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Protein-based computers are ripe for spectacular scientific advances because we know a great deal about these circuits' molecular components. But we are only beginning to understand how they process information and make decisions. Of the many types of information processing systems known to us, the least well understood are the complex, intracellular molecular reaction networks that control the physiology of living cells and organisms. Protein-based computers are very different from their silicon-based counterparts, and the intellectual tools necessary to understand, intervene in, and reengineer these information processing systems are likely to be quite different from the paradigms that have been so successful in electrical engineering and computer science.