Modelle, Mechanismen, Komplexität. Zur Philosophie der Systembiologie

• Applicant: Professor Dr. Olaf Wolkenhauer
• Subject Area: Theoretical Philosophy
• Term: from 2011 to 2015
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 201038283

• Final Report Year: 2015

Final Report Abstract

Mathematical modelling plays an increasingly important role in molecular and cell biology. In contrast to other areas, like the engineering sciences, the role of models in the life sciences is quite different. The systems under consideration are complex, their mechanisms and parameter values mostly unknown. This project focused on the role of models, and more specifically the role of abstraction for understanding and explanation. While some projects may aim for a biochemical realism of model, other models are deliberately simplistic, compared to the actual number of components involved. The same type of representation (e.g. ODEs) can thus serve very different purposes. A result of our project is the conclusion that there is a need for a model ontology that practitioners could use to explain/justify the type of model they are pursuing. Neither the biological context, nor the mathematical representation by itself can communicate the purpose of a model and its value in the process of answering biological questions. The communication between interdisciplinary teams would benefit from a philosophical perspective and model ontology.

Publications

• (2011). System approaches of Weiss and Bertalanffy and their relevance for systems biology today. Seminars Cancer Biology 21:150 -155
  Drack M, Wolkenhauer O
  
• The Complexity of Cell-Biological Systems. In: Philosophy of Complex Systems Vol. 10; 345-385; Hooker CA (ed.); series: Handbook of the Philosophy of Science; North-Holland 2011. ISBN 9780444520760
  Wolkenhauer O, Muir A
  
• (2012). Diagrams as locality aids for explanation and model construction in cell biology. Biology and Philosophy 27; 705-721
  Jones N, Wolkenhauer O
  
• (2012). Integration in action. EMBO reports 13: 769-771
  Green S, Wolkenhauer O
  
• (2012). The role of theorem proving in systems biology. Journal of Theoretical Biology 300: 57-61
  Wolkenhauer O, Shibata D, Mesarovic MD
  
• (2013): Interdisciplinarity as both necessity and hurdle for progress in the life sciences. In: Andersen H et al. eds. New Challenges to Philosophy of Science - The Philosophy of Science in a European perspective 4. Springer Verlag, 2013, 225-235
  Wolkenhauer O, Hofmeyr J
  
• (2013): The search for organizing principles as a cure against reductionism in systems medicine. FEBS Journal, 280 (23): 5938-48
  Wolkenhauer O, Green S
  
• Do simple models lead to generality in ecology? Trends Ecol Evol. 2013 Oct; 28(10):578-83
  Evans MR, Grimm V, Johst K, Knuuttila T, de Langhe R, Lessells CM, Merz M, O'Malley MA, Orzack SH, Weisberg M, Wilkinson DJ, Wolkenhauer O, Benton TG
  
• Encyclopedia of Systems Biology. Springer 2013. lSBN 9781441998620
  Dubitzky W, Wolkenhauer O, Yokata H, Cho K-H (eds.)
  
• The Role of Theory and Modelling in Medical Research. Front. Pysiol. 4:377
  Wolkenhauer, O
  
• Tracing organizing principles: Learning from the history of systems biology. History and Philosophy of the Life Sciences, 35 (4), 553 - 576
  Green S, Wolkenhauer O
  
• Enabling multiscale modeling in systems medicine. Genome Medicine 2014, 6:21
  Wolkenhauer O, Auffray C, Brass O, Clairambault J, Deutsch A, Drasdo D, Gervasio F, Preziosi L, et al.
  
• Pushing limits by embracing complexity. lET Syst Biol. 2014 Dec;8(6):244-250
  Wolkenhauer, O
  
• Why model? Front. Physiol. 5:21
  Wolkenhauer, O
  
• Modelle und ihre Befragbarkeit als Grundlage biomedizinischer Erkenntnis. Erwägen-Wissen-Ethik. Vol 26 (2015)
  Wolkenhauer, O