SBI – Department of Systems Biology and Bioinformatics
Faculty of Computer Science and Electrical Engineering
University of Rostock
Ulmenstrasse 69 | 18057 Rostock
Germany
+49 381 498-7571
olaf.wolkenhauer@uni-rostock.de
Transformation of scientific knowledge in the life sciences - changes in the understanding of the living cell (ExCell)
ExCell is a joint project investigating the changed understanding of the living cell in science. The task for the project partners is to investigate the transformation of scientific knowledge in the life sciences in a comprehensive and interdisciplinary way. For the first time, the shift in paradigm, concerning the understanding of cellular processes in the context of the digital revolution in light microscopy and systems biology, is scrutinized.
Our sub-project is concerned with representation methods in the life sciences and the notion of the cell as a system. Methods such as “life cell imaging”, “gene expression analysis”, “proteomics” and “high-throughput techniques” allow for new experimental approaches to investigate the behaviour of biological cells. The data exploited are converted with the help of mathematical, graphical and computer models from systems biology, into a form that can be interpreted easily. The representation of complex cellular processes leads to a radical change in the standard representational practice of cells, away from a static perspective towards a dynamic, process-oriented representational manner is evident, together with a significant increase in abstraction. In the course of an examination with respect to philosophy of science and image theory (Bildtheorie) we ask within the sub-project, on the one hand, about the conditions for creation of systems biology models of the cell. On the other hand, the interpretation of such models and their heuristic role for the life sciences is examined, based on approved concepts, such as that of pathways. Models, no matter how abstract, are always intended images. Hence existing image theories are tested, whether they are suitable to capture recent forms of light microscopy and systems biology imaging and modelling of cell processes. Theoretical modifications should be developed, if necessary.
We are examining graphical representations of pathways as they are used in systems biology. This research is guided by philosophical knowledge towards formal ontologies. As a result we expect a clearer understanding of the pathway concept and how it relates to other concepts like that of crosstalk.