Micro-controllers and their programming is a well-understood domain in computer-science. What is not well understood is the evolution of the programs executed in micro-controllers and the evolution of micro-controllers as such. If we examine micro-controllers with high-density code, the brittleness of the program-code for evolution is readily apparent. In addition, it is extremely difficult, if not impossible, to implement these micro-controllers in biomolecular systems.
In the process of our systematic attempts to simplify micro-controller structures in the direction of molecular systems, a few common features come into focus:
a) counting, a standard operation in micro-controllers, has no real counterpart in simple biochemical systems.
b) read-write-registers (memory is seen in this context as registers as well) are a precious resource in biochemistry and other means of information processing need to be considered. Conformational changes for example are an obvious choice to store information.
c) long sequential algorithms are not robust in noisy biochemical environments with imperfect procedures.
d) digital arithmetic, a natural basis in conventional computing, seems to be more or less irrelevant in biochemical systems.
e) pure Boolean operations may be more limited in biochemical systems.