New directions in genomics: Systems and synthetic biology (2005-2010)
Affiliated staffJane Calvert (Innogen), John Dupré (Egenis)
Systems biology is a new approach to biology which makes use of computational tools and mathematical modelling to analyse the vast amounts of data that have been generated by genome sequencing and other 'omic' projects. It requires the collaboration of scientists from many different disciplines, including physicists, mathematicians, computer scientists, engineers and biologists. Because of its potential to transform biology and healthcare, systems biology has been heralded as the future of genomics and has received high levels of investment around the globe.
Systems biology raises numerous interesting philosophical and social issues, from system conceptualization and the evaluation of modelling techniques to the social achievement of interdisciplinarity. The project began 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 (see O’Malley and Dupré, 2005). With Jane Calvert, we also examined some of the potential socioethical issues raised by systems biology (see O'Malley et al. 2007). In response to the growing body of work in synthetic biology, I and some of my systems biology collaborators undertook an examination of some of the epistemic issues raised by this integration of biological practice and engineering principles (O'Malley et al., 2008; O'Malley, 2010).
In order to focus this more general attention to systems and synthetic biology, I 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 produce a philosophical history of the various modes of experimentation involved in the huge success story of miRNA research, as it turned the study of gene regulation into a system-oriented investigation. This project broadened into an associated study with these collaborators and Chris Haufe (Chicago) on philosophies of funding and science policy (O'Malley et al., 2009). Another area of focused research takes in philosophical issues in the systems science of obesity, specifically in relation to the themes of integration, intervention and translation. This sub-project is being carried out in collaboration with Karola Stotz at the University of Sydney.
O'Malley, M.A., and Stotz, K. (2011). Intervention, integration and translation in obesity research: Genetic, developmental and metaorganismal approaches. Philosophy, Ethics, and Humanities in Medicine, 6(2).
O'Malley, M.A., Elliott, K.C., and Burian, R.M. (2011). From genetic to genomic regulation: Iterativity in microRNA research. Studies in the History and Philosophy of Biological and Biomedical Sciences, 41 (4): 407-417.
Haufe, C., Elliott, K.C., Burian, R.M., and O'Malley, M.A. (2010). Machine science: what's missing (a response to Evans and Rzhetsky) Science, 330: 317-318 (for other responses, see Leonelli, Gianfelici, and Evans & Rzhetsky's reply).O'Malley, M.A. (2010). Exploration, iterativity and kludging in synthetic biology. Comptes Rendus Chimie, forthcoming (corrected proof now online). O'Malley, M.A. 'Making knowledge in synthetic biology: Design meets kludge'. Biological Theory (special issue on synthetic biology), 4(4): 378-389, 2010.
O'Malley, M.A., Elliot, K.C., Haufe, C., and Burian, R.M. (2009). Philosophies of funding, Cell, 138 (4): 611-615.
O'Malley, M.A., Powell, A., Davies, J.F., and Calvert, J. (2008). Knowledge-making distinctions in synthetic biology, BioEssays, 30 (1): 57-66.
Powell, A., O'Malley, M.A., Müller-Wille, S.E.W., Calvert, J., and Dupré, J. (2007). 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): 5-32 (or view a preprint of Disciplinary baptisms).
Davies, J.F., and O'Malley, M.A. (2008). Review of Systems Biology: Philosophical Foundations, edited by Fred C. Boogerd et al. Biological Theory, 2 (4): 420-423.
O'Malley, M. A., Calvert, J., and Dupré, J. (2007). The socioethical study of systems biology. American Journal of Bioethics, 7 (4): 67-78 (plus 5 commentaries).
O'Malley, M. A., Calvert, J., and Dupré, J. (2007). Response to our commentators. American Journal of Bioethics, 7 (4): W7-W9.
O’Malley, M. A., and Dupré, J. (2005). Fundamental issues in systems biology. BioEssays, 27: 1270–1276.
Philosophy of Systems Biology Workshop Report, 30 November 2006
See the commentaries written by Mark Greener in EMBO reports (2008, 9 (9): 835-837; 2008, 9 (11): 1067-1069). These articles feature our comments on synthetic biology and questions about life.