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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 current research focuses on philosophical and historical issues in microbiology, with a particular interest in metagenomics and microbial systems biology. This project continues and extends my earlier work on evolutionary microbiology and microbial genomics, which I carried out while part of the Doolittle lab at Dalhousie University (Halifax, Nova Scotia). My other interests include the use of evolutionary theory in the social sciences, as well as the philosophy and sociology of science in general.
Projects: New directions in genomics: Systems biology, Synthetic biology, Metagenomics and Microbiology and Questioning the Tree of Life.
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. Read the paper here.
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.
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. Read the Darwin microbiology paper(pdf).
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, 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. Read the preprint.
This is one of a group of three papers (plus an introduction by C.Kenneth Waters) on exploratory experimentation in recent molecular life sciences. The other papers are by Richard Burian and Kevin Elliott. Preprints of the other articles are available on the PhilSci archive: http://philsci-archive.pitt.edu/archive/00003981/ http://philsci-archive.pitt.edu/archive/00003982/ http://philsci-archive.pitt.edu/archive/00003988/ 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. Read the abstract here (subscription required for the full paper).
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., 'Introduction: Towards a philosophy of microbiology', Studies in History and Philosophy of Biological and Biomedical Sciences, 38 (4), 2007, pp. 775-779. Read the paper here (subscription required).
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. Read the paper here (subscription required).
O'Malley, M. A., 'The nineteenth-century roots of 'Everything is everywhere', Nature Reviews Microbiology, 5, 2007, pp. 647-651. Read the paper here.
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. Read the paper here.
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. Socioethical issues preprint
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. Fundamental issues preprint
Calvert, J., O’Malley, M.A. and Bostanci, A., 'Whole genome patenting', Nature Reviews Genetics, 6, 6, 2005, pp. 502-506. Read the paper here. 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. Read the paper here (subscription required).
Book chapters
Maureen A O'Malley, '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. Click here to read a description of the book.
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, 2009, 18 (2), pp 186-194. Click here for the whole symposium.
O'Malley, M.A. and Nicholson, D.J., review of Brian Garvey's Philosophy of Biology. Notre Dame Philosophical Reviews, October 2008. Read the review. 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). 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).
O'Malley, M.A. 'Making knowledge in synthetic biology: Design meets kludge'. Biological Theory (special issue on synthetic biology), 2010. Preprint available soon.
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, Molecular Phylogeny of Microorganisms, (Norwich: Horizon). Read the preprint on Construction and deconstruction (pdf).
O'Malley, M.A. 'Ernst Mayr, the Tree of Life, and philosophy of biology'. Biology and Philosophy, forthcoming spring 2010 (special issue on the tree of life).
O'Malley, M.A., Martin, W., and Dupre, J. 'The Tree of Life: Introduction to an evolutionary debate'. Biology and Philosophy, forthcoming spring 2010 (special issue on the tree of life).
Recent presentations
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).
'Everything is everywhere': historical conceptions of microbial biogeography. Presented at the History of Science Society Conference (with PSA and 4S), Vancouver (November, 2006)
The historical context of Beijerinck's and Baas Becking's denial of geographical patterns in microbial biogeography. Presented to the Doolittle, Roger and Archibald labs, and the Evolution Study Group, Dalhousie University, Halifax, Nova Scotia (October, 2006)
Historical conceptions of microbial ecology. Presented at a workshop on 'Philosophical and Social Dimensions of Microbiology', held at the University of Exeter (July, 2006).
Microbial genetics: reproduction, replication and inheritance in microorganisms. Presented at the Max Planck Institute for the History of Science, in a workshop on 'Reproduction in the Century of the Gene', Berlin (March, 2006).
Philosophical and social dimensions of systems biology. Presented at the BBSRC's UK Centres for Integrative Systems Biology meeting, Imperial College, London (February, 2006).
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