Author: Kalevi Kull
Company: ZBI

Genomics and membrane computing in a semiotic framework

Solomon Marcus
Solomon.Marcus@imar.ro

At the crossroad of molecular biology, computer science, linguistics, and mathematics, under the stimulus of the recent Human Genome Project and of the emergence of genomics, important semiotic problems are challenging us, in a perspective far away from the framework of classical semiotics. The gene-protein interaction points out a syntactic-semantic interplay, where similarity is a basic tool of investigation. But, as Richard Karp shows, this line of research leads to questions of high computational complexity. Algorithmic and computational biosemiotics seems to be a field that no longer can be ignored.
We point out the non-conventional semiotic scenario resulting from this approach, the itinerary from invisible entities to visible aspects of inheritance, we show how linguistic metaphors rise new problems and how the Human Genome Project is a semiotic enterprise and how computational biosemiotics enters the scene. We discuss the interaction of reads, clones, exons and introns and the way similar genomes express closely related species.
Membrane computing is a recent field of investigation, as a variant of biological computation simulating the processes at the membrane level and exploiting the surfaces inside surfaces processes shown to play an essential role in the emergence of life (see Paun 2002).

References

Paun, Gheorghe 2002. Membrane Computing. Berlin: Springer Verlag.