Research History

One unifying theme of the traditional disciplines of engineering is that they deal rigorously with complex systems in the material world— considerably more rigorously than any other set of disciplines. Among engineers there are those who apply their skills to understanding systems designed by others—a process frequently called reverse engineering.

As long as there have been engineers, a few of them have applied reverse engineering to biological systems-- complex systems designed not by other engineers, but by nature. Over the Lewis Lab’s 35-year existence, from 1967 to 2002, reverse engineering of biological systems was its business. Core funding for this work was provided by the National Institutes of Health. Funding was supplemented with several grants from the National Science Foundation, the National Aeronautic and Space Administration, the Office of Naval Research, the Joint Services Electronics Program, and the Committee on Research of the University of California.

For the first fifteen years, the lab was focused on two kinds of biological systems-- nervous systems and ecological systems. Throughout the last twenty years, the focus was confined to signal processing in the vertebrate inner ear. My principal goal was to identify ways that engineering concepts and tools could be used to deepen our understanding of biological systems. Initially, the biological objects of my research were incidental and selected opportunistically for that goal.

That is not to say that I was satisfied with superficial knowledge of those biological objects. In attempting to understand any part of the nervous system, for example, the reverse engineer is obliged to begin by estimating what it is that that part of the nervous system is doing to help the species survive and flourish. Given that estimate of function, the reverse engineer can attempt to deduce how that particular function is accomplished. Without the estimate of function, the deductions of the reverse engineer would have no guiding purpose. Before spending large amounts of time in the second step, therefore, the prudent reverse engineer would invest heavily in the first—pursuing all avenues necessary to make the estimate of function (selective advantage) rise to the level of strong inference. At the very least, those avenues include morphology and physiology, developmental biology, behavioral biology, ecology and evolution. Regarding the vertebrate inner ear, the Lewis Lab has pursued all of these. This, of course, required deep commitment to the ear and its biology.

Much of our ecological research during the first fifteen years, however, was not aimed specifically at the vertebrate inner ear. Instead, it was aimed at understanding the dynamics of organism populations—often with the goal of devising strategies for controlling or managing those populations.

The history of the lab is reflected well by the activities of its doctoral students and the dissertations they produced.

Doctoral Dissertations

1969

Earl M. Mayeri (Biophysics) “Integration in the lobster cardiac ganglion” (research conducted at Bodega Marine Laboratory, co-mentor = Donald M. Wilson, Stanford Biology)

1971

Michael J. Murray (EECS) “The biology of a carnivorous mollusc: anatomical, behavioral, and electrophysiological observations on Navinax inermis”

Robert G. Plantz (EECS) “A dynamic analysis of semicircular-canal evoked eye movements"

1972

Y.Y. Zeevi (Biophysics) “Structural functional relationships in single neurons; scanning electron microscopy and theoretical studies”

1973

Keh-lon Lee (EECS) “A new approach to modeling schistosomiasis and its control”

Michael Hassul (EECS) “Single-unit studies in the vestibulo-cerebellum of turtle”

1974

J. Sherwood Charlton (EECS) “Characterization of an intermediate process in the lateral eye photoreceptors of Limulus polyphemus”

1975

Yuji Hazeyama (EECS) “ The modification of A-V shunt flow by changes in the hypothalamic temperature in dogs” (research conducted at Lawrence Berkeley Laboratory, co-mentor = Ernest L. Dobson, LBL)

Cheuk-wa Li (EECS) “Structure and development of hair cells in the acoustico- lateralis system of the bullfrog” (co-mentor = Howard A. Bern, Zoology)

Ivan F. Weeks (Biophysics) "Deterministic simulation in ecology"

1979

Sai-piu Chan (EECS) “Search and encounter interaction as basis for nonlinearities in population modeling”

1980

Miguel F. Acevedo (Biophysics) “Tropical forests dynamics: a modeling approach” [1978 MSII (EECS) “On a Markovian model of forest succession: its application to tropical forests”]

1982

Nasser Ali Farahbakhsh (EECS) “Modeling the phototransduction in ventral photoreceptor of limulus”

Richard A. Baird (EECS) “Correspondences between structure and function in the bullfrog otoconial organs”

1983

Abraham L. Elterman (Biophysics) “A stochastic analysis of the transmission dynamics and of the eradication of schistosomiasis endemics”

1988

Ellen L. Leverenz (Biophysics) “Signal processing in the amphibian papilla of the bullfrog”

1989

Penelope A. Globus (Biophysics) “The ionophoretic injection of DNA into plant cells”

1991

Xiaolong Yu (EECS) “Signal processing mechanics in the bullfrog ear inferred from neural spike trains”

1992

Bruce R. Parnas (EECS) “Studies with a neuronal modeling system for the mammalian auditory pathway”

Stephen W. Moore (Bioengineering) “Direct measurement of dynamic biomechanical properties of amphibian embryonic tissues”

1993

David Egert (Bioengineering) “The physiological bases of tuning in the bullfrog sacculus”

1994

Charles C. Della Santina (Bioengineering) “Silicon regeneration-type multi- microelectrodes for electrophysiology in the eighth cranial nerve” (research carried out in part at Stanford; co-mentor = Gregory T.A. Kovacs, Stanford EE)

Bennett H. Bonham (EECS) “Properties and activity-dependent development of model audiory brain stem neurons”

1996

Kathryn A. Cortopassi (Bioengineering) “A comparison of acoustic and equilibrium primary afferent nerve fibers from the bullfrog lagena: examining the evolution and performance of vertebrate inner ear sensors”

Gregory J. Wolodkin (EECS) “System identification methods for a class of structured nonlinear systems” (co-mentor = Kameshwar Poolla, ME/EE)

1997

Walter M. Yamada (Neurobiology) “Second-order Wiener kernel analysis of auditory afferent axons of the North American bullfrog and Mongolian gerbil responding to noise”

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