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Title: Dr. Job Title: Egenis Senior Research Fellow Tel: 01392 269136 Fax: 01392 264676 Email: M.A.O\'Malley@exeter.ac.uk Building: Byrne House, Streatham Campus, University of Exeter Room Number: FF1
My research is primarily concerned with philosophical analyses of changing modes of biological practice. I focus on fields such as systems and synthetic biology, as well as metagenomics. These connect to microbiology more generally, where I have major interests in microbial phylogeny and biogeography. I often examine particular episodes of philosophically interesting microbiological research, such as the ways in which microbial rhodopsins have been discovered and explored. All these foci come together in a general picture of how biological practice might be changing in light of molecular microbial knowledge, and what the consequences are for broader understandings of the life sciences.
Projects:
Systems and synthetic biology
Metagenomics and Microbiology
Questioning the Tree of Life
Microbial rhodopsin research in translation
O'Malley, M.A. 'Making knowledge in synthetic biology: Design meets kludge'. Biological Theory (special issue on synthetic biology), 4 (4), 2010, pp. 378-389. Dupré, J., and O'Malley, M.A. 'Varieties of living things: Life at the intersection of lineage and metabolism'. Philosophy & Theory in Biology, Vol 1, 2009.
Bapteste, E., O'Malley, M.A., Beiko, R.G., et al. 'Prokaryotic evolution and the tree of life are two different things', Biology Direct, 4 (34), 2009. (This paper is accompanied by three reviews, written by W. Ford Doolittle, Nicolas Galtier and John M. Logsdon).
O'Malley, M.A., Elliot, K.C., Haufe, C., and Burian, R.M. 'Philosophies of funding', Cell, 138 (4), 2009, pp. 611-615.
O'Malley, M.A. 'What did Darwin say about microbes, and how did microbiology respond?' Trends in Microbiology, 17(8), 2009, pp. 341-347.
O'Malley, M.A. 'Everything is everywhere: but the environment selects': Ubiquitous distribution and ecological determinism in microbial biogeography. Studies in History and Philosophy of Biological and Biomedical Sciences, 39 (3), 2008, pp. 314-325.
O'Malley, M.A. 'Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case', History and Philosophy of the Life Sciences, 29 (3), 2008, pp. 337-358. O'Malley, M.A., Powell, A., Davies, J.F., and Calvert, J., 'Knowledge-making distinctions in synthetic biology', BioEssays, 30 (1), 2008, pp. 57-65.
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.
O'Malley, M.A., and Dupré, J., 'Introduction: Towards a philosophy of microbiology', Studies in History and Philosophy of Biological and Biomedical Sciences, 38 (4), 2007, pp. 775-779.
Dupré, J., and O'Malley, M.A., 'Metagenomics and biological ontology'. Studies in History and Philosophy of Biological and Biomedical Sciences, 38 (4), 2007, pp. 834-846.
O'Malley, M. A., 'The nineteenth-century roots of 'Everything is everywhere' , Nature Reviews Microbiology, 5, 2007, pp. 647-651.
O'Malley, M. A., and Dupré, J., 'Size doesn't matter: towards a more inclusive philosophy of biology' , Biology and Philosophy, 22 (2), 2007, pp. 155-191.
O'Malley, M. A., Calvert, J., and Dupré, J., 'The study of socioethical issues in systems biology', American Journal of Bioethics, 7 (4), 2007, pp. 67-78.
O'Malley, M. A., Calvert, J., and Dupré, J., 'Response to our commentators', American Journal of Bioethics, 7 (4), 2007, W7-W9.
O'Malley, M. A., and Dupré, J., 'Fundamental issues in systems biology', BioEssays, 27, 2005, pp. 1270-76.
Calvert, J., O’Malley, M.A. and Bostanci, A., 'Whole genome patenting', Nature Reviews Genetics, 6 (6), 2005, pp. 502-506. O'Malley, M. A. and Boucher, Y., 'Paradigm change in evolutionary microbiology', Studies in History and Philosophy of Biological & Biomedical Sciences, 36, 2005, pp. 183-208.
Book chapters
O'Malley, M.A. 'Construction and deconstruction: The influence of lateral gene transfer on the evolution of the Tree of Life'. In Oren, A., and Papke, T. (Eds.), 2010, pp 151-166, Molecular Phylogeny of Microorganisms, (Norwich: Horizon). Read the preprint of Construction and deconstruction (pdf).
O'Malley, M.A. and Dupré, J. ' Philosophical themes in metagenomics'. In D. Marco (Ed.), Metagenomics: Theory, Methods and Applications, 2009, Hethersett, Norwich: Horizon Scientific Press. Dupré, J., and O'Malley, M.A. 'A metagenomic world view: Comment on 'Metagenomic metaphors: New images of the human from "translational" research'', by Eric T. Juengst. In M. Drenthen et al. (Eds.), New Visions of Nature, 2009, Springer.
O'Malley, M.A. 'Evolutionary approaches in the social sciences', in W. Outhwaite and S. P. Turner (Eds.), The Sage Handbook of Social Science Methodology, London: Sage, 2007, pp. 333-357.
Book reviews
O'Malley, M.A. Review of Microcosm: E.coli and the New Science of Life, by Zimmer, C., (part of a review symposium, Life through a microbial lens, with Susan Spath, Jesse Zanefeld, Rob Knight and Carl Zimmer), Metascience, 18 (2), 2009, pp. 186-194.
O'Malley, M.A. and Nicholson, D.J., Review of Brian Garvey's Philosophy of Biology. Notre Dame Philosophical Reviews, October 2008. Davies, J.F. and O'Malley, M.A., 'Toward a philosophy of systems biology, Review of Systems Biology: Philosophical Foundations (ed), Fred C. Boogerd et al', Biological Theory, 2 (4), 2008, pp. 420-423.
O'Malley, M. A., Review of Evolution in Four Dimensions (ed), Eva Jablonka and Marion J. Lamb. Acta Biotheoretica, 54, 2006, pp. 93-98.
Forthcoming
O'Malley, M.A. (2010). Exploration, iterativity and kludging in synthetic biology. Comptes Rendus Chimie, forthcoming. Preprint available on request.
O'Malley, M.A. (2010, forthcoming). Decentring humans? Imagining a microbially inspired sociology. (Review of Myra Hird's The Origins of Sociable Life: Evolution After Science Studies, 2009, Palgrave Macmillan). Metascience. Preprint available on request. O'Malley, M.A. (2010, forthcoming). 'What microbes can do: A sensory guide to microbiology' (essay review of John L. Ingraham's March of the Microbes: Sighting the Unseen, 2010, Belknap). Biological Theory. Preprint available on request.
O'Malley, M.A., Elliott, K.C., and Burian, R.M. (2010, forthcoming). 'From genetic to genomic regulation: Iterativity in microRNA research'. Studies in the History and Philosophy of Biological and Biomedical Sciences. Preprint available on request.
O'Malley, M.A., and Müller-Wille, S.E.W. (2010, in press). The cell as nexus: Connections between the history, philosophy and science of cell biology. Studies in the History and Philosophy of Biological and Biomedical Sciences (special issue on the history and philosophy of cell research). Corrected proof available.
O’Malley, M.A. (2010). The first eukaryote cell: An unfinished history of contestation. Studies in History and Philosophy of Biological and Biomedical Sciences C, forthcoming (special issue on the history and philosophy of cell biology). Corrected proof available.
O'Malley, M.A. 'Ernst Mayr, the Tree of Life, and philosophy of biology'. Biology and Philosophy, forthcoming 2010 (special issue on the tree of life). Online First preview.
O'Malley, M.A., Martin, W., and Dupre, J. 'The Tree of Life: Introduction to an evolutionary debate'. Biology and Philosophy, forthcoming 2010 (special issue on the tree of life). Online First preview.
Recent presentations
Tree preservation: The Tree of Life as heuristic. Presented at the London 'Beyond the Tree of Life' meeting (July 10-11). Iterativity and kludging in systems and synthetic biology. Presented at the Department of Philosophy Seminar, University of Bristol (May 7, 2010).
Iterativity in the practice and philosophy of biological research. Presented at the Data-Driven Workshop, University of Exeter (April 15, 2010).
Everything is everywhere: but the environment selects: Microbial biogeography, past and present. Presented at the Plymouth Marine Laboratory (March 3, 2010).
Philosophy of evolution, Ernst Mayr, and the Tree of Life. Presented at the workshop Perspectives on the Tree of Life, Halifax, Nova Scotia (July 30-August 1, 2009). Philosophy of biology, Ernst Mayr, and the Tree of Life. Presented at the biennial meeting of the International Society for the History, Philosophy and Social Study of Biology, Brisbane, Australia (July 12-16, 2009).
Philosophy and the Tree of Life. Presented at the start-up meeting for the BMBF Study Group, Evolution and Classification in Biology, Linguistics and the History of Science, Heinrich Heine University, Düsseldorf (June 11-12, 2009).
Epistemological distinctions in synthetic biology. Presented at the International Conference: From Synthetic Chemistry to Synthetic Biology, Collège de France, Paris (May 5, 2009).
Making knowledge in synthetic biology. Presented at the Historical and Philosophical Foundations of Synthetic Biology Workshop, Ecole Normale Supérieure, Paris (April 17-18, 2009).
Varieties of living things: Life at the intersection of lineage and metabolism. Presented at IHPST, Paris (November 21, 2008).
A philosophical history of microbiology. Presented to the Doolittle, Roger, Archibald and Gray labs plus associates, Dalhousie University, Halifax, Nova Scotia (July 17, 2008).
Philosophical and sociological issues in systems biology. Presented at the Lille Spring School on Modelling Complex Biological Systems in the Context of Genomics, Villeneuve (April 7-11, 2008).
The microbial world: edges and boundaries. Presented at the Edges and Boundaries of Biological Objects Workshop, University of Utah (March 13-15, 2008).
Philosophy of systems biology: reduction, emergence and pluralism. Presented to the Doctoral Training Centre in Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester (January, 2008).
Philosophy of genomics: an overview. Presented at the AHRC SW Regional Meeting, Bristol (December, 2007).
Metagenomics and the proteorhodopsin case: exploratory experimentation and its transformative effects. Presented at the biennial meeting of the International Society for the History, Philosophy and Social Studies of Biology, Exeter, UK (July, 2007).
Historical and political shifts in microbiology: biogeography and superorganisms. Presented at the FordFest Symposium, Halifax, Nova Scotia (June, 2007).
The historical roots of 'Everything is everywhere' in microbial biogeography. Presented to the Regional Conference for History and Philosophy of Science, University of Colorado at Boulder (April, 2007).
Philosophy of science for systems biologists: 1. Reductionism, holism and pluralism; 2. Models, theories and simulations. Presented to the Doctoral Training Centre in Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester (January, 2007).
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