There Is Nothing More Practical Than a Good Theory ! (?)

Olaf Wolkenhauer

Organisms, cells, genes, and proteins are complex structures of interdependent and subordinate components whose relationships and properties are largely determined by their function in the whole. Investigating the concept of a 'pathway' the aim of this contribution is to discuss a formal, conceptual framework in which to investigate intra- and inter-cellular dynamic processes. The approach is signal- and system-oriented, rooted in dynamic systems theory. The basic idea is that in order to explain the functioning and function of a cell, we need to understand it in terms of dynamic processes. Comparing and generalizing the most commonly used mathematical theories to study dynamic interactions of molecules within cells and in communication between cells, we ask whether it is possible to generalize and integrate mathematical pathway models to investigate cell functions in silico. Is the concept of a "pathway" suitable for a systems approach? Could an appropriately large set of pathway models represent a cell? Which conceptual framework (e.g. stochastic processes, differential equations, formal languages) is most appropriate and can we establish a conceptual framework which integrates those?