Prof. Olaf Wolkenhauer

Research Interest

Making Sense out of Data; Giving Meaning to Models...
is the motto for my research group. We use systems theory to provide both, a conceptual basis and a working method for the scientific explanation of biological phenomena.

I am interested in data analysis and mathematical modelling - with applications to molecular and cell biology. Nowadays this is called Systems Biology, respectively Bioinformatics. I believe that cell function, like life itself is not a property of the components involved but emerges from their dynamic interactions and organisation: The genome provides the notes but the music is played elsewhere. In this context I am trying to answer the following questions: How do the components within a cell interact, so as to bring about its structure and realise its functioning (intra-cellular dynamics)? How do cells interact, so as to develop and maintain higher levels of structural and functional organisation (inter-cellular dynamics)? My approach is mathematical; I believe there is nothing more practical than a good theory (model)!

The goal is a deeper understanding of th spatio-temporal interactions among components of a cell, among cells, and their interaction with the environment. Systems biology is an approach by which (molecular and cell-) biological questions are addressed through integrating experiments in iterative cycles with the mathematical modeling, simulation, and theory [*]. Systems biology brings about a shift of focus in the life sciences: moving on from the identification and molecular characterisation of components of the cell, towards an understanding of functional activity. Since systems theory is the study of organisation per se, it seems natural to define systems biology as a merger of (dynamic) systems theory and (cell) biology [**]. This is indeed how it was originally envisaged in 1968 [***]. My systems-theoretic perspective on the functional organisation of the cell (as opposed to its structural organisation) is motivated by the conviction that the way the components of the cell are put together, whether we call it structure, order, or organisation, is as material in its causal effects as matter itself. Objects and relations between objects have identical ontological status: Life is a relation among molecules and not a property of any molecule; Causation as the principle of explanation of change, is a relation, not between things, but between changes of states of things.

[*] O.Wolkenhauer: Why Systems Biology Is (Not) Called Systems Biology (pdf). BioForum Europe, April 2007, 2-3
O.Wolkenhauer et al. Advancing systems biology for medical applications (pdf). IET Syst. Biol., 2009, Vol. 3, Iss. 3, pp. 131-136
O. Wolkenhauer: Interview (pdf). The Reasoner, Vol. 5, Nr. 9, September 2011
[**] O.Wolkenhauer: Engineering Approaches: What can we learn from it in systems biology? (pdf). Contribution to the 'Forward Look Report on Systems Biology' by the European Science Foundation, 2007
[***] O.Wolkenhauer, M.Mesarovic: Feedback Dynamics and Cell Function: Why Systems Biology is called Systems Biology (pdf). Molecular BioSystems, Vol.1, No.1, 14-16, May 2005

I am not only interested in building models but also in understanding the role of systems theory, modeling and mathematical models in science. The close link between my philosophical outlook and my work in systems biology, is apparent in a recent publication, coauthored with Jannie Hofmeyr: An Abstract Cell Model that describes the Self-Organization of Cell Function in Living Systems (pdf), which appeared in the Journal of Theoretical Biology (2007). The paper addresses autonomous self-fabrication and self-organisation as a feature of living systems (Video, 8 min, 7 mb (wma)). Together with Allan Muir, I I have written about 'The complexity of Cell-Biological Systems' (In: Philosophy of Complex Systems Vol. 10; 345-385; Hooker CA (ed.), 2011). A summary of my "philosophical" musings on systems theory and systems biology can be found in an interview with The Reasoner, Vol. 5, Nr. 9, September 2011.

Miscellaneous Documents and Links

• In remembrance of Allan Muir
• Collection of some of my favorite quotations, aphorisms and thoughts that have motivated and influenced my thinking.
• A review (pdf) of D. Ellerman: Adjoints and emergence: applications of a new theory of adjoint functors. Axiomathes (2007) 17:19-39.
• The Beauty of Mathematics - A Rough Sketch for a Proof (pdf), submitted for publication)
• Selbstorganisation: Ein charakterische Eigenschaft lebender Systeme (November 2007): Video, 8 min, 7 mb (wma) oder Pdf-Datei (pdf)

I don't play chess but I am interested in the question of how complexity emerges from simplicity. Here are some notes I prepared while reading chess books and which may be useful for a novice:

• Chess notes, focussing on Black and the KIA (pdf)
• One-page summary of e4 chess openings (pdf)
• Graphical summary of e4 openings (pdf)
• Graphical summary of d4 openings (pdf)
• Tabular summary of d4 openings (pdf)
• Tabular summary of the Scandinavian opening (pdf)

Academic Background

Biografie auf Deutsch

My first degrees (Dipl.Ing. and BEng.) in control engineering are from the University of Applied Sciences in Hamburg, Germany and the University of Portsmouth, U.K. in 1994. My PhD (1997) was on the application of possibility theory to data analysis, research I conducted at UMIST, Manchester. Following a research lectureship at the Control Systems Centre at UMIST, an invited visiting position at the Technical University Delft, Netherlands in 1999-2000, I held a joint senior lectureship with the Department of Biomolecular Sciences and the Department of Electrical Engineering and Electronics, at UMIST. After ten years at the Control Systems Centre, I accepted in 2003 the C4 Chair in Systems Biology and Bioinformatics, Department of Computer Science at the University of Rostock, Germany. I was a visiting Professor in the School of Mathematics at The University of Manchester between 2003 and 2006. Since October 2004 I have an adjunct position in the Department of Electrical Engineering and Computer Science at Case Western Reserve University, where I collaborate with Mihajlo Mesarovic. Together with Kwang-Hyun Cho, I am the founding editor of the journal Systems Biology. Since 2005, I am a fellow of the Stellenbosch Institute for Advanced Study (STIAS), where I collaborate with Jan-Hendrik Hofmeyr. I am a founding member of the Centre for Logic, Philosophy and History of Science at the University of Rostock.

Publications

For a list of publications refer to the page "Publications".