Publications

Books

O’Malley MA (2014). Philosophy of Microbiology. Cambridge University Press (in press). Click here for an overview of the book.

Journal articles

O’Malley MA, Brigandt I, Love AC, Crawford JW, Gilbert JA, Knight R, Mitchell SD, and Rohwer F (2014, forthcoming). Multilevel research strategies and biological systems. Philosophy of Science.

O’Malley MA (2013). When integration fails: Prokaryote phylogeny and the tree of life. Studies in History and Philosophy of Biological and Biomedical Sciences, 44(4): 551–562.

Evans MR, Grimm V, Johst K, Knuuttila T, de Langhe R, Lessells CM, Merz M, O’Malley MA, Orzack SH, Weisberg M, Wilkinson DJ, Wolkenhauer O, Benton TG (2013). Do simple models lead to generality in ecology? Trends in Ecology and Evolution, 28(10):578–583. (See response by Lonergan, and our response to him — details in Letters below.)

Soyer OS, O’Malley MA (2013). Evolutionary systems biology: what it is and why it matters. BioEssays, 35: 696–705.

O’Malley MA (2013). Philosophy and the microbe: a balancing act. Biology and Philosophy, 28(2): 153–159.

O’Malley MA, Simpson AGB, and Roger AJ (2013). The other eukaryotes in light of evolutionary protistology. Biology and Philosophy 28(2): 299–330.

O’Malley MA, and Soyer OS (2012). The roles of integration in molecular systems biology. Studies in History and Philosophy of Biological and Biomedical Sciences, 43(1): 58–68 (part of a special issue on data-driven research).

O’Malley MA (2011). Constructive personalized medicine: The potential integration of synthetic biology and personalized medicine. Current Pharmacogenomics and Personalized Medicine, 9(3): 177–183.

O’Malley MA, and Koonin EV (2011). How stands the Tree of Life a century and a half after The Origin? Biology Direct, 6:32 (part of a special issue on Beyond the Tree of Life).

Grote M, and O’Malley MA (2011). Enlightening the life sciences: The history of halobacterial and microbial rhodopsin research. FEMS Microbiology Reviews, 35(6): 1082–1099.

O’Malley MA (2011). Exploration, iterativity and kludging in synthetic biology. Comptes Rendus Chimie, 14(4): 406–412.

O’Malley MA, 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 MA, and Leonelli S (2011). The scientific importance of asking questions at meetings: Why virtual debate is not enough. BioEssays, 33(1): 35–37.

O’Malley MA, Elliott KC, and Burian, RM (2010). From genetic to genomic regulation: Iterativity in microRNA research. Studies in the History and Philosophy of Biological and Biomedical Sciences, 41(4): 407–417.

O’Malley MA (2010). The first eukaryote cell: An unfinished history of contestation. Studies in the History and Philosophy of Biological and Biomedical Sciences, 41(3): 212–224 (in the special issue on the history and philosophy of cell research).

O’Malley MA, and Müller-Wille SEW (2010). 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, 41(3): 169–171 (in the special issue on the history and philosophy of cell research).

O’Malley MA, Martin W, and Dupré J (2010). The Tree of Life: Introduction to an evolutionary debate. Biology and Philosophy, 25: 441-453 (in the special issue on the tree of life).

O’Malley MA (2010). Ernst Mayr, the Tree of Life, and philosophy of biology. Biology and Philosophy, 25: 529–552 (in the special issue on the tree of life).

O’Malley MA (2010). Making knowledge in synthetic biology: Design meets kludge. Biological Theory, 4(4): 378–389 .

Dupré J, and O’Malley MA (2009). Varieties of living things: Life at the intersection of lineage and metabolism. Philosophy & Theory in Biology, 1. Reprinted as:
Dupré J, and O’Malley MA (2014). Vita [Life]. In Michelini F, Davies JF (Eds), Frontiere della Biologia: Prospettive Filosofiche Sulle Scienze Della Vita [Frontiers of Biology: Philosophical Reflections on the Life Sciences]. Milano: Mimesis Edizioni.
Dupré J, and O’Malley MA (2012). Chapter 12. In Dupré J (Ed), Processes of Life: Essays in the Philosophy of Biology. Oxford University Press.
Dupré J, and O’Malley MA (2012). The continuity of life and non-life. In Wolfe LT, Normandin S (Eds), Vitalism and the Scientific Image in Post-Enlightenment Life Science, 1800–2010. Springer.

Bapteste E, O’Malley MA, Beiko RG, 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 Doolittle WF, Galtier N, and Logsdon JM).

O’Malley MA, Elliot KC, Haufe C, and Burian RM (2009). Philosophies of funding. Cell, 138(4): 611–615.

O’Malley MA (2009). What did Darwin say about microbes, and how did microbiology respond?. Trends in Microbiology, 17(8): 341–347.

O’Malley MA (2008). ‘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): 314–325.

O’Malley MA (2008). Exploratory experimentation and scientific practice: Metagenomics and the proteorhodopsin case. History and Philosophy of the Life Sciences, 29(3): 337–358.

O’Malley MA, Powell A, Davies JF, and Calvert J (2008). Knowledge-making distinctions in synthetic biology. BioEssays, 30(1): 57–65.

Powell A, O’Malley MA, Müller-Wille SEW, 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.

O’Malley MA, and Dupré J (2007). Introduction: Towards a philosophy of microbiology. Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4):775–779.

Dupré J, and O’Malley MA (2007). Metagenomics and biological ontology. Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4): 834–846. Reprinted as:
Dupré J, and O’Malley MA (2012). Chapter 11. In Dupré J (Ed), Processes of Life: Essays in the Philosophy of Biology. Oxford University Press.

O’Malley MA (2007). The nineteenth-century roots of ‘Everything is everywhere’. Nature Reviews Microbiology 5: 647–651.

O’Malley MA, and Dupré J (2007). Size doesn’t matter: towards a more inclusive philosophy of biology. Biology and Philosophy, 22(2): 155–191. Reprinted as:
Dupré J, and O’Malley MA (2012). Chapter 10. In Dupré J (Ed), Processes of Life: Essays in the Philosophy of Biology. Oxford University Press.

O’Malley MA, Calvert J, and Dupré J (2007). The study of socioethical issues in systems biology. American Journal of Bioethics, 7(4): 67–78.

O’Malley MA, and Dupré J (2005). Fundamental issues in systems biology. BioEssays, 27: 1270–1276.

O’Malley MA, Bostanci A, and Calvert J (2005). Whole genome patenting. Nature Reviews Genetics, 6(6): 502–506.

O’Malley MA and Boucher Y (2005). Paradigm change in evolutionary microbiology. Studies in History and Philosophy of Biological & Biomedical Sciences, 36: 183–208.

Letters and encyclopædia entries

Evans MR, Benton TG, Grimm V, Lessells CM, O’Malley MA, Moustakas A, and Weisberg M (2014). Data availability and model complexity, generality, and utility: A reply to Lonergan. Trends in Ecology and Evolution, 29: 302–3.

O’Malley MA (2013). Metagenomics. In Dubitzky W, et al. (Eds) Encyclopedia of Systems Biology. Springer (preprint available).

O’Malley MA (2013). Metaorganism. In Dubitzky W, et al. (Eds) Encyclopedia of Systems Biology. Springer (preprint available).

Haufe C, Elliott KC, Burian RM, and O’Malley MA (2010). Machine science: what’s missing (a response to Evans and Rzhetsky).Science, 330: 317–318 (for other responses, see replies of Leonelli, Gianfelici, and Evans and Rzhetsky).

Grote M, and O’Malley MA (2010). History of science is good for you. Nature Reviews Microbiology, 8: 752.

O’Malley MA, Calvert J, and Dupré J (2007). Response to our commentators. American Journal of Bioethics, 7(4): W7–W9.

Edited special issues of journals

O’Malley MA (2013) Special issue on Philosophy and the Microbe. Biology and Philosophy 28(2).

O’Malley MA, and Boucher Y (Eds) (2011). Special thematic series on Beyond the Tree of Life (11 papers). Biology Direct.

O’Malley MA, and Müller-Wille SEW (Eds) (2010). Special issue on the history and philosophy of cell biology and cell theory (6 papers). Studies in History and Philosophy of Biological and Biomedical Sciences C, 41(3).

O’Malley MA (Ed) (2010). Special issue on The tree of life (15 papers). Biology and Philosophy, 25(4).

O’Malley MA, Dupré J (Eds) (2007). Special issue on philosophy of microbiology (6 papers). Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4).

Book chapters

O’Malley MA (2012). Evolutionary systems biology: historical and philosophical perspectives on an emerging synthesis. In Soyer OSS (Ed), Evolutionary Systems Biology (Springer) pp. 1–28.

Duncan MJ, Bourrat P, DeBerardinis J, and O’Malley MA (2012). Small things, big consequences: microbiological perspectives on biology. In Kamporakis K (Ed), The Philosophy of Biology: A Companion for Educators (Springer) pp. 373–394. (preprint available).

O’Malley MA (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 (Hethersett, Norwich: Horizon Scientific Press) pp. 151–166. (preprint available).

O’Malley MA, and Dupré J (2009). Philosophical themes in metagenomics. In Marco D (Ed), Metagenomics: Theory, Methods and Applications (Hethersett, Norwich: Horizon Scientific Press) pp. 183–207.

Dupré J, and O’Malley MA (2009). A metagenomic world view: Comment on ‘Metagenomic metaphors: New images of the human from "translational" research’, by Juengst ET. In Drenthen M et al. (Eds), New Visions of Nature (Dordrecht: Springer) pp. 147–153.

O’Malley MA (2007). Evolutionary approaches in the social sciences. In Outhwaite W, and Turner SP (Eds), The Sage Handbook of Social Science Methodology (London: Sage) pp. 333–357.

Book Reviews

O'Malley MA (2014). Exemplary philosophy of science: How to do it. Essay review of Fagan MB (2013), Philosophy of Stem Cell Biology: Knowledge in Flesh and Blood. Studies in the History and Philosophy of Biological and Biomedical Sciences, 45: 49–52.

O’Malley MA (2013). Review of Pradeu T (2012), The Limits of the Self: Immunology and Biological Identity. British Journal for the Philosophy of Science (advance access).

O’Malley MA (2011). Decentring humans? Imagining a microbially inspired sociology. Review of Hird M (2009), The Origins of Sociable Life: Evolution After Science Studies. Metascience, 20: 127–130.

O’Malley MA (2010). What microbes can do: A sensory guide to microbiology. Essay review of Ingraham JL (2010), March of the Microbes: Sighting the Unseen. Biological Theory, 5(2): 182–186.

O’Malley MA (2009). Review of Zimmer C (2008), Microcosm: E. coli and the New Science of Life (part of a review symposium, Life through a microbial lens, with Susan Spath, Jesse Zanefeld, Rob Knight and Carl Zimmer. Metascience, 18(2): 186–194.

O’Malley MA, and Nicholson DJ (2008). Review of Garvey B (2007), Philosophy of Biology. Notre Dame Philosophical Reviews, October 2008.

Davies JF, and O’Malley MA (2008). Toward a philosophy of systems biology. Review of Boogerd FC et al (Eds) (2007), Systems Biology: Philosophical Foundations. Biological Theory, 2(4): 420–423.

O’Malley MA (2006). Review of Jablonka E, and Lamb MJ (2005), Evolution in Four Dimensions. Acta Biotheoretica, 54: 93–98.

Recent presentations

Microbes First! Presented at Philosophy of Biology at Dolphin Beach 7, Moruya NSW (August 16–18, 2013).

Beyond tractability: other reasons for microbes as model systems. Presented in a symposium on ‘Microbes as Model Systems’ at ISHPSSB 2013, Montpellier (July 7–12, 2013).

Philosophies for the funding of scientific research. Presented in a symposium on ‘Scientific Research Funding:Practices, Problems, Philosophies’ at The 4th biennial conference of the Society for the Philosophy of Scientific Practice, San Diego (June 26–29, 2013).

Biological systems from molecular, ecological and microbiological points of view. Presented in a symposium on ‘Molecules, Organisms, Systems: Developing Multilevel Integrated Insights Into Biological Processes’ at the PSA 2012 Biennial Meeting, San Diego (November 15–17, 2012).

Synthetic biology as heuristic. Presented at ‘Synthetic Biology in Question’, hosted and sponsored by Biological Futures in a Globalized World, Seattle (November 13–14, 2012)

Philosophy of paradigms and phylogeny. Presented in a symposium on ‘Paradigm Shifting in Phylogeny’ at the Annual Meeting of the Society for Molecular Biology and Evolution, Dublin (July 23–26, 2012).

Prokaryote evolution: Is there something special about it? Presented at the Center for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax NS, (July 5, 2012).