Weizmann Institute Scientist Designs The First General-Purpose Mechanical Computing Device To Serve As The Basis For A Biological Computer

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The first general-purpose mechanical computer designed for biomolecular and pharmaceutical applications has been developed by Prof. Ehud Shapiro of the Computer Science and Applied Mathematics Department at the Weizmann Institute of Science.  The mechanical computer will be presented today at the Fifth International Meeting on DNA-Based Computers at the Massachusetts Institute of Technology.

In terms of the logic behind it, Shapiro's mechanical computer is very similar to biomolecular machines of the living cell such as the ribosome. Therefore, a future biomolecular version of the device may ultimately lead to the construction of general-purpose programmable computers of subcellular size. If scientists succeed to build such a computer, it may be able to operate in the human body and interact with the body's biochemical environment, thus having far-reaching biological and pharmaceutical applications.

"For example, such a computer could sense anomalous biochemical changes in the tissue and decide, based on its program, what drug to synthesize and release in order to correct the anomaly," Prof. Shapiro says.

The Turing machine


Unlike existing electronic computers, which are based on the computer architecture developed by John von Neumann in the U.S. in the 1940s, the new mechanical computer is based on the Turing machine, conceived as a paper-and-pencil computing device in 1936 by the British mathematician Alan Turing.  
The theoretical Turing machine consists of a potentially infinite tape divided into cells, each of which can hold one symbol, a read/write head, and a control unit which can be in one of a finite number of states. The operation of the machine is governed by a finite set of rules that constitute its "software program."  
In each cycle the machine reads the symbol in the cell located under the read/write head, writes a new symbol in the cell, moves the read/write head one cell to the left or to the right, and changes the control state, all according to its program rules. Although the Turing machine is a general-purpose, universal, programmable computer and is key to the theoretical foundations of computer science, it has not been used in real applications. Shapiro's mechanical device embodies the theoretical Turing machine, and as such is a general-purpose programmable computer.

The mechanical computer


The device employs a chain of three-dimensional building blocks to represent the Turing machine's tape, and uses another set of building blocks to encode the machine's program rules.  In each cycle the device processes one "rule molecule."  The device is designed so that the processing of the molecule modifies the polymer representing the Turing machine's tape in accordance with the intended meaning of the rule.

At the conference, Shapiro will present a 30-cm high plastic model of his mechanical computer. He hopes that in the future, with the advent of improved techniques for the analysis and synthesis of biomolecular machines, the actual computer could possibly be built from biological molecules, so that it would measure about 25 millionths of a millimeter in length, roughly the size of a ribosome.

The computer and the ribosome

In fact, Prof Shapiro designed the mechanical computer with the ultimate goal of implementing it with biological molecules. The computer is not more complicated than existing biomolecular machines of the living cell such as the ribosome, and all its operations are part of the standard repertoire of these machines. 
These operations include the mechanical equivalents of polymer elongation, cleavage and ligation, as well as moving along a polymer and being controlled by coordinated structural changes. The ribosome is the molecular machine of the living cell that performs the final step of interpretation of the genetic code by translating messenger RNA, which is transcribed from DNA, into protein.
A key similarity between Shapiro's mechanical computer and the ribosome is that a "program rule" molecule specifies a computational step of the computer similarly to the way a transfer RNA molecule specifies a translation step of the ribosome.

The computer is similar to the ribosome in that both operate on two polymers simultaneously, and their basic cycle consists of processing an incoming molecule that matches the currently held molecules on the first polymer, elongating the second polymer, and moving sideways. However, unlike the ribosome, which only "reads" the messenger RNA in one direction, the computer edits the tape polymer and may move in either direction.

A future interactive biological computer

The computer design may allow it to respond to the availability and to the relative concentrations of specific molecules in its environment, and to construct program-defined polymers, releasing them into the environment. If implemented using biomolecules, such a device may operate in the human body,  interacting with its biochemical environment in a program-controlled manner. In particular, given a biomolecular implementation of the computer that uses RNA as the tape polymer, the computer may release cleaved tape polymer segments that function as messenger RNA, performing program-directed synthesis of proteins in response to specific biochemical conditions within the cell. Such an implementation could give rise to a family of computing devices with broad biological and pharmaceutical applications.

About Prof. Shapiro


Prof. Shapiro received his Ph.D. from Yale University and joined the Weizmann Institute in 1982. During the 1980s he was involved with the Japanese Fifth Generation Computer Project and published numerous scientific papers in the area of concurrent logic programming languages.

In the early 1990s, Shapiro´s innovative research in programming languages led to the establishment of Ubique, a company that develops interactive online environments. Shapiro took a leave from Weizmann to establish Ubique, and when the company was bought by America Online, Inc., he moved to the U.S. to assist in incorporating Ubique's Virtual Places technology in America Online's internet services.
When America Online sold Ubique to Lotus/IBM in 1998, Shapiro returned to his research post at the Weizmann Institute. The mechanical design of Shapiro's computer model was performed by K. Karunaratne from Korteks and M. Schilling from Schilling 3D Design, both from San Diego, CA.

The Weizmann Institute of Science is a major scientific research graduate study located in Rehovot, Israel. Its 2,500 scientists, students and support staff are engaged in more than 1,000 research projects across the spectrum of contemporary science.