Language Theory and Molecular Genetics: Generative Mechanisms Suggested by DNA Recombination

The stimulus for the development of the theory presented in this chapter is the string behaviors exhibited by the group of molecules often referred to collectively as the informational macromolecules. These include the molecules that play central roles in molecular biology and genetics: DNA, RNA, and the polypeptides. The discussion of the motivation for the generative systems is focused here on the recombinant behaviors of double stranded DNA molecules made possible by the presence of specific sets of enzymes. The function of this introduction is to provide richness to the reading of this chapter. It indicates the potential for productive interaction between the systems discussed and molecular biology, biotechnology, and DNA computing. However, the theory developed in this chapter can stand alone. It does not require a concern for its origins in molecular phenomena. Accordingly, only the most central points concerning the molecular connection are given here. An appendix to this chapter is included for those who wish to consider the molecular connection and possible applications in the biosciences. Here we present only enough details to motivate each term in the definition of the concept of a splicing rule that is given in the next section. The splicing rule concept is the foundation for the present chapter.