30 found
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  1.  5
    How Causal Are Microbiomes? A Comparison with the Helicobacter Pylori Explanation of Ulcers.Kate E. Lynch, Emily C. Parke & Maureen A. O’Malley - 2019 - Biology and Philosophy 34 (6):62.
    Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...)
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  2.  2
    How Causal Are Microbiomes? A Comparison with the Helicobacter Pylori Explanation of Ulcers.Kate E. Lynch, Emily C. Parke & Maureen A. O’Malley - 2019 - Biology and Philosophy 34 (6):62.
    Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...)
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  3.  36
    How Causal Are Microbiomes? A Comparison with the Helicobacter Pylori Explanation of Ulcers.Kate E. Lynch, Emily C. Parke & Maureen A. O’Malley - 2019 - Biology and Philosophy 34 (6):62.
    Human microbiome research makes causal connections between entire microbial communities and a wide array of traits that range from physiological diseases to psychological states. To evaluate these causal claims, we first examine a well-known single-microbe causal explanation: of Helicobacter pylori causing ulcers. This apparently straightforward causal explanation is not so simple, however. It does not achieve a key explanatory standard in microbiology, of Koch’s postulates, which rely on manipulations of single-microorganism cultures to infer causal relationships to disease. When Koch’s postulates (...)
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  4.  39
    The Roles of Integration in Molecular Systems Biology.Maureen A. O’Malley & Orkun S. Soyer - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):58-68.
  5.  36
    Making Knowledge in Synthetic Biology: Design Meets Kludge.Maureen A. O’Malley - 2009 - Biological Theory 4 (4):378-389.
    Synthetic biology is an umbrella term that covers a range of aims, approaches, and techniques. They are all brought together by common practices of analogizing, synthesizing, mechanicizing, and kludging. With a focus on kludging as the connection point between biology, engineering, and evolution, I show how synthetic biology’s successes depend on custom-built kludges and a creative, “make-it-work” attitude to the construction of biological systems. Such practices do not fit neatly, however, into synthetic biology’s celebration of rational design. Nor do they (...)
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  6.  31
    When Integration Fails: Prokaryote Phylogeny and the Tree of Life.Maureen A. O’Malley - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4a):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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  7.  14
    The Roles of Integration in Molecular Systems Biology.Maureen A. O’Malley & Orkun S. Soyer - 2012 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 43 (1):58-68.
  8.  21
    Methodological Strategies in Microbiome Research and Their Explanatory Implications.Maureen A. O’Malley & Derek J. Skillings - 2018 - Perspectives on Science 26 (2):239-265.
    Microbiome research is the analysis of the aggregated molecular components of a defined microbial community.1 Our examination of this field will focus on how causality is assigned in microbiome analyses, and what methodological strategies are used to identify communities or components of those communities as causal contributors to host states. Earlier microbiome research was conducted at a broad scale via bio informatic analyses of environmental samples, then backed up by whole community transfer experiments. These "top-down" findings, in which the whole (...)
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  9. Metagenomics and Biological Ontology.John Dupré & Maureen A. O’Malley - 2007 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 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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  10.  6
    Reproduction Expanded: Multifenerational and Multilineal Units of Evoultion.Maureen A. O’Malley - 2016 - Philosophy of Science 83 (5):835-847.
    Reproduction is central to biology and evolution. Standard concepts of reproduction are drawn from animals. Nonstandard examples of reproduction can be found in unicellular eukaryotes that distribute their reproductive strategies across multiple generations, and in mutualistic systems that combine different modes of reproduction across multiple lineages. Examining multigenerational and multilineal reproducers and how they align fitness has implications for conceptualizing units of evolution.
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  11.  10
    Microbiome Causality: Further Reflections.Kate E. Lynch, Emily C. Parke & Maureen A. O’Malley - 2020 - Biology and Philosophy 35 (2):1-16.
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  12.  36
    The First Eukaryote Cell: An Unfinished History of Contestation.Maureen A. O’Malley - 2010 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 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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  13.  14
    Major Problems in Evolutionary Transitions: How a Metabolic Perspective Can Enrich Our Understanding of Macroevolution.Maureen A. O’Malley & Russell Powell - 2016 - Biology and Philosophy 31 (2):159-189.
    The model of major transitions in evolution devised by Maynard Smith and Szathmáry has exerted tremendous influence over evolutionary theorists. Although MTE has been criticized for inconsistently combining different types of event, its ongoing appeal lies in depicting hierarchical increases in complexity by means of evolutionary transitions in individuality. In this paper, we consider the implications of major evolutionary events overlooked by MTE and its ETI-oriented successors, specifically the biological oxygenation of Earth, and the acquisitions of mitochondria and plastids. By (...)
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  14.  30
    Paradigm Change in Evolutionary Microbiology.Maureen A. O’Malley & Yan Boucher - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 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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  15.  4
    The First Eukaryote Cell: An Unfinished History of Contestation.Maureen A. O’Malley - 2010 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 41 (3):212-224.
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  16.  16
    Metagenomics and Biological Ontology.John Dupré & Maureen A. O’Malley - 2005 - Studies in History and Philosophy of Biological and Biomedical Sciences 38 (4):834-846.
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  17.  55
    From Genetic to Genomic Regulation: Iterativity in microRNA Research.Maureen A. O’Malley, Kevin C. Elliott & Richard M. Burian - 2010 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 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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  18.  33
    Towards a Philosophy of Microbiology.Maureen A. O’Malley & John Dupré - 2007 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 38 (4):775-779.
  19.  28
    Philosophy and the Microbe: A Balancing Act. [REVIEW]Maureen A. O’Malley - 2013 - Biology and Philosophy 28 (2):153-159.
  20.  6
    Paradigm Change in Evolutionary Microbiology.Maureen A. O’Malley & Yan Boucher - 2005 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 36 (1):183-208.
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  21.  15
    The Other Eukaryotes in Light of Evolutionary Protistology.Maureen A. O’Malley, Alastair G. B. Simpson & Andrew J. Roger - 2013 - 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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  22.  97
    ‘Everything is Everywhere: But the Environment Selects’: Ubiquitous Distribution and Ecological Determinism in Microbial Biogeography.Maureen A. O’Malley - 2008 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 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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  23.  8
    ‘Everything is Everywhere: But the Environment Selects’: Ubiquitous Distribution and Ecological Determinism in Microbial Biogeography.Maureen A. O’Malley - 2008 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 39 (3):314-325.
  24.  17
    The Cell as Nexus: Connections Between the History, Philosophy and Science of Cell Biology.Maureen A. O’Malley & Staffan Müller-Wille - 2010 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 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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  25.  24
    Exemplary Philosophy of Science: How to Do It. [REVIEW]Maureen A. O’Malley - 2014 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 45 (1):149-152.
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  26.  24
    A Philosophical Perspective on Evolutionary Systems Biology.Maureen A. O’Malley, Orkun S. Soyer & Mark L. Siegal - 2015 - Biological Theory 10 (1):6-17.
    Evolutionary systems biology is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context (...)
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  27.  13
    What Microbes Can Do: A Sensory Guide to Microbiology: March of the Microbes: Sighting the Unseen John L. Ingraham Cambridge, MA: Belknap Press of Harvard University Press, 2010.Maureen A. O’Malley - 2010 - Biological Theory 5 (2):182-186.
  28.  10
    The Cell as Nexus: Connections Between the History, Philosophy and Science of Cell Biology.Maureen A. O’Malley & Staffan Müller-Wille - 2010 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 41 (3):169-171.
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  29.  8
    What Microbes Can Do: A Sensory Guide to Microbiology: March of the Microbes: Sighting the Unseen John L. Ingraham Cambridge, MA: Belknap Press of Harvard University Press, 2010. [REVIEW]Maureen A. O’Malley - 2010 - Biological Theory 5 (2):182-186.
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  30.  15
    Decentring Humans? Imagining a Microbially Inspired Sociology: Myra J. Hird: The Origins of Sociable Life: Evolution After Science Studies. Houndsmills, Basingstoke: Palgrave Macmillan, 2009, V+202pp, £50.00 HB.Maureen A. O’Malley - 2011 - Metascience 20 (1):127-130.
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