming Undergraduate Education for Future Research Biologists biology course. The laboratory described here follows a similar crawl, walk, run format as the physics laboratory proposed above. Students would obtain hands-on experiences with how the basic laws of physics control life from an engineering perspective. This approach would also be synergistic with the idea of integrating more engineering concepts into biology courses. Students would consider the following types of questions: What solutions did nature find to solving a certain problem? How does the system function? What are the crucial functional elements? Why do they work together? These are essentially engineering questions. The crawl phase would focus on the ramifications of Newton’s mechanics: Conservation of energy: energy input and storage, measurement of energy consumption, external and/or internal mechanical work, energy efficiency. Muscles as force actuators; moments created by muscles; calculating the point of gravity; force analysis of a system with one, two, and more joints; set-up a mass-spring system. Attach an accelerometer to the mass, and measure the response. Building a simple robotic system that can move and carrying out a mechanical analysis of the construct. The walk phase would focus on electrical phenomena ranging from charges and charge separation in solution, to electronics and instrumentation: Building RC circuits; mimicking an action potential of a nerve cell; simple coupled RC circuits. Circuit analysis. Osmotic pressure versus hydrostatic pressure; building a cell; pressure measurements; analysis of systems with varying pore sizes and/or sizes of charged particles. Modeling the kinetics of charge separation. Visualizing and analyzing the path of charged molecules/particles in microfluidic devices. Experimentation and modeling. The run phase would focus on optics and spectroscopy. Optical microscopy has emerged as a primary experimental tool for biologists, so students would learn the basic optical laws, as well as the essential components and methods in optical microscopy. Fluorophores are frequently employed by biologists as spectroscopic probes. The way that fluorophores absorb
OCR for page 85
Bio 2010: Transforming Undergraduate Education for Future Research Biologists and emit light and the competing de-excitation pathways by which fluorophores can give off their energy are important concepts. Proper analysis of the signals and images captured with optical microscopes is crucial to avoid misinterpretation of data and erroneous conclusions. Assuming that in the future optics will play a stronger role in the classroom physics curriculum, the following topics could be covered: Building a human eye from optical components. Analysis of its performance; corrective optics for the human eye. Light sources and optical components (filters, lenses, lambda/half and lambda/quarter plates, polarizers). Introduction to optical microscopy; illumination, building of a simple telescope or microscope. Differential interference microscopy. Confocal microscopy. Photophysics of light absorption and emission, competing deactivation pathways; kinetic analysis. Chemistry Laboratory Chemistry laboratory courses frequently focus on teaching specific research techniques. Experience indicates that students are more excited about courses in which they feel they are discovering something new, not just trying to duplicate an established experiment. The two objectives can be combined into a project-based laboratory. For example, in a synthetic organic chemistry experiment, different groups of students could perform the reaction at different temperatures. This would enable them to determine a rate constant for the reaction, and also its energy of activation, and for different times, to see the effect on yield of the product. Another possibility is to determine the effect of reaction conditions, such as the duration of synthesis, on the ratio of the desired product to other products. All of this is relevant to optimizing a synthesis, a common real-life research goal in industry. The variation in results among students performing the same experiment would also introduce them to statistical analysis of experimental data. Chemistry laboratory courses are also excellent places to teach some fundamental aspects of the science. For example, infrared and nuclear magnetic resonance spectroscopies are most appreciated if students examine
OCR for page 86
Bio 2010: Transforming Undergraduate Education for Future Research Biologists “unknowns” by these techniques and then deduce their chemical structures, perhaps also being given a mass spectrum. Some simple experiments with enzymes can teach a lot. For example, students as a class can follow an enzymatic reaction using optical spectroscopy of quenched samples (so they do not need to tie up the spectrometers) at different times, but with varying pH’s and/or the addition of inhibitors with varying substrate concentrations. This would let them determine and try to understand the rate laws involved and the reason for a pH dependence. Genomics Laboratory Project-based laboratories are also well suited for the acquisition of computer and programming skills. Genomics lends itself particularly well to project-based learning. For example, students could be asked to carry out computer searches to track down what is known about a particular gene. This would involve exploring (1) the internal structure of the gene: exons, introns, promoter, and transcription factor binding sites; (2) how its expression is regulated; (3) homologs, orthologs, and other aspects of its evolution; (4) the structure and function of the protein; (5) interactions of the protein with other proteins and with small molecules; and (6) diseases caused by mutations in the coding and noncoding regions of the gene. Students in such a laboratory could also be presented with challenges such as predicting alternative splicing patterns or three-dimensional structure. Sophisticated project-based experiments in genomics are being carried out by undergraduates at many institutions using DNA arrays. The Genome Consortium for Active Teaching (GCAT), founded at Davidson College and now comprising more than 35 faculty members around the country, has made DNA arrays accessible to undergraduates for original experiments in which the expression levels of many genes are monitored for pairs of distinctive biological states (e.g., growth in a rich versus a minimal medium). The consortium provides yeast, Arabidopsis, and E. coli expression arrays at a relatively modest price. Protocols for the preparation of RNA and for hybridization are also provided. Undergraduates carry out the biological experiments, isolate the mRNA, and perform the hybridization. The arrays are then sent to GCAT for scanning on their array reader. Students analyze the resulting expression data to determine which genes are differentially expressed and to pose questions for further experimentation.
Representative terms from entire chapter: