Publications

Publications by type:

Books

O’Malley MA (2014). Philosophy of Microbiology. Cambridge University Press.

Sniegowski P (2016). Philosophy of Microbiology, by Maureen A. O'Malley. Quarterly Review of Biology, 91: 99.

Şerban M, Green S (2016). Why the small things in life matter: Philosophy of biology from the microbial perspective. Philosophy of Science, 83: 152‐158.

Ben-Barak I (2015). Philosophy of Microbiology, by Maureen A. O'Malley. Australasian Journal of Philosophy, doi:10.1080/00048402.2015.1101479.

Bunyard BA (2015). Philosophy of Microbiology. FUNGI, 8 (3): 44–45.

Kaiser MI (2015). Philosophy of Microbiology. Maureen A. O’Malley. International Studies in the Philosophy of Science.

McConwell AK (2015). Review: Philosophy of Microbiology. British Journal for Philosophy of Science. DOI: 10.1093/bjps/axv033

Pedroso M (2015). Starting small: Using little microbes to tackle big philosophical questions. Studies in History and Philosophy of Biological and Biomedical Sciences, 53: 126–128.

Capozzi V, Russo P, Spano G (2015). The great microbial beauty. Trends in Microbiology, 3(6): 334.

Clarke E (2015). Review: Philosophy of Microbiology. Notre Dame Philosophical Reviews, 2015.03.44.

Harold F (2015). Review: Philosophy of Microbiology. Microbe Magazine, 10(2): 83.

Woolfson A (2015). The meaning of microbes. Science, 347(6224):832.

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Journal articles

O'Malley MA, Wideman JG, Ruiz-Trillo I (2016). Losing complexity: The role of simplification in macroevolution. Trends in Ecology and Evolution, 31:608–621. Publisher's copy temporarily available for download here (until September 8).

O'Malley MA (2016, in press). Reproduction expanded: Multigenerational and multilineal units of evolution. Philosophy of Science.

O'Malley MA (2016, forthcoming). Microbiology, philosophy, and education. FEMS Microbiology Letters. Preprint available here.

O'Malley MA (2016, corrected proof). The ecological virus. Studies in History and Philosophy of Biological and Biomedical Sciences.

O'Malley MA, Powell R (2016). Major problems in evolutionary transitions: How a metabolic perspective can enrich our understanding of macroevolution. Biology and Philosophy, 31: 159–169.
See commentary by Matt Herron on his Fierce Roller blog: Part 1, Part 2, and Part 3, plus our response to Matt.

O'Malley MA (2016). Histories of molecules: Reconciling the past. Studies in History and Philosophy of Science, 55: 69–83.

O'Malley MA (2015). Endosymbiosis and its implications for evolutionary theory. Proceedings of the National Academy of Sciences USA, 112: 10270–10277.

O'Malley MA, Travisano M, Velicer GJ, Bolker JA (2015). How do microbial populations and communities function as model systems? Quarterly Review of Biology, 90: 269–293.

O'Malley MA, Soyer OS, Siegal ML (2015). A philosophical perspective on evolutionary systems biology. Biological Theory, 10(1):6–7 (part of a special section on evolutionary systems biology).

O’Malley MA, Brigandt I, Love AC, Crawford JW, Gilbert JA, Knight R, Mitchell SD, and Rohwer F (2014). Multilevel research strategies and biological systems. Philosophy of Science, 81:811–828.

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, and 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 and 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 (2013). 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.

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Book chapters

O'Malley MA (2016, forthcoming). Is evolution fundamental when it comes to defining biological ontology? No. In Dasgupta S, Westlake B (Eds), Current Controversies in Philosophy of Science (Routledge). Preprint available here.

Brigandt I, Green S, O'Malley MA (forthcoming). Systems biology and mechanistic explanation. In Glennan S, Illari P (Eds), The Routledge Handbook of Mechanisms and Mechanistic Philosophy (Routledge). Preprint available here.

O'Malley MA (forthcoming). W. Ford Doolittle: evolutionary provocations and a pluralistic vision. In Dietrich MR, Harman O (Eds), Dreamers, Romantics and Visionaries in the Life Sciences. (Chicago: University of Chicago Press). Preprint available here.

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.

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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, 6.

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

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Book reviews

O'Malley MA (2015). Molecular organisms: A review of John Archibald's 'One Plus One Equals Two'. Biology and Philosophy, 31: 571–589.

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 (2014). Review of Pradeu T (2012), The Limits of the Self: Immunology and Biological Identity. British Journal for the Philosophy of Science, 65(1): 179–183.

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, 2008.10.21.

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.

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Other contributions

O'Malley MA (2016). The microbial nature of humans. In Schaechter E (Ed), In the Company of Microbes: 10 Years of Small Things Considered (ASM Press) pp. 42–46. Original blogpost on Small Things Considered here.

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.

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Recent presentations

Bottom-up microbiome research and its implications for holobionts. Presented at CGEB Seminar Series, Dalhousie University (July 7, 2016).

Causal relationships in host-microbe systems. Presented at New Frontiers in Ecological Developmental Biology and Microbiota-Host Co-Construction, University of Bordeaux (June 14–16, 2016).

Experimental 'versus' historical approaches to the origin of life. Presented at Understanding Life: New Perspectives from Philosophy and Biology, University of Bern (May 26–27, 2016).

Microbiome research: a philosophical perspective. Presented at BioPerspectives: New Perspectives in Philosophy of Biology, L'Institut d'Études Scientifiques de Cargèse, Corsica (April 29–May 1, 2016).

Concrete models. Presented at Philosophy and Practice of Modelling, University of Sydney (August 20, 2015).

Philosophical reflections on microbiology. Presented at Who Are We? Humans, Microbes, and Their Interactions, Eugene, Oregon (August 2, 2015).

Correlation and causation in microbiome research. Presented at The Gordon Research Conference on Microbial Population Biology, Proctor Academy NH (July 19‐24, 2015)

The early eukaryote garden of Eden and the loss of complexity. Presented in a symposium on ‘From complex to simple: Evolution by simplification, and its philosophical implications’ at ISHPSSB 2015, Montreal (July 5-10, 2015)

Metabolic explanation and early evolution. Presented at The Origin of Life: Second Conference on History and Philosophy of Astrobiology, Höör, (May 8–10, 2015).

The Tree of Life: Introduction to an evolutionary debate. Presented at Life on Earth and Beyond: The History and Philosophy of the Origin of Life, Ven (May 4–6, 2015).

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Philosophy of microbiology. Presented at the lunchtime seminar of the Charles Perkins Centre, Sydney (April 21, 2015).

Microbiology and the modern synthesis. Presented at Revisiting the History of the Modern Synthesis, University of Chicago (November 10, 2014).

Reproduction without bottlenecks: Multilineal units of evolution. Presented in a symposium on Complex Life Cycles, Reproduction and Evolution at PSA 2014, Chicago (November 6–9, 2014).

Philosophical reflections on endosymbiosis: Implications for evolutionary theory. Presented at the Sackler symposium on Symbioses Becoming Permanent: The Origins and Evolutionary Trajectories of Organelles, Beckman Center, UC Irvine (October 15–17, 2014).

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).

Microbial ecology, past and present: Some key philosophical issues. Presented at the biennial meeting of the International Society for the History, Philosophy and Social Studies of Science, Salt Lake City (July 10–15, 2011).

The dynamics of scientific practice: Integration and iteration in molecular systems biology. Presented at the biennial meeting of the Society for the Philosophy of Science in Practice, Exeter (June 22–24, 2011).

Engineering and design in synthetic biology. Presented at the PhytoMetaSyn conference, Nature Redesigned, Banff (March 24–25, 2011).

Rational design in synthetic biology. Presented at the Paris EGN-OECD Conference, Delivering Global Promise Through the Life Sciences (Dec 6–7, 2010).

Rational design in synthetic biology. Presented at the Manchester Science Festival, Artificial Life: Promises and Pitfalls, Manchester (October 26, 2010).

Tree preservation: The Tree of Life as heuristic. Presented at the London `Beyond the Tree of Life’ meeting (July 10–11, 2010).

Questioning the Tree of Life. Presented at the First European Summer School on Life and Cognition, Donostia-San Sebastián (June 22–26, 2010).

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