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 152
Bio 2010: Transforming Undergraduate Education for Future Research Biologists E Physics and Engineering Panel Summary The panel on physics and engineering met on February 25-26, 2001, at the National Academy of Sciences building. The panel devoted most of its effort to the discussion of appropriate content for an introductory physics course. They also considered the role of engineering in the study of biology and ways to help students understand the concept of systems that is so crucial to engineering, and becoming more central to biomedical research. EXPERTISE OF MEMBERS OF THE PANEL John Hopfield is Howard A. Prior Professor in the Life Sciences and Professor of Molecular Biology at Princeton University. His research encompasses neurobiology and computing networks. He is a member of the National Academy of Sciences, the American Academy of Arts and Sciences, and the American Philosophical Society. He has received the MacArthur Fellowship and the APS prize in Biophysics and was named California Scientist of the Year for 1991. He has taught in physics departments (from first-year physics to graduate condensed matter physics), in chemistry departments (first-year chemistry to graduate biophysical chemistry), and now in a molecular biology department, where he teaches a senior course related to how networks of neuron-like elements compute. He has a bachelor’s degree from Swarthmore College and PhD from Cornell.
OCR for page 153
Bio 2010: Transforming Undergraduate Education for Future Research Biologists Daniel Axelrod is a professor of physics at the University of Michigan. His research is on the development of optical microscopy techniques to study dynamics at biological surfaces and membranes. He has taught extensively, including courses on Physics and Music, Biophysical Principles of Microscopy, Techniques in Molecular Biophysics, Dynamics of Biophysical Processes, Science and Strategy in the Nuclear Arms Race, Living with Physics, and Introductory Modern Physics. He is a Fellow of the Biophysical Society and has received the Excellence in Teaching Award from the University of Michigan. He has a bachelor’s degree in physics and math from Brooklyn College and a PhD in physics from the University of California at Berkeley. Scott Fraser is the co-director of the Center for Computational Molecular Biology and Anna L. Rosen Professor of Biology at California Institute of Technology. His research explores the mechanisms involved in the assembly of the vertebrate nervous system, in particular, the patterning of cell lineages, cell migration, and axonal connections. He is involved in developing new imaging technologies (modification of optics of light microscopes, new software for acquisition, and manipulation of data) at the Biological Imaging Center of the Beckman Institute with a goal of developing methods to observe single cells in intact developing embryos. He is the recipient of the Marcus Singer Medal and the McKnight Scholar Award and is a fellow of the American Academy of Arts and Sciences. He received the Kaiser-Permanente Award for Best Medical School Teaching and the Silver Beaker Award for Best Medical School Faculty Member. Among the many courses he has taught at Caltech are Principles of Modern Microscopy, Fundamentals of Modern Biology, and Developmental Neurobiology. In addition he has taught summer courses at Cold Spring Harbor. He received his bachelor’s degree from Harvey Mudd College and his PhD from Johns Hopkins University. Jonathon Howard is a professor of physiology and biophysics at the University of Washington. He was recently named a director at the Max Planck Institute for Molecular Cell Biology and Genetics. His research is on the mechanical properties of cells and molecules focusing on the motor protein kinesin. He was a PEW Scholar in 1990 and was awarded a Guggenheim Fellowship in 1996. He has a bachelor’s degree in pure mathematics and a PhD in neurobiology, both from Australian National University.
OCR for page 154
Bio 2010: Transforming Undergraduate Education for Future Research Biologists Mimi Koehl is a professor in the Integrative Biology Department at the University of California at Berkeley. Her research involves the application of fluid dynamics and solid mechanics to study how biological structures function in nature. She utilizes this approach to investigate the various ways in which organisms withstand and utilize the movement of water or air around them. She has been awarded the Presidential Young Investigator Award and two achievement awards from Gettysburg College. She has received NATO, Guggenheim, and MacArthur fellowships. Her teaching experience includes Animal Biology, Physiology, Biomechanics and Structure, The Mechanics of Organisms, The Biology of Rocky Seashores, and Living Machines. She is on the scientific advisory board for The Shape of Life, a National Geographic television series about animal form, function, and evolution. She was elected as a member of the National Academy of Sciences in 2001. She received her bachelor’s degree from Gettysburg College in Pennsylvania and her PhD in zoology from Duke University. Carl Luchies is a professor of mechanical engineering at the University of Kansas at Lawrence. He is also the director of the Human Performance Laboratory, located in the Center on Aging, University of Kansas Medical Center. His research is on biomechanics including human balance and mobility. He previously taught at Hope College in Holland, Michigan, where he developed a liberal-arts-based engineering education program. He has taught courses in computer-aided design, statics, solid mechanics, material science, vibrations, thermodynamics, and fluid mechanics. He received his bachelor’s degree from Calvin College and PhD from the University of Michigan. Jose Onuchic is a professor of physics at the University of California at San Diego. His research in theoretical biophysics and chemical physics focuses on theory of chemical reactions in condensed matter and rational design of functional proteins. He is a member of the Molecular Biophysics Training Grant Steering Committee at UCSD and served on UCSD’s Task Force on Biological Sciences. He was awarded the Engineering Institute Prize, Sao Paulo, Brazil, in 1980 and the International Centre for Theoretical Physics Prize in Honor of Professor Werner Heisenberg, Trieste, Italy, in 1988. He was named an associate member of the Academia de Ciencias do Estado de Sao Paulo, a Beckman Young Investigator, a Fellow of the American Physical Society, and a Senior Fellow of SDSC, a national laboratory for computational science and engineering. He is part of a team recently awarded a
OCR for page 155
Bio 2010: Transforming Undergraduate Education for Future Research Biologists biocomplexity grant from NSF. He received his bachelor’s degrees in electrical engineering and physics from Universidade de Sao Paulo in Brazil and his PhD from California Institute of Technology Viola Vogel is director of the Center for Nanotechnology and professor of bioengineering at the University of Washington. Her research program is focused on investigating how to control the assembly of molecular building blocks into supramolecular complexes with predictable architecture. It involves nanoscale surface patterning, molecular motors and switches, biomaterials, assembly of extracellular matrix proteins, cell/surface interactions, biomineralization, surface analysis, optical spectroscopy, and microscopy. She received her PhD in physics from Johann-Wolfgang Goethe University in Frankfurt/Main REPORT OF THE PHYSICS AND ENGINEERING PANEL The panel devoted most of its effort to the discussion of appropriate content for an introductory physics course. The concepts that they felt were appropriate are listed in the body of the report. The panel concluded that physics plays three roles in the education of the future research biologist. First, there are the specific and quantitative principles of physics on which a microscopic understanding of biology is ultimately based, and on which much of the instrumentation of biological research is also based. Understanding better how these principles are reflected in biology becomes important as biological research becomes more quantitative, develops further quantitative models, and becomes even more heavily reliant on experimental physical techniques. Second, and more abstract, physics is a more mature science with far less complexity than biology, in which a student can more easily learn about the interactive relationship between experiments, theory, modeling, and analysis. Third, much of physics is about the behavior of dynamical systems. Biologists need to understand dynamics, for biology is fundamentally a driven, dissipative system, not an equilibrium system. For most students, 1 to 1.5 years of a physics course with an appropriate curriculum can make significant progress toward accomplishing these three objectives. Additional physics-based and engineering-based courses emphasizing biology should also be available at major institutions. The panel anticipates that an increasing number of physics/engineering majors or double majors in physics/engineering and biology will go into graduate education in biology.
OCR for page 156
Bio 2010: Transforming Undergraduate Education for Future Research Biologists The panel listed three questions that might be asked about the content of an introductory physics course: What background is needed? How can that background material be structured into a course? What other material needs to be added in order to make the course understandable? An appropriate yearlong course of more or less conventional format but revised content is described in the main text of the report. Given the increased emphasis of that course on physical measurement techniques, dynamical systems, modeling, and quantitative analysis, the panel felt that it was appropriate to address the question of balance between chemistry, physics, engineering, mathematics, and computer science in the new curriculum. In view of the importance for biology of materials that cannot be addressed within a oneyear physics course, offering an optional additional physics course is strongly recommended by the panel. Ideas for this course are outlined below. The panel felt that the biologists of 2010—on the average—would be better served by these additions to the physics curriculum than an obliga-tory third quarter (or second semester) of organic chemistry. Potential Additions to the Physics Concepts Described in the Body of the Report The physics concepts listed in the body of the report could potentially fit into a yearlong introductory course. However, the panel felt that additional concepts of physics would also be useful to biology students. The following list indicates those topics they recommend adding to the curriculum in schools where biology students are able to take a four-quarter or three-semester sequence of physics. Some of these topics might also be substituted for concepts in the list found in the body of the report, depending on the interests of the students or the instructor. Particle in a box; energy levels; spectroscopy from a quantum viewpoint Representation of optical spectra as a distribution of oscillators absorbing and emitting energy Forster Transfer; quenching; photon-counting noise/statistics Other microscopies: electron, scanning tunneling, atomic force Networks – Neural/chemical/genetic (This goes well with electrical circuit analysis—should also do a laboratory with real circuits. This area connects well to biological examples.) Spontaneous static pattern formation and symmetry breaking (mag-
OCR for page 157
Bio 2010: Transforming Undergraduate Education for Future Research Biologists netization—from microscopics to the magnetic phase transition; the liquid-gas interface; handedness of quartz crystals Spontaneous dynamical pattern formation (wind-driven surface waves in water, stripe formation in sedimentation, circulation patterns in water heated from below, the BZ reaction, slime mold aggregation) Chaos and periodicity; chaotic systems in physics (coupled oscillators, onset of turbulence) and in biology (population dynamics, heartbeat) Electromagnetism and magnetic properties of matter: B, H, dipole fields, forces on magnetized particles, how fMRI originates from magnetic properties of hemoglobin; magnetic bacteria and nerve cells. The panel envisions the teaching of a one-year course derived from the physics concepts in the body of the report. Some portions of such an introductory physics course could be relatively conventional. The course might well begin with classical mechanics (because it is the basis for a kinetic understanding of chemistry). Gravity would be included—not because it is historic and conventional (which it is) but because it is an excellent pedagogical subject for understanding mechanics. The course might initially treat heat in the usual fashion as the “byproduct” of dissipative forces and explore the second law of thermodynamics from the conventional 19th-century viewpoint. However, added to the chosen subset of topics from today’s introductory physics is a focus on the parts of physics relevant to biology at the molecular level, and on aspects of macrocsopic physics relevant to biological functions. A totally different pedagogy, of more relevance to molecular biology, beginning at the microscopic level, might be developed as an alternative course of study. The level of the course would depend to some degree on the amount of material students have already learned in their high school science courses. The existence of superb simulation tools for visualizing the predictions of a set of physics equations should be strongly used in homework problem sets. These tools free the student from the tyranny of only considering the limited “special problems” that are exactly solvable, allow the student to experiment beyond their ability to carry out the manipulations of classical mathematics, are wonderful tools any time statistical ideas are a part of the physics, and, in addition, are now important tools for any scientist. These tools can be introduced as almost “canned programs,” but the progress through the year should require more and more ability of the students to alter parts of the programs, and ultimately to generate their own programs. The list of concepts in the body of the report has been trimmed to be
OCR for page 158
Bio 2010: Transforming Undergraduate Education for Future Research Biologists taught plausibly in a one-year course. Topics have been sacrificed from within the customary one-year physics curriculum. These include all aspects of magnetism, inductance, Maxwell’s Equations, angular momentum, and special relativity. Some time might be saved if chemistry and physics courses are appropriately coordinated, though such cooperation is not natural to university faculties. Similarly, if the mathematics courses can teach complex numbers early, they could be made use of within the physics curriculum for x-ray structure determinations, oscillations, resonance, and stability analysis. Also a major effort must be made to include simple biological examples in the problem sets. Every attempt should be made to win acceptance of such a new physics course by non-biological majors, in addition to the various possible biomajors (biology, biochemistry, molecular biology). In an ideal world, a freshman could take either the traditional general physics course or the biology-oriented physics course (B-Physics) as her or his physics requirement. The two courses should be equally challenging and equally based on mathematics, but differ in emphasis. Many majors should be encouraged to accept the B-Physics course as an alternative, including chemistry, math, computer science, and engineering majors. Having several majors accept one course as meeting requirements avoids having students become trapped in a particular major because they have chosen a particular introductory physics course. Also, by giving students flexibility in their curriculum, they will be encouraged to explore opportunities they otherwise might not explore. While a few premeds may appropriately take the B-physics course, its emphasis on physical understandings at the molecular level, and the mathematical sophistication are inappropriate for general premeds. At most universities, an effort to accommodate premeds in the same course would require a substantial dilution of the material presented. While much can be said in favor of redesigning physics courses for premeds, this course is not the appropriate vehicle. While a conventional laboratory might be adequate, it seems more sensible to consider fundamental changes in laboratory as well as course materials. One possible rationale is based on the usual kind of relationship between course and laboratory physics. A second possible rationale is based on using the laboratory experience to teach principles of engineering as they apply to biology. Sample sets of laboratories for each rationale are sketched in the following two sections. The purpose of the lab would be to reinforce lecture concepts, introduce new concepts particularly suitable to laboratory exploration, illustrate physical principles, and/or experience bio-
OCR for page 159
Bio 2010: Transforming Undergraduate Education for Future Research Biologists applications. Error analysis, uncertainty, fluctuations, and noise are probably best treated as part of laboratory experience rather than as topics in physics. Examples from biology should be used when available, and can already start in the section on Newtonian and macroscopic mechanics. Properties of materials (bone, tendon, hair) and biological fluid flows or motions of bacteria or bioparticles in water provide excellent opportunities. The laboratory should begin with sessions based on step-by-step instruction, data sheets, equations given, and minimal writing. In a later phase, there should be guidelines—laboratories based on examples of how to do things, concepts, and a memo report (~1 page). Over the year they should evolve to open-ended questions with minimal reporting (~2 pages). This is a “Crawl, Walk, Run” approach. Students should work as a team consisting of two or three students for all labs. While the work done in lab should be done as a team, all writing assignments should be done by each student to develop writing skills. Whenever possible, students should learn by doing. If students are required to think through the process, they will have a much better understanding of the concepts. It may not be feasible to have a physical lab for all the desired laboratory experiences. Physical laboratories are preferred whenever possible, but both physical and virtual labs should be utilized. LabVIEW and Matlab both offer excellent environments for students to learn laboratory concepts. Web-based learning should also be utilized when particular experiments are not available or may be hard to reproduce locally. Details on the content for such a lab can be found in Chapter 4. Connections to Engineering in the Biology Curriculum It is important to bring some ideas from engineering into the education of biology students. The word function is used in a similar context in engineering and biology, and this context does not exist in pure science or mathematics. Biology, with the impetus to dissect systems to understand their components (top-down), has evolved in the past decade into a molecular science. Now that the human genome is known, and the molecular players of many cell-signaling pathways are identified, biology is turning increasingly to the understanding of complex systems. Understanding function at the systems level requires a way of thinking that is common to many engineers. An engineer takes building blocks to build a system with desired features (bottom-up). Creating (or re-creating) function by building a complex system, and getting it to work, is the ultimate proof that all essential
OCR for page 160
Bio 2010: Transforming Undergraduate Education for Future Research Biologists building blocks and how they work in synchrony are truly understood. Getting a system to work typically requires (a) an understanding of the fundamental building blocks, (b) knowledge of the relation between the building blocks, (c) the system’s design, or how its components fit together in a productive way, (d) system modeling, (e) construction of the system, and (f) testing the system and its function(s). Understanding cells, organs, and finally animals and plants at the systems level will require that the biologist borrow approaches from engineering, and that engineering principles are introduced early in the education of biologists. Biology research is really about trying to understand how biology works. What actually constitutes such an understanding is often best grappled within an engineering context, where systems have been designed and do work. Students should be frequently confronted throughout their biology curriculum with questions and tasks such as how they would design “xxx,” and how they would test to see whether their conceptual design actually works. They should be asked to simulate their system, determine its rate constants, determine regimes of stability and instability, investigate regulatory feedback mechanisms, and other challenges. The engineering view has a role in the general biology curriculum, or could be introduced as special-topics biology courses or as specific courses within engineering biomedical engineering/biomaterials programs. Some examples of topics with engineering aspects that might be included within the ordinary biology curriculum can be found in the body of the report. Another appropriate subject is the study of molecules and supramolecular structures from both a biochemical and a mechanical perspective. The students should also be thinking of kinetics, rate constants, and other topics addressed in the outline of the physics course. Assuming that biochemistry is already well covered, these concepts with an emphasis on mechanics could be developed in the context of motor proteins, assembly and de-assembly of the cytoskeleton, condensation of DNA, etc. The students could be asked to analyze raw data quantitatively to see the relationship between physical structure, reaction pathways, and function or model the dynamics (e.g., dynamic instabilities) of a system with a given set of parameters. Seminars Seminars on research, directed to lower-division undergraduates, can illustrate the relevance of mathematical and computer modeling and analysis. They are effective ways to convey the importance of quantitative and
OCR for page 161
Bio 2010: Transforming Undergraduate Education for Future Research Biologists modeling approaches to research in biology. While not directly part of the physics/engineering curriculum for biology, and perhaps best given under the aegis of a biology department, they can have an immense impact on the views of students as to what is of importance. Many engineering curricula require a capstone design experience, in which students undertake one project that ties together many of the topics they have learned throughout their college career. Borrowing successful models from engineering, a biology capstone course might be required. This course could be a design experience, a research experience, or a combination of the two. The goal should be to give a major experience that requires the students to bring together their diverse knowledge to accomplish the goals of the projects. The students should work as teams under the close guidance of a faculty member. The course should be a one-semester course, although a two-semester sequence is not uncommon in engineering. The teams should be required to accomplish something more than a paper product (i.e., writing a small research proposal should not be sufficient). Instead of research, the students could focus on the development of a biorelated product. In any event, a significant report and presentation should be required. Efforts should be made to have biology students work on multidisciplinary projects with engineering, biomedical engineering, physics, chemistry, and other majors. The committee brainstormed the following ideas for advanced seminar courses, and some aspects of these courses would also make appropriate capstone projects. They involve bringing together diverse aspects of students’ previous education in order to increase their understanding of more complex systems: The Mechanics of Organisms as described in Case Study #5 in the body of the committee report. Determination of Structure, the chemistry and biology of proteins using methods of diffraction and spectroscopy and including the topics of fluorescence, Fourier transforms, electron spins, and display of 3-D data. Biological Imaging including the properties of light, thin lens laws, resolution, and diffraction orders, the lens as a Fourier transform, fluorescence, confocal microscopy, MRI, electron microscopy, tomography, and deconvolution. Molecular Biophysics of signal transduction at the cell surface and inside the cell, including the statistics of receptor ligand interactions, life in low Reynolds number, kinases and phosphatases, G-protein coupled cas-
OCR for page 162
Bio 2010: Transforming Undergraduate Education for Future Research Biologists cades, the cytoskeleton and cell adhesion, transcription factors and genetic cascades, and the multiple roles of individual proteins and cross-talk between different pathways (beta catenin for example). Biomedical Systems: a bioengineering/biophysics approach to human physiology. Topics would include organ physiology, hormones and endocrine loops, paracrine effects, systems analysis of control loops, the importance of temporal aspects of hormones, and examples such as cardiac control loops and circadian rhythms. Biological Motors and Molecular Machines.
Representative terms from entire chapter: