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  1. Maureen A. O'Malley (2014). Exemplary Philosophy of Science: How to Do It. Studies in History and Philosophy of Science Part C 45 (1):149-152.
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  2. Maureen A. O'Malley (2013). Philosophy and the Microbe: A Balancing Act. [REVIEW] Biology and Philosophy 28 (2):153-159.
  3. Maureen A. O'Malley (2013). Small Things, Big Consequences: Microbiological Perspectives on Biology. In Kostas Kampourakis (ed.), The Philosophy of Biology: A Companion for Educators. Springer. 1--373.
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  4. Maureen A. O'Malley (2013). When Integration Fails: Prokaryote Phylogeny and the Tree of Life. Studies in History and Philosophy of Science Part C 44 (4):551-562.
    Much is being written these days about integration, its desirability and even its necessity when complex research problems are to be addressed. Seldom, however, do we hear much about the failure of such efforts. Because integration is an ongoing activity rather than a final achievement, and because today’s literature about integration consists mostly of manifesto statements rather than precise descriptions, an examination of unsuccessful integration could be illuminating to understand better how it works. This paper will examine the case of (...)
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  5. Maureen A. O'Malley, Alastair G. B. Simpson & Andrew J. Roger (2013). The Other Eukaryotes in Light of Evolutionary Protistology. Biology and Philosophy 28 (2):299-330.
    In order to introduce protists to philosophers, we outline the diversity, classification, and evolutionary importance of these eukaryotic microorganisms. We argue that an evolutionary understanding of protists is crucial for understanding eukaryotes in general. More specifically, evolutionary protistology shows how the emphasis on understanding evolutionary phenomena through a phylogeny-based comparative approach constrains and underpins any more abstract account of why certain organismal features evolved in the early history of eukaryotes. We focus on three crucial episodes of this history: the origins (...)
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  6. Maureen A. O'Malley & Orkun S. Soyer (2012). The Roles of Integration in Molecular Systems Biology. Studies in History and Philosophy of Science Part C 43 (1):58-68.
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  7. Maureen A. O'Malley (2010). The First Eukaryote Cell: An Unfinished History of Contestation. Studies in History and Philosophy of Science Part C 41 (3):212-224.
    The eukaryote cell is one of the most radical innovations in the history of life, and the circumstances of its emergence are still deeply contested. This paper will outline the recent history of attempts to reveal these origins, with special attention to the argumentative strategies used to support claims about the first eukaryote cell. I will focus on two general models of eukaryogenesis: the phagotrophy model and the syntrophy model. As their labels indicate, they are based on claims about metabolic (...)
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  8. Maureen A. O'Malley, Kevin C. Elliott & Richard M. Burian (2010). From Genetic to Genomic Regulation: Iterativity in microRNA Research. Studies in History and Philosophy of Science Part C 41 (4):407-417.
    The discovery and ongoing investigation of microRNAs suggest important conceptual and methodological lessons for philosophers and historians of biology. This paper provides an account of miRNA research and the shift from viewing these tiny regulatory entities as minor curiosities to seeing them as major players in the post-transcriptional regulation of genes. Conceptually, the study of miRNAs is part of a broader change in understandings of genetic regulation, in which simple switch-like mechanisms were reinterpreted as aspects of complex cellular and genome-wide (...)
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  9. Maureen A. O'Malley & Staffan Müller-Wille (2010). The Cell as Nexus: Connections Between the History, Philosophy and Science of Cell Biology. Studies in History and Philosophy of Science Part C 41 (3):169-171.
    Although the cell is commonly addressed as the unit of life, historians and philosophers have devoted relatively little attention to this concept in comparison to other fundamental concepts of biology such as the gene or species. As a partial remedy to this neglect, we introduce the cell as a major point of connection between various disciplinary approaches, epistemic strategies, technological vectors and overarching biological processes such as metabolism, growth, reproduction and evolution. We suggest that the role of the cell as (...)
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  10. Maureen A. O’Malley (2010). Ernst Mayr, the Tree of Life, and Philosophy of Biology. Biology and Philosophy 25 (4):529-552.
    Ernst Mayr’s influence on philosophy of biology has given the field a particular perspective on evolution, phylogeny and life in general. Using debates about the tree of life as a guide, I show how Mayrian evolutionary biology excludes numerous forms of life and many important evolutionary processes. Hybridization and lateral gene transfer are two of these processes, and they occur frequently, with important outcomes in all domains of life. Eukaryotes appear to have a more tree-like history because successful lateral events (...)
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  11. Maureen A. O’Malley, William Martin & John Dupré (2010). The Tree of Life: Introduction to an Evolutionary Debate. [REVIEW] Biology and Philosophy 25 (4):441-453.
    The ‘Tree of Life’ is intended to represent the pattern of evolutionary processes that result in bifurcating species lineages. Often justified in reference to Darwin’s discussions of trees, the Tree of Life has run up against numerous challenges especially in regard to prokaryote evolution. This special issue examines scientific, historical and philosophical aspects of debates about the Tree of Life, with the aim of turning these criticisms towards a reconstruction of prokaryote phylogeny and even some aspects of the standard evolutionary (...)
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  12. Maureen A. O'Malley (2008). 'Everything is Everywhere: But the Environment Selects': Ubiquitous Distribution and Ecological Determinism in Microbial Biogeography. Studies in History and Philosophy of Science Part C 39 (3):314-325.
    Recent discoveries of geographical patterns in microbial distribution are undermining microbiology’s exclusively ecological explanations of biogeography and their fundamental assumption that ‘everything is everywhere: but the environment selects’. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will (...)
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  13. Maureen A. O’Malley (2008). 'Everything is Everywhere: But the Environment Selects': Ubiquitous Distribution and Ecological Determinism in Microbial Biogeography. Studies in History and Philosophy of Science Part C 39 (3):314-325.
    Recent discoveries of geographical patterns in microbial distribution are undermining microbiology’s exclusively ecological explanations of biogeography and their fundamental assumption that ‘everything is everywhere: but the environment selects’. This statement was generally promulgated by Dutch microbiologist Martinus Wilhelm Beijerinck early in the twentieth century and specifically articulated in 1934 by his compatriot, Lourens G. M. Baas Becking. The persistence of this precept throughout twentieth-century microbiology raises a number of issues in relation to its formulation and widespread acceptance. This paper will (...)
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  14. John Dupré & Maureen A. O'Malley (2007). Metagenomics and Biological Ontology. Studies in History and Philosophy of Science Part C 38 (4):834-846.
    Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...)
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  15. John Dupré & Maureen A. O’Malley (2007). Metagenomics and Biological Ontology. Studies in History and Philosophy of Science Part C 38 (4):834-846.
    Metagenomics is an emerging microbial systems science that is based on the large-scale analysis of the DNA of microbial communities in their natural environments. Studies of metagenomes are revealing the vast scope of biodiversity in a wide range of environments, as well as new functional capacities of individual cells and communities, and the complex evolutionary relationships between them. Our examination of this science focuses on the ontological implications of these studies of metagenomes and metaorganisms, and what they mean for common (...)
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  16. Maureen A. O'Malley & John Dupré (2007). Towards a Philosophy of Microbiology. Studies in History and Philosophy of Science Part C 38 (4):775-779.
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  17. Maureen A. O’Malley & John Dupré (2007). Introduction: Towards a Philosophy of Microbiology. Studies in History and Philosophy of Science Part C.
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  18. Maureen A. O’Malley & John Dupré (2007). Size Doesn't Matter: Towards a More Inclusive Philosophy of Biology. [REVIEW] Biology and Philosophy 22 (2):155-191.
    Philosophers of biology, along with everyone else, generally perceive life to fall into two broad categories, the microbes and macrobes, and then pay most of their attention to the latter. ‘Macrobe’ is the word we propose for larger life forms, and we use it as part of an argument for microbial equality. We suggest that taking more notice of microbes – the dominant life form on the planet, both now and throughout evolutionary history – will transform some of the philosophy (...)
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  19. Maureen A. O'Malley & Yan Boucher (2005). Paradigm Change in Evolutionary Microbiology. Studies in History and Philosophy of Science Part C 36 (1):183-208.
    Thomas Kuhn had little to say about scientific change in biological science, and biologists are ambivalent about how applicable his framework is for their disciplines. We apply Kuhn’s account of paradigm change to evolutionary microbiology, where key Darwinian tenets are being challenged by two decades of findings from molecular phylogenetics. The chief culprit is lateral gene transfer, which undermines the role of vertical descent and the representation of evolutionary history as a tree of life. To assess Kuhn’s relevance to this (...)
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