| WEEK # | TOPICS | READINGS |
|---|---|---|
| 1 | Introduction |  Galilei, G. (1638). Excerpt from Dialogues Concerning Two New Sciences. Translated by H. Crew and A. de Salvio. New York, NY: Reprinted by Dover Publications, 1954. ISBN: 9780486600994. Nabi, I. "On the Tendencies of Motion." In The Dialectical Biologist. Edited by R. Levins and R. C. Lewontin. Cambridge, MA: Harvard University Press, 2006. ISBN: 9780674202832.Howard, D. A. "Albert Einstein as a Philosopher of Science." Phys Today (December 2005): 34-40. |
| 2 | The Process of Model Building | Zwislocki, J. "Analysis of the Middle-Ear Function. Part I: Input Impedance." J Acoust Soc Am 34 (1962): 1514-1523. Kringlebotn, M. "Network Model for the Human Middle Ear." Scand. Audiol 17 (1988): 75-85. Pascal, J., A. Bourgeade, M. Lagier, and C. Legros. "Linear and Nonlinear Model of the Human Middle Ear." J Acoust Joc Am 104 (1998): 1509-1516. |
| 3 | Analytic vs. Computational | Lynch, T. J., V. Nedzelnitsky, and W. T. Peake. "Input Impedance of the Cochlea in Cat." J Acoust Soc Am 72 (1982): 108-130. Puria, S., and J. B. Allen. "A Parametric Study of Cochlear Input Impedance." J Acoust Soc Am 89 (1991): 287-309. Shera, C. A., and G. Zweig. "A Symmetry Suppresses the Cochlear Catastrophe." J Acoust Soc Am 89 (1991): 1276-1289. |
| 4 | Detailed vs. Heuristic I | Kalluri, S., and B. Delgutte. "Mathematical Models of Cochlear Nucleus on set Neurons. II. Model with Dynamic Spike-Blocking State." J Comput Neurosci 14 (2003): 91-110. Zhou, Y., L. H. Carney, and H. S. Colburn. "A Model for Interaural Time Difference Sensitivity in the Medial Superior Olive: Interaction of Excitatory and Inhibitory Synaptic Inputs, Channel Dynamics, and Cellular Morphology." J Neurosci 25 (2005): 3046-3058. Goldstein, M. H., and N. Y. S. Kiang. "Synchrony of Neural Activity in Electric Responses Evoked by Transient Acoustic Stimuli." J Acoust Soc Am 30 (1958): 107-114. |
| 5 | Special Topic I: Dimensional Analysis and Scaling | Galilei, G. Excerpts from Dialogues Concerning Two New Sciences. Translated by H. Crew and A. de Salvio. New York, NY: Reprinted by Dover Publications, 1954. ISBN: 9780486600994. Thompson, D. W. "On Magnitude." In On Growth and Form: A New Edition. New York, NY: Cambridge University Press by Dover Publications, 1942. ISBN: 9780521066228. McMahon, T. "Size and Shape in Biology." Science 179 (1973): 1201-1204. West, G. B., J. H. Brown, and B. J. Enquist. "The Fourth Dimension of Life: Fractal Geometry and Allometric Scaling of Organisms." Science 284 (1999): 1677-1679. |
| 6 | Field Trip | Elhilali, M., J. B. Fritz, D. J. Klein, J. Z. Simon, and S. A. Shamma. "Dynamics of Precise Spike Timing in Primary Auditory Cortex." J Neurosci 24 (2004): 1159-1172. |
| 7 | Detailed vs. Heuristic II | Smith, E. C., and M. S. Lewicki. "Efficient Auditory Coding." Nature 439 (2006): 978-982. Kayser, C., C. I. Petkov, M. Lippert, and N. K. Logothetis. "Mechanisms for Allocating Auditory Attention: An Auditory Saliency Map." Curr Bio 15 (2005): 1943-1947. |
| 8 | Special Topic II: Curve Fitting, Resampling, and Monte Carlo | Gott, J. R. "Implications of the Copernican Principle for our Future Prospects." Nature 363 (1993): 315-319. Yedid, G., and G. Bell. "Macroevolution Simulated with Autonomously Replicating Computer Programs." Nature 420 (2002): 810-812. |
| 9 | Forward vs. Inverse | Zweig, G. "Finding the Impedance of the Organ of Corti." J Acoust Soc Am 89 (1991): 1229-1254. Neely, S. T. "A Model of Cochlear Mechanics with Outer Hair Cell Motility." J Acoust Soc Am 94 (1993): 137-146. Kolston, P. J., and J. F. Ashmore. "Finite Element Micromechanical Modeling of the Cochlea in Three Dimensions." J Acoust Soc Am 99 (1996): 455-467. |
| 10 | Special Topic III: Chaos and the Limits to Prediction | Lorenz, E. N. "Deterministic Nonperiodic Flow." J Atmos Sci 20 (1963): 130-141. Fiegenbaum, M. J. "Universal Behavior in Nonlinear Systems." Los Alamos Science 1 (1980): 4-27. |
| 11 | Special Topic IV: Molecular Mathematical Biology | Turing, A. M. "The Chemical Basis of Morphogenesis." Phil Trans Roy Soc Lond B 237 (1952): 37-72. Yuh, C. -H., H. Bolouri, and E. H. Davidson. "Genomic Cis-Regulatory Logic: Experimental and Computational Analysis of a Sea Urchin Gene." Science 279 (1998): 1896-1902. Dassow, G. von, E. Meir, E. M. Munro, and G. M. Odell. "The Segment Polarity Network is a Robust Developmental Module." Nature 406 (2000): 188-192. |
| 12 | Student Selections I | White, R. D., and K. Grosh. "Microengineered Hydromechanical Cochlear Model." Proc Nat Acad Sci USA 102 (2005): 1296-1301. Allen, J. B., and S. T. Neely. "Modeling the Relation between the Intensity Just-Noticeable Difference and Loudness for Pure Tones and Wideband Noise." J Acoust Soc Am 102 (1997): 3628-3646. |
| 13 | Student Selections II | Xu, Y., and L. M. Collins. "Predicting the Threshold of Single-Pulse Electrical Stimuli using a Stochastic Auditory Nerve Model: The Effects of Noise." IEEE Trans Biomed Engr 50 (2003): 825-835. O'Gorman, D. E., J. A. White, and C. A. Shera. "Realistically Irregular and Desynchronized Neural Firing without Physiological Noise." In preparation. 2006. |
| 14 | The Relation between Theory and Experiment | Hodgkin, A. L., A. F. Huxley, and B. Katz. "Measurement of Current-Voltage Relations in the Membrane of the Giant Axon of Loligo." J Physiol 116 (1952): 424-448. Hodgkin, A. L., and A. F. Huxley. "Currents Carried by Sodium and Potassium through the Membrane of the Giant Axon of Loligo." J Physiol 116 (1952a): 449-472. ———. "The Components of Membrane Conductance in the Giant Axon of Loligo." J Physiol 116 (1952b): 473-496. ———. "The Dual Effect of Membrane Potential on Sodium Conductance in the Giant Axon of Loligo." J Physiol 116 (1952c): 497-506. ———. "A Quantitative Description of Membrane Current and its Application to Conductance and Excitation in Nerve." J Physiol 117 (1952d): 500-544. |
| 15 | Recapitulation | Levins, R., and R. C. Lewontin. "Conclusion: Dialectics." In The Dialectical Biologist. Cambridge, MA: Harvard University Press, 2006. ISBN: 9780674202832. Weinberg, S. "Two Cheers for Reductionism." In Dreams of a Final Theory. New York, NY: Random House, 1992. |
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