Category:Systems Biology

Systems Biology

Systems Biology is an interdisciplinary field interested in the study of self-organization in biological systems. Originally beginning with a view to analyse the processes that define success in the field of self-organising systems, the focus has widened; from top-down analysis, through bottom-up analysis towards a third method of middle-out understanding.

Major breakthroughs of understanding have been in the field of philosophy and metaphysics and these have improved both the clarity and accuracy of predictive models.

Lenny Moss (Exeter) argued for an alternative metaphysical premise; that nature explores greater levels of detachment (and complexity) and that its potential to do so can never be formally exhausted. This is the abundance-seeking phenomenon which contrasts with the environmental scarcity of Niche theory; where a 'space of opportunity' exists in the environment and this can be explored by the biological systems within it, through their increase in detachment and complexity.

"Cells have to be understood via these concepts as members of populations 
exploring phenotype space via competitive coherence strategies (growing 
versus surviving, specializing versus diversifying)" Vic Norris (Rouen)

The growth areas of the field include the concept of: "...‘understanding’ versus prediction and control, the role of hypotheses, the need for reductionism, the importance (or otherwise) of data comprehensiveness, and how interdisciplinarity could be most successfully achieved." Jane Calvert (Exeter)

Original report: Egenis, University of Exeter, November 30th – December 1st, 2006

Sub Disciplines of Systems Biology

Mathematics - For modelling the processes

Philosophy - For explaining and predicting the models efficacy

Philosophical underpinnings of the subject

Auffray, C., Imbeaud, S., Roux-Rouquié, M., and Hood, L. (2003). Selforganized living systems: Conjunction of a stable organization with chaotic fluctuations in biological space-time. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences,361: 1125-1139.

Boogerd, F. C., Bruggeman, F. J., Richardson, R. C., Stephan, A., and Westerhoff, H. V. (2005). Emergence and its place in nature: A case study of biochemical networks. Synthese, 145: 131-64.

Bruggeman, F. J., Westerhoff, H. V., and Boogerd, F. C. (2002). BioComplexity: A pluralist research strategy is necessary for a mechanistic explanation of the 'live' state. Philosophical Psychology, 15: 411- 440.

Guespin, J. (1998).Réductionnisme et globalisme en biologie. [Available on request from the author.]

Guespin-Michel, J., and Ripoll, C. (2000). La pluridisciplinarité dans les sciences de la vie : un nouvel obstacle pistémologique, la non linéarité. [Available on request from the author.]

Norris, V., Amar, P., Bernot, G., Delaune, A., Derue, C., et al. (2004). Questions for cell cyclists. Journal of Biological Physics and Chemistry, 4: 124–130.

Norris, V., Cabin, A., and Zemirline, A. (2005). Hypercomplexity. Acta Biotheoretica, 53: 313-330. Philosophical papers on emergence.

Bedau, M. (1997). Weak emergence. Nous, 31: 375-399.

Cunningham, C. (2000).The re-emergence of emergence. Philosophy of Science, 68: S62-S75.

Klee, R. L. (1984). Micro-determinism and concepts of emergence, Philosophy of Science, 51: 44-63. 9

Silberstein, M., and McGeever, J. (1999). The search for ontological emergence. The Philosophical Quarterly, 49: 182-200.

Other network Links

www.cellsignet.org.uk: - a "Cell Signalling Network" with a balanced membership from biology and the mathematical sciences, facilitating the development of an active and cohesive cross-disciplinary community at the mathematics/systems biology interface.

Current Network System Biologists