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On Design Principles for a Molecular Computer

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On Design Principles for a Molecular Computer ARTICLES ON DESIGN PRINCIPLES FOR A MOLECULAR COMPUTER If the unique information-processing capabilities of protein enzymes could be adapted for computers, then evolvable, more efficient systems for such applications as pattern recognition and process control are in principle possible. MICHAEL CONRAD It is only recently that a serious interest in the possibil- systems, which are ultimately based on the conforma- ity of using carbon-based materials for computing has tional properties of protein enzymes, suggest this ap- developed in the scientific community. Formerly, indi- proach (see Figures l-3). Although elaborate conforma- viduals expressing an interest in exploring this possibil- tion is probably incompatible with good conductivity, it ity would have been advised to implement their com- allows for the lock-and-key type interactions that en- puting concepts in existing electronic technologies. In- able enzymes to recognize specific molecular objects by deed, to the best of my knowledge, no molecular com- exploring their shapes.’ Shape-based specificity is a puting device has so far been constructed or shown to form of tactile pattern recognition. Admittedly, en- be imminent. However, a convergence of developments zymes make for much slower switches than transistors in a number of fields, including polymer chemistry, (typically 0.1 millisecond, as compared to.a nanosec- various biotechnologies, the physics of computation, ond). To simulate the sensory and control functions and computer science, has changed the situation. Theo- they perform, however, would require an enormous retical arguments suggest that more efficient and adapt- number of switching processes in a digital computer. able modes of computing are possible, while emerging Designs that use functions of this sort as primitives- biotechnologies point to possibilities for implementa- predefined elements that are irreducible as far as the tion. Their common ground is molecular computing. computing power of the machine is concerned-can One immed:iate objective is to produce a von reasonably be expected to yield significant increases in Neumann-type computer in carbon, rather than silicon computational power for such tasks as pattern recogni- [3]. The assumption is that carbon chemistry may facil- tion and process control. In addition, enzymes have the itate the construction of smaller and faster devices. At- virtue of being adaptable switches, which makes them tention has therefore been focused on the possibilities amenable to tailoring for particular functions through for organic sw:itching devices and conducting polymers trial-and-error evolution. The evolution process pro- [21,41], and secondarily on the problems of contact ceeds by variation of the sequence of amino acids in and reliability. Certainly, work in this area is poten- the enzyme, followed by selection and propagation of tially important. Even so, it is likely that molecular the best-performing sequences (see Figure 4). computing will prove to be much more valuable out- However, these advantages can only be exploited at side the context of conventional von Neumann com- the expense of programmability, which is the major puters. Critically important computing needs such as feature of today’s computers. This idea can be stated in adaptive pattern recognition and process control may the form of a trade-off principle: A system cannot at the be refractory to simple decreases in size and increases same time be effectively programmable, amenable to evolu- in speed. Instead of suppressing the unique properties tion by variation and selection, and computationally effi- of carbon polymers, we should consider how to harness cient. The von Neumann computer opts for programma- them to fill these needs. bility. The trade-off theorem suggests that an alterna- The information-processing capabilities of biological ’ The argument is that the conformational flexibility of biopolymers is con- 0 1985 ACM OOOl-0782/135/0500-041%750 comitant to the lack of conjugation required for electronic conductivity [43]. 464 Communications of the ACM May 1985 Volume 28 Number 5 Articles tive domain of computing is in principle possible, have access to the same computational resources at the where programmability is exchanged for efficiency and same time, is also possible, but, in general, only at the adaptability. Biological systems, as the products of evo- expense of effective programmability (for a discussion lution, must operate in this alternative domain. of parallelism and speedup, see [26]). ESSENTIAL FEATURES OF VON NEUMANN The von Neumann computer also has fundamental COMPUTERS shortcomings: Let us first list some of the fundamental features of von 6. Inefficiency. Von Neumann computers make ineffi- Neumann computers. These features have become so cient use of available space, time, and energy resources. familiar that it is possible to forget how remarkable The vast majority of processors are dormant at any they really are [6]: given time. 1. Programming languages exist. It is a fact of experi- 7. Sensitivity. The sensitivity of programs to change ence that if we can conceive of an algorithm we can is a matter of common and usually unpleasant experi- always express it directly in any of a large number of ence. computer languages (e.g., ALGOL, LISP, Pascal). A basic feature of all such languages is that they are defined by The strengths of the von Neumann design (properties a finite, discrete base set of symbolic primitives. Were l-5) are all control properties. Intensive efforts are un- these symbols not finite in number, a user’s manual der way in computer science to retain these control could not be finite either. Were the symbols not dis- properties while removing the constraints on efficiency crete, it would be necessary to perform calculations to and adaptability [properties 6 and 7). The trade-off prin- ascertain what algorithm a program actually expresses. ciple suggests that the strengths of the von Neumann The psychological sense of directness conveyed by to- computer are inextricably linked to its limitations. day’s computer languages is derived from these proper- ties. THE TURING-CHURCH THESIS 2. Effective programmability. Once a program is writ- The capabilities computer scientists generally associate ten, it is always possible to effectively communicate it with the von Neumann computer are summed up in to an actual machine. From a user’s point of view, this the famous thesis of Turing and Church (a recent gen- communication process may be mediated by an inter- eral discussion can be found in [zJ]). One statement of preter, which can read and follow any particular pro- this thesis is any effectively computable function is com- gram, or by a compiler, which sets the state of the putable by a formal process involving simple operations on machine so as to execute the desired program. strings of symbols. A program is a rule that generates such a process. The classic Turing formalization of a 3. Structural programmability. Digital computers all computing process is illustrated in Figure 6. The Turing employ a small repertoire of simple switches (e.g., logic machine program can be rewritten in any general- gates and on-off devices). Each switch constitutes a purpose algorithmic language. These various formaliza- switching primitive. It is always possible to write a pro- tions all define the same class of functions-the partial gram in a language that directly maps the structure of recursive functions. To prove this, it is only necessary the machine and the state of each component [8, 141. to show that they are all equivalent up to the point of This property, structural programmability, is the basis for simulation, that is, up to the coding of strings of sym- all other forms of programmability in today’s com- bols into other strings of symbols. This equivalence puters. The network in Figure 5 illustrates the concept supports the Turing-Church thesis, although it does not of structural programmability. It shows how algorithms actually prove it. Indeed, proof is impossible, since the expressed in terms of the symbolic primitives of a claim is that an informal concept of computation is highly simplified programming language can be ex- equivalent to any of a large number of formal models of pressed directly in terms of the switching primitives of computation. Disproof, however, is possible if a con- the network. Of course, the diagram of the network is vincing counterexample can be found. Computer scien- also a language, and the “switching” primitives in it are tists generally accept Turing-Church because no such also symbolic primitives. However, they are symbolic counterexample has ever been discovered. primitives that can easily be realized as switches. The Turing-Church thesis is sometimes interpreted narrowly as encompassing only the processes of logic 4. Universality. Were there no limitations on time and space, the von Neumann computer could run any and mathematics. The strongest interpretation is that conceivable program. It is also universal in that, so far any physically realizable system or process must be effec- as is known, it can simulate any physically realizable tively computable. If a physically realizable system or process in nature (more on this in the next section). process were not effectively computable, it could be used as a new primitive of computation, thereby en- 5. Sequentiality. It is possible for the von Neumann larging the class of functions computable by systems in computer to execute a single elementary operation at a nature. For the purpose of this article, I accept this time. True parallelism, as where two or more programs strong form of the Turing-Church thesis, first because May 1985 Volume 28 Number 5 Communicationsof the ACM 465 Articles energy-dependent folding T-t,Y The sequence of nucleotide bases in DNA, which stores are pictured with dark springs, and weak bonds, which the information accumulated during the course of eV0k.b determine the folded structure, by light springs.
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