Bringing DNA computers to life
posted 2006-05-02 21:10:39 latest updated 2006-05-02 21:11:46
computer science Tapping the computing power of biological molecules gives rise to tiny machines that can speak directly to living cells

When British mathematician Alan Turing conceived the notion of a universal programmable computing machine, the word “computer” typically referred not to an object but to a human being. It was 1936, and people with the job of computer, in modern terms, crunched numbers. Turing’s design for a machine that could do such work instead— one capable of computing any computable problem—set the stage for theoretical study of computation and remains a foundation for all of computer science. But he never specifi ed what materials should be used to build it. Turing’s purely conceptual machine had no electrical wires, transistors or logic gates. Indeed, he continued to imagine it as a person, one with an infi nitely long piece of paper, a pencil and a simple instruction book. His tireless computer would read a symbol, change the symbol, then move on to the next symbol, according to its programmed rules, and would keep doing so until no further rules applied. Thus, the electronic computing machines made of metal and vacuum tubes that emerged in the 1940s and later evolved silicon parts may be the only “species” of nonhuman computer most people have ever encountered, but theirs is not the only possible form a computer can take. Living organisms, for instance, also carry out complex physical processes under the direction of digital information. Biochemical reactions and ultimately an entire organism’s operation are ruled by instructions stored in its genome, encoded in sequences of nucleic acids. When the workings of biomolecular machines inside cells that process DNA and RNA are compared to Turing’s machine, striking similarities emerge: both systems process information stored in a string of symbols taken from a fi xed alphabet, and both operate by moving step by step along those strings, modifying or adding symbols according to a given set of rules. These parallels have inspired the idea that biological molecules could one day become the raw material of a new computer species. Such biological computers would not necessarily offer greater power or performance in traditional computing tasks. The speed of natural molecular machines such as the ribosome is only hundreds of operations a second, compared with billions of gate-switching operations a second in some electronic devices. But the molecules do have a unique ability: they speak the language of living cells. The promise of computers made from biological molecules lies in their potential to operate within a biochemical environment, even within a living organism, and to interact with that environment through inputs and outputs in the form of other biological molecules. A biomolecular computer might act as an autonomous “doctor” within a cell, for example. It could sense signals from the environment indicating disease, process them using its preprogrammed medical knowledge, and output a signal or a therapeutic drug.

By Ehud Shapiro and Yaakov Benenson/Scientific American 2006

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