Semiotic structures and meaningful information in biological systems

The project aims at the semantic aspect of biological information. We will develop novel methods to objectively identify and describe semiotic sub-systems of living cells. The basic idea relies on the identification of organic codes (as recently reviewed by Barbieri, Naturwissenschaften 95, 577-599, 2008) and on how these codes are physically instantiated. First, we develop formal concepts and measures that allow to describe and quantify organic codes based on experimental observations. Second, for validation, we will apply this method to already known biological codes (e.g. the genetic code) and to an in-silico artifcial chemistry, in which chemical information processing can appear spontaneously and can evolve. Third, we will apply these methods to concrete biological signalling systems, in which the codes are more difficult to identify. In particular we investigate (a) microbial communication systems (chemotactic signaling in social amoeba, quorum sensing) and (b) kinetochore proteins and their involvement in the control of mitosis (especially the spindle assembly checkpoint). As bene¿t this project will deliver a novel way to describe and understand biological systems from a semantic perspective. We will be able to compare and classify biological information processing at the molecular level. The semantic description may also enable us to explain the evolution of bacterial languages and to design novel cellular circuits in the context of synthetic biology.