Semiotic Structures and Meaningful Information in Biological Systems

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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, we will apply these methods to a concrete biological signalling system in which the codes are difficult to identify: inner and outer kinetochore proteins and their involvement in structure formation and the control of mitosis (especially the spindle assembly checkpoint). The required data are measured in the Diekmann group (in the second funding period: extended and more specific data sets), while in the Dittrich group the data are modelled in order to theoretically describe cell cycle dependent inner and outer kinetochore assembly and function. As an additional benefit, 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.