Linked bibliography for the SEP article "Philosophy of Microbiology" by Maureen A. O’Malley and Emily C. Parke

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If everything goes well, this page should display the bibliography of the aforementioned article as it appears in the Stanford Encyclopedia of Philosophy, but with links added to PhilPapers records and Google Scholar for your convenience. Some bibliographies are not going to be represented correctly or fully up to date. In general, bibliographies of recent works are going to be much better linked than bibliographies of primary literature and older works. Entries with PhilPapers records have links on their titles. A green link indicates that the item is available online at least partially.

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Alegado, Rosanna A, Laura W Brown, Shugeng Cao, Renee K Dermenjian, Richard Zuzow, Stephen R Fairclough, Jon Clardy, and Nicole King, 2012, “A Bacterial Sulfonolipid Triggers Multicellular Development in the Closest Living Relatives of Animals”, ELife, 1: e00013. doi:10.7554/elife.00013 (Scholar)
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Attah, Nuhu Osman, Marina DiMarco, and Anya Plutynski, 2020, “Microbiomes: Proportional Causes in Context”, Biology & Philosophy, 35(1): art. 22. doi:10.1007/s10539-020-9738-3 (Scholar)
Avery, Oswald T., MacLeod, Colin M., and McCarty, Maclyn, 1944, “Studies on the Chemical Nature of the Substance Inducing Transformation of Pneumococcal Types: Induction of Transformation by a Desoxyribonucleic Acid Fraction Isolated from Pneumococcus Type III”, Journal of Experimental Medicine, 79: 137–158. (Scholar)
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Beatty, John, 2006, “Replaying Life’s Tape”, The Journal of Philosophy, 103(7): 336–362. doi:10.5840/jphil2006103716 (Scholar)
Beckwith, Jon, 2011, “The Operon as Paradigm: Normal Science and the Beginning of Biological Complexity”, Journal of Molecular Biology, 409(1): 7–13. doi:10.1016/j.jmb.2011.02.027 (Scholar)
Beekman, Madeleine and Tanya Latty, 2015, “Brainless but Multi-Headed: Decision Making by the Acellular Slime Mould Physarum polycephalum”, Journal of Molecular Biology, 427(23): 3734–3743. doi:10.1016/j.jmb.2015.07.007 (Scholar)
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Blount, Zachary D., Christina Z. Borland, and Richard E. Lenski, 2008, “Historical Contingency and the Evolution of a Key Innovation in an Experimental Population of Escherichia coli”, Proceedings of the National Academy of Sciences USA, 105(23): 7899–7906. doi:10.1073/pnas.0803151105 (Scholar)
Blount, Zachary D., Jeffrey E. Barrick, Carla J. Davidson, and Richard E. Lenski, 2012, “Genomic Analysis of a Key Innovation in an Experimental Escherichia coli Population”, Nature, 489(7417): 513–518. doi:10.1038/nature11514 (Scholar)
Booth, Austin, 2014, “Symbiosis, Selection, and Individuality”, Biology & Philosophy, 29(5): 657–673. doi:10.1007/s10539-014-9449-8 (Scholar)
Botstein, David and Gerald R. Fink, 2011, “Yeast: An Experimental Organism for 21st Century Biology”, Genetics, 189(3): 695–704. doi:10.1534/genetics.111.130765 (Scholar)
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Brock, Thomas D., 1990, The Emergence of Bacterial Genetics, Cold Spring Harbour, NY: Cold Spring Harbor Laboratory Press. (Scholar)
Bulloch, William, 1938, The History of Bacteriology, London: Oxford University Press. (Scholar)
Burki, Fabien, Andrew J. Roger, Matthew W. Brown, and Alastair G.B. Simpson, 2020, “The New Tree of Eukaryotes”, Trends in Ecology & Evolution, 35(1): 43–55. doi:10.1016/j.tree.2019.08.008 (Scholar)
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Clarke, Ellen, 2013, “The Multiple Realizability of Biological Individuals”:, Journal of Philosophy, 110(8): 413–435. doi:10.5840/jphil2013110817 (Scholar)
Cleland, Carol E., 2007, “Epistemological Issues in the Study of Microbial Life: Alternative Terran Biospheres?”, Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4): 847–861. doi:10.1016/j.shpsc.2007.09.007 (Scholar)
Coyne, Jerry A. and H. Allen Orr, 1998, “The Evolutionary Genetics of Speciation”, Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 353(1366): 287–305. doi:10.1098/rstb.1998.0210 (Scholar)
Dagan, Tal and William Martin, 2009, “Getting a Better Picture of Microbial Evolution En Route to a Network of Genomes”, Philosophical Transactions of the Royal Society B: Biological Sciences, 364(1527): 2187–2196. doi:10.1098/rstb.2009.0040 (Scholar)
Davis, Rowland H., 2003, The Microbial Models of Molecular Biology: From Genes to Genomes, New York: Oxford University Press. doi:10.1093/acprof:oso/9780195154368.001.0001 (Scholar)
Doolittle, W. Ford, 1999, “Phylogenetic Classification and the Universal Tree”, Science, 284(5423): 2124–2128. doi:10.1126/science.284.5423.2124 (Scholar)
Doolittle, W. Ford and Eric Bapteste, 2007, “Pattern Pluralism and the Tree of Life Hypothesis”, Proceedings of the National Academy of Sciences USA, 104(7): 2043–2049. doi:10.1073/pnas.0610699104 (Scholar)
Doolittle, W. Ford and Olga Zhaxybayeva, 2009, “On the Origin of Prokaryotic Species”, Genome Research, 19(5): 744–756. doi:10.1101/gr.086645.108 (Scholar)
Dupré, John, 2001, “In Defence of Classification”, Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 32(2): 203–219. doi:10.1016/s1369-8486(01)00003-6 (Scholar)
Dupré, John and Maureen A. O’Malley, 2007, “Metagenomics and Biological Ontology”, Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences, 38(4): 834–846. doi:10.1016/j.shpsc.2007.09.001 (Scholar)
Embley, T. Martin and Tom A. Williams, 2015, “Steps on the Road to Eukaryotes”, Nature, 521(7551): 169–170. doi:10.1038/nature14522 (Scholar)
Eme, Laura, Anja Spang, Jonathan Lombard, Courtney W. Stairs, and Thijs J. G. Ettema, 2017, “Archaea and the Origin of Eukaryotes”, Nature Reviews Microbiology, 15(12): 711–723. doi:10.1038/nrmicro.2017.133 (Scholar)
Endersby, Jim, 2007, A Guinea Pig’s History of Biology: The Plants and Animals Who Taught Us the Facts of Life, London: William Heinemann. (Scholar)
Enquist, Brian J., Andrew J. Abraham, Michael B. J. Harfoot, Yadvinder Malhi, and Christopher E. Doughty, 2020, “The Megabiota Are Disproportionately Important for Biosphere Functioning”, Nature Communications, 11: art. 699. doi:10.1038/s41467-020-14369-y (Scholar)
Ereshefsky, Marc, 1998, “Species Pluralism and Anti-Realism”, Philosophy of Science, 65(1): 103–120. doi:10.1086/392628 (Scholar)
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Ereshefsky, Marc and Makmiller Pedroso, 2013, “Biological Individuality: The Case of Biofilms”, Biology & Philosophy, 28(2): 331–349. doi:10.1007/s10539-012-9340-4 (Scholar)
Falkowski, Paul G., Tom Fenchel, and Edward F. Delong, 2008, “The Microbial Engines That Drive Earth’s Biogeochemical Cycles”, Science, 320(5879): 1034–1039. doi:10.1126/science.1153213 (Scholar)
Fox, Jeremy W. and Richard E. Lenski, 2015, “From Here to Eternity—The Theory and Practice of a Really Long Experiment”, PLOS Biology, 13(6): e1002185. doi:10.1371/journal.pbio.1002185 (Scholar)
Franklin[-Hall], L. R., 2007, “Bacteria, Sex, and Systematics*”, Philosophy of Science, 74(1): 69–95. doi:10.1086/519476 (Scholar)
Fry, A J, M R Palmer, and D M Rand, 2004, “Variable Fitness Effects of Wolbachia Infection in Drosophila melanogaster”, Heredity, 93(4): 379–389. doi:10.1038/sj.hdy.6800514 (Scholar)
Gause, G.F., 1934a, The Struggle for Existence, Baltimore, MD: Williams and Wilkins. (Scholar)
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Gest, H., 2004, “The Discovery of Microorganisms by Robert Hooke and Antoni van Leeuwenhoek, Fellows of The Royal Society”, Notes and Records of the Royal Society of London, 58(2): 187–201. doi:10.1098/rsnr.2004.0055 (Scholar)
Gillies, Donald, 2016, “Establishing Causality in Medicine and Koch’s Postulates”, International Journal of History and Philosophy of Medicine, 6: 10603. (Scholar)
–––, 2019, “Commentary on Kate E. Lynch, Emily C. Parke, and Maureen A. O’Malley: ‘How Causal Are Microbiomes? A Comparison with the Helicobacter pylori Explanation of Ulcers’”, Biology & Philosophy, 34(6): art. 56. doi:10.1007/s10539-019-9707-x">10.1007/s10539-019-9707-x (Scholar)
Godfrey-Smith, Peter, 2015, “Reproduction, Symbiosis, and the Eukaryotic Cell”, Proceedings of the National Academy of Sciences USA, 112(33): 10120–10125. doi:10.1073/pnas.1421378112 (Scholar)
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Gogarten, J. Peter, W. Ford Doolittle, and Jeffrey G. Lawrence, 2002, “Prokaryotic Evolution in Light of Gene Transfer”, Molecular Biology and Evolution, 19(12): 2226–2238. doi:10.1093/oxfordjournals.molbev.a004046 (Scholar)
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Guerrero, Ricardo, Carlos Pedrós-Alió, Isabel Esteve, Jordi Mas, David Chase, and Lynn Margulis, 1986, “Predatory Prokaryotes: Predation and Primary Consumption Evolved in Bacteria”, Proceedings of the National Academy of Sciences USA, 83(7): 2138–2142. doi:10.1073/pnas.83.7.2138 (Scholar)
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Hastings, Alan, 2020, “Long-Term Predator–Prey Cycles Finally Achieved in the Lab”, Nature, 577(7789): 172–173. doi:10.1038/d41586-019-03603-3 (Scholar)
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Hershey, A. D. and Martha Chase, 1952, “Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage”, The Journal of General Physiology, 36(1): 39–56. doi:10.1085/jgp.36.1.39 (Scholar)
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Hooks, Katarzyna B., Jan Pieter Konsman, and Maureen A. O’Malley, 2019, “Microbiota-Gut-Brain Research: A Critical Analysis”, Behavioral and Brain Sciences, 42: e60. doi:10.1017/S0140525X18002133 (Scholar)
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Jacob, François and Jacques Monod, 1961, “Genetic Regulatory Mechanisms in the Synthesis of Proteins”, Journal of Molecular Biology, 3(3): 318–356. doi:10.1016/s0022-2836(61)80072-7 (Scholar)
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O’Malley, Maureen A., William Martin, and John Dupré, 2010, “The Tree of Life: Introduction to an Evolutionary Debate”, Biology & Philosophy, 25(4): 441–453. doi:10.1007/s10539-010-9208-4 (Scholar)
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O’Malley, Maureen A. and Russell Powell, 2016, “Major Problems in Evolutionary Transitions: How a Metabolic Perspective Can Enrich Our Understanding of Macroevolution”, Biology & Philosophy, 31(2): 159–189. doi:10.1007/s10539-015-9513-z (Scholar)
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