Readings

Course readings.

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.