New directions in genomics: The philosophy of systems biology
Researcher Name: Maureen O'Malley
Affiliated Staff: Jane Calvert (Egenis/Innogen), Jonathan Davies (Egenis PhD), John Dupré (Egenis Director),
Dan Nicholson (Egenis PhD) and Alexander Powell (Egenis PhD)
Project Start Date: 01.10.2005
Project End Date: 30.09.2012
Contact Details: Lead researcher: Maureen O'Malley
Email: M.A.O'Malley@exeter.ac.uk
Funder: This project was funded by the Arts and Humanities Research Council from 2006-2008.
Background: Our project is based on a distinction between two overlapping modes of practising and thinking about systems biology. One we call pragmatic systems biology and the other systems-theoretic biology. Pragmatic systems biologists see a system as an interacting collection of molecules and other components. More theoretically driven systems biologists see systems as special levels of biological organization. This distinction has implications for modelling practice. Pragmatic systems biologists normally model the interaction of molecules from the bottom-up. Systems-theoretic biologists, on the other hand, tend to model systems from the top-down. For both systems biologies, the simple diagrammatic models that are routinely encountered in biology are insufficient for modelling systems. Both groups believe that systems modelling has to be mathematical in order to capture the complexities of higher-level biological organization.
For the last two years we have been sharing our philosophical and sociological insights into systems biology in a teaching programme at the Doctoral Training Centre in the Manchester Centre for Integrative Systems Biology. www.mcisb.org/dtc Students from diverse scientific backgrounds are being trained as systems biologists at this new and flourishing institute, and we contribute to their training with a basic understanding of the philosophical and sociological issues associated with the field.
Aims and Objectives: We are investigating a number of philosophical questions in relation to each form of systems biology.
The nature and properties of systems. Are systems merely collections of molecules, or entities with novel emergent properties? What are those properties? Which biological entities can be conceived of as systems?
Reductionism. Reductionism is classically the attribution of ultimate reality to components, with higher-level entities considered to be no more than the sum of those components. Is pragmatic systems biology still reductionist?
Emergence. What does emergence mean for systems biologists and how do they put this philosophical concept to practical use
Downward causation: system effects on components. The most robust form of anti-reductionism accords reality to systems and attributes causal powers to them. How is downward causation understood in systems biology? And how should causation more generally be thought of in relation to systems? In 2008, we began a collaboration on experimental strategies in microRNA research with Richard Burian (Virginia Tech) and Kevin Elliott (South Carolina) . Our aim in this project is to complete a philosophical history of the various modes of experimentation involved in the huge success story of miRNAs. This study is also leading to an associated project with the above collaborators and Chris Haufe (Virginia Tech) on philosophies of funding and science policy. See our paper Philosophies of Funding . A third level of additional research is on philosophical and historical issues in the science of obesity. This sub-project is being carried out in collaboration with Karola Stotz at the University of Sydney.
Research Methods:
Key Findings: Our early analysis of systems biology uncovered two main epistemological trends in how systems biology was being practised: systems-theoretic biology and pragmatic systems biology. This analysis also raised some fundamental philosophical questions for systems biology to address. Further work has looked at the historical context of systems biology’s development, with a particular focus on how it was named in relation to the older disciplines of genetics, molecular biology and genomics.
Wider implications for policy:
Project Update:
Publications: O'Malley, M.A., Elliot, K.C., Haufe, C., and Burian, R.M., 'Philosophies of funding ', Cell , 138 (4), 2009, pp 611-615.
Davies, J.F., and O'Malley, M.A., Review of 'Systems Biology: Philosophical Foundations' , Fred C. Boogerd et al. (Eds), Biological Theory , 2 (4), 2008, pp 420-423.
Powell, A., O'Malley, M.A., Müller-Wille, S.E.W., Calvert, J., and Dupré, J., 'Disciplinary baptisms: A comparison of the naming stories of genetics, molecular biology, genomics and systems biology', History and Philosophy of the Life Sciences , 29 (1), 2007, pp 5-32. Disciplinary baptisms preprint (pdf).
O’Malley, M. A., and Dupré, J. (2005). Fundamental issues in systems biology. BioEssays , 27: 1270–1276. Read the Fundamental issues preprint .
External Links:
Further information: Philosophy of Systems Biology Workshop Report (pdf)
Gateway to Post-Genomic Science . An annotated bibliographic database of key scientific papers in genomics, systems biology, synthetic biology, metagenomics, sociogenomics, sociomicrobiology.
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