Past ResearchThis page summarizes the following past research projects at the universities of Exeter and Sydney: As an archival page its content is not maintained, so please use your favourite search engine if hyperlinks are broken or to check current affiliations of the researchers mentioned; similarly email me for a PDF whenever a preprint or draft version is missing.
2011–2015: Transitions and translations in scientific practice
1. Systems and synthetic biology: Multilevel efforts to model and construct cellular processes on the basis of large-scale molecular datasets
Aims and plans
- To examine how scientists integrate mathematical and experimental research
- To develop practical understandings of translation and integration as they function in these fields
- To apply insights from these fields to existing philosophical accounts of research and scientific practice
- To enrich understanding of exploratory, integrative and iterative approaches in today's molecular biology
- To examine the implications of evolving scientific practice for existing philosophies of funding
2. Metagenomics: The analysis of molecules sampled from microbial communities in their natural environments
Aims and plans
- To examine the development of this field and how it creates knowledge
- To examine how metagenomics interacts with microbial ecology and biogeography, particularly in regard to the practice of science and concepts about it
- To compare metagenomic practices and microbial ecology more generally to traditional ways of doing plant and animal ecology
- To analyse underlying concepts in metagenomics, especially in relation to ideas about organisms and superorganisms, cooperation and competition, and the organization of life in general
- To develop insight into the integrative and translational aspects of metagenomics (e.g., obesity drugs, bioremediation)
3. Phylogenomics: The use of genomic and other large-scale datasets to reconstruct evolutionary history and understand the functions of molecules
Aims and plans
- To examine how new methods and huge datasets are influencing ideas about evolution and its representation
- To discuss with phylogeneticists and molecular evolutionists the implications of new methods and data for the concept of the tree of life, as well as species and other evolutionary units
- To analyse the implications of these changes for evolutionary theory in general and microbial evolution in particular
- To develop a translational understanding of phylogenomics in regard to environmental remediation and human health
4. Philosophy of microbiology: Bringing it all together
The common themes in the three projects above are microbes and microbiological knowledge. Microbial systems are the model systems for systems and synthetic biology, the basis of metagenomics, and the source of the biggest problems for phylogenomic reconstructions of the tree of life.
Because philosophy of biology has largely been about plant and animal research, and because microbiology is such a fascinating source of philosophical insight, I've brought all my research interests together in a book titled Philosophy of Microbiology (CUP, 2014).
Also addressing philosophical themes in microbiology is a special issue of Biology and Philosophy on Philosophy and the Microbe. Both scientists and philosophers contributed papers, which discuss a wide range of microbial phenomena (including viruses, protists and other unicellular eukaryotes, as well as prokaryotes) and microbiological practices.
This theme continues into my current research (2015+).
2005–2011: Egenis projects
1. 2009–2011: Microbial rhodopsin research in translation
Co-funded by Egenis and the Max Planck Institute for the History of Science, Berlin, and carried out in collaboration with Mathias Grote.
Grote M, O'Malley M.A., Enlightening the life sciences: The history of halobacterial and microbial rhodopsin research. FEMS Microbiology Review, 35 (6): 1082-1099, November 2011.
Grote, M., and O'Malley, M.A., History of science is good for you. Nature Reviews Microbiology, 8, 2010, p.752.
Grote, M (2010). Surfaces of action: Cells and membranes in electrochemistry and the life sciences. Studies in History and Philosophy of Biological and Biomedical Sciences (special issue on the history and philosophy of cell research), 41 (3): 183-193.
O'Malley, M.A. (2008). Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case. History and Philosophy of the Life Sciences, 29 (3): 335-358.
Membranes, Surfaces, Boundaries: Interstices in the History of Science, Technology and Culture, October 2010, MPIWG Berlin.
2. 2008–2010: Questioning the Tree of Life
Funded by the Leverhulme Trust, and carried out in collaboration with John Dupré and all the network members below.
The first meeting of the network took place at the Philosophy of Science Association (PSA) meeting, November 6-9 2008 in Pittsburgh (USA). Read the TOL PSA report for an overview of this workshop and a discussion of plans for future activities.
Further dissemination of the project took place in Brisbane, at the ISHPSSB meeting in July, 2009. Session details. Mark Ragan’s presentation has already been published as a paper in Biology Direct, Trees and networks before and after Darwin.
The next group gathering took place in Halifax, Nova Scotia, from July 30 to August 1, 2009. View the Perspectives workshop report. The project culminated with a workshop, Beyond the Tree of Life, held in London in July 2010. Read details of all the talks in the Beyond the Tree of Life London workshop report.
Eric Bapteste (UPMC, Paris), Yan Boucher (MIT), Richard Burian (Virginia Tech), Ford Doolittle (Dalhousie), Marc Ereshefsky (Calgary University), Laura Franklin-Hall (NYU), Peter Gogarten (University of Connecticut), Jeffrey Lawrence (University of Pittsburgh), Jim Mallet (UCL), Bill Martin (Heinrich-Heine Universität, Düsseldorf), Elliott Sober (University of Wisconsin) and Joel Velasco (Cornell).
John Archibald (Dalhousie), Rob Beiko (Dalhousie), Joe Bielawski (Dalhousie), Frédéric Bouchard (University of Montreal), Lisa Gannett (Saint Mary's University), Eugene Koonin (NCBI), Ulrich Kutschera (Kassel), Nick Lane (UCL), Francois-Joseph Lapointe (Montreal), Christophe Malaterre (IHPST, Paris), James McInerney (NUI Maynooth, Ireland), Gordon McOuat (King’s College University, NS), Greg Morgan (Stevens Institute of Technology, NJ), Staffan Müller-Wille (Exeter), Thomas Pradeu (IHPST, Sorbonne), Olivier Rieppel (The Field Museum, Chicago), Andrew Roger (Dalhousie), Jan Sapp (York University, Toronto), Susan Spath, (independent scholar, California), Peter Stevens (St Louis, Missouri), Davide Vecchi (Universidad de Santiago de Chile) and Rob Wilson (Alberta).
A special issue of Biology Direct was published in June, 2011 titled Beyond the Tree of Life and containing nine papers from network members.
A special issue of Biology and Philosophy was published in September, 2010 on the Tree of Life.
Bapteste, E., O'Malley, M.A., Beiko, R.G., et al. (2009). Prokaryotic evolution and the tree of life are two different things. Biology Direct, 4: 34 (This paper is accompanied by three reviews, written by W. Ford Doolittle, Nicolas Galtier and John M. Logsdon).
O'Malley, M.A. (2010). Construction and deconstruction: The influence of lateral gene transfer on the evolution of the Tree of Life. In Oren, A., and Papke, T. (Eds.), Molecular Phylogeny of Microorganisms, Norwich: Horizon pp. 151-166.
3. 2005–2012: New directions in biology — metagenomics and microbiology
This project was funded by the Arts and Humanities Research Council (UK), and carried out in collaboration with John Dupré.
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. (2010). 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, 5 (2): 182-186
O'Malley, M.A. (2010). The first eukaryote cell: An unfinished history of contestation. Studies in the History and Philosophy of Biological and Biomedical Sciences (special issue on the history and philosophy of cell research), 41 (3): 212-224
Dupré, J., and O'Malley, M.A. Varieties of living things: Life at the intersection of lineage and metabolism. Philosophy & Theory in Biology, 1, 2009.
O'Malley, M.A. What did Darwin say about microbes, and how did microbiology respond? Trends in Microbiology, 17 (8), 2009: 341-347.
O'Malley, M.A., and Dupré, J. Philosophical themes in metagenomics, in D. Marco (ed.), Metagenomics: Theory, methods and applications. Hethersett, Norwich: Horizon Scientific Press, 2009.
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 Zaneveld, Rob Knight and Carl Zimmer), Metascience, 18 (2), 2009: 186-194.
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. Springer, 2009.
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: 335-358 (Preprint available). [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.
O'Malley, M. A. The nineteenth-century roots of 'Everything is everywhere'. Nature Reviews Microbiology, 5, 2007: 647-651.
Dupré, J., and O’Malley, M. A. Metagenomics and biological ontology. Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4), 2007: 834-846.
O'Malley, M. A., and Dupré, J. Size doesn't matter: Towards a more inclusive philosophy of biology. Biology and Philosophy, 22 (2), 2007: 155-191.
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: 775-779.
Workshop on ‘Philosophical and Social Dimensions of Microbiology’, July 2007.
4. 2005–2010: New directions in genomics — systems and synthetic biology
This project was funded by the Economic and Social Sciences Research Council (UK), and carried out in collaboration with John Dupré and Jane Calvert
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