DNA Splicing: Computing by Observing

Motivated by several techniques for observing molecular processes in real-time we introduce a computing device that stresses the role of the observer in biological computations and that is based on the observed behavior of a splicing system. The basic idea is to introduce a marked DNA strand into a test tube with other DNA strands and restriction enzymes. Under the action of these enzymes the DNA starts to splice. An external observer monitors and registers the evolution of the marked DNA strand. The input marked DNA strand is then “accepted” if its observed evolution follows a certain expected pattern. We prove that using simple observers (finite automata), applied on finite splicing systems (finite set of rules, i.e., enzymes and finite set of axioms, i.e., initial strands), the class of recursively enumerable languages can be recognized. This is the preliminary version of a paper that was published in Natural Computing, 8,1, 2009. The original publication is available at http://www.springerlink.com