Broad Area Colloquium For AI-Geometry-Graphics-Robotics-Vision
(CS 528)

Injecting Life With Computers

Ehud Shapiro
Weizmann Institute of Science
Special time: Thursday, October 7, 3:00PM
Special location: Gates 104
http://graphics.stanford.edu/ba-colloquium/

Abstract

Although electronic computers are the only "computer species" we are accustomed to, the mathematical notion of a programmable computer has nothing to do with wires and logic gates. In fact, Alan Turing's notional computer, which marked in 1936 the birth of modern computer science and still stands at its heart, has greater similarity to natural biomolecular machines such as the ribosome and polymerases than to electronic computers. Recently, a new "computer species" made of biological molecules has emerged. These simple molecular computers inspired by the Turing machine, of which a trillion can fit into a microliter, do not compete with electronic computers in solving complex computational problems; their potential lies elsewhere. Their molecular scale and their ability to interact directly with the biochemical environment in which they operate suggest that in the future they may be the basis of a new kind of "smart drugs": molecular devices equipped with the medical knowledge to perform disease diagnosis and therapy inside the living body. They would detect and diagnose molecular disease symptoms and, when necessary, administer the requisite drug molecules to the cell, tissue or organ in which they operate. In the talk we review this new research direction and report on preliminary steps carried out in our lab towards realizing its vision.

References

About the Speaker

Born in Jerusalem in 1955, the guiding light for Ehud Shapiro's scientific endeavors was the philosophy of science of Karl Popper, with which he became acquainted through a high-school project supervised by Moshe Kroy from the Department of Philosophy, Tel Aviv University. Shapiro served in the Israeli Defense Forces from 1973 till 1977 as a tank's crewman, commander and officer, followed by undergraduate studies in Tel Aviv University in Mathematics and Philosophy, completed with distinction in 1979. Shapiro's PhD work with Dana Angluin in Computer Science at Yale attempted to provide an algorithmic interpretation to Popper's philosophical approach to scientific discovery, resulting in both a computer system for the inference of logical theories from facts and a methodology for program debugging, developed using the programming language Prolog. His thesis, "Algorithmic Program Debugging", was published by MIT Press as a 1982 ACM Distinguished Dissertation, followed in 1986 by "The Art of Prolog", a textbook co-authored with Leon Sterling.

Coming to the Department of Computer Science and Applied Mathematics at the Weizmann Institute of Science in 1982 as a post-doctoral fellow, Shapiro was inspired by the Japanese Fifth Generation Computer Systems project to invent a high-level programming language for parallel and distributed computer systems, named Concurrent Prolog. A two-volume book on Concurrent Prolog and related work was published by MIT Press in 1987. Shapiro's work had a decisive influence on the strategic direction of the Japanese national project, and he cooperated closely with the project throughout its 10-years duration.

In 1993, Shapiro took leave of absence from his tenured position at Weizmann to found Ubique Ltd., an Israeli Internet software pioneer. Building on Concurrent Prolog, Ubique developed "Virtual Places", a precursor to today's broadly-used Instant Messaging systems. Ubique was sold to America Online in 1995, and following a management buy out in 1997 was sold again to IBM in 1998, where it continues to develop SameTime, IBM's leading Instant Messaging product based on Ubique's technology.

Preparing for return to academia, Shapiro ventured into self-study of molecular biology. Initially curious about the origin of life, Shapiro was sidetracked into attempting to build a computer from biological molecules, guided by a vision of "A Doctor in a Cell": A biomolecular computer that operates inside the living body, programmed with medical knowledge to diagnose diseases and produce the requisite drugs. Lacking experience in molecular biology, Shapiro realized his first design for a molecular computer as a LEGO-like mechanical device built using 3D stereolithography, which was patented upon his return to Weizmann in 1998. At Weizmann, actual construction of a molecular computer began by his PhD student, Yaakov Benenson in cooperation with colleagues at Weizmann and the Technion. The computer used DNA molecules as input, output and software, and DNA-manipulating enzymes as hardware. A report on the programmable, automonous molecular computing machine was published by Nature in 2002, followed in 2003 by a report in PNAS on the use of a DNA molecule as the source of both data and fuel for a molecular computer. Shapiro and his team at the Laboratory for Biomolecular Computers at the Deportment of Biological Chemistry continue to advance the "Doctor in a Cell" vision, with the more modest and immediate goal being "A Doctor in a Test-tube": A molecular computer that uses molecular disease markers as input and, when diagnosing a disease, produces the requisite drug molecules as output.

Ehud Shapiro lives in Nataf, a small village nestled in the Judea Mountains, with his three boys Yonatan (15), Boaz (13) and Haggai (11).

Contact: bac-coordinators@cs.stanford.edu

Back to the Colloquium Page