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  1. The Attempt on the Life of the Tree of Life: Science, Philosophy and Politics.W. Ford Doolittle - 2010 - Biology and Philosophy 25 (4):455-473.
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  • Why is There Anything Except Physics?Barry Loewer - 2009 - Synthese 170 (2):217 - 233.
    In the course of defending his view of the relation between the special sciences and physics from Jaegwon Kim’s objections Jerry Fodor asks “So then, why is there anything except physics?” By which he seems to mean to ask if physics is fundamental and complete in its domain how can there be autonomous special science laws. Fodor wavers between epistemological and metaphysical understandings of the autonomy of the special sciences. In my paper I draw out the metaphysical construal of his (...)
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  • Size Doesn’T Matter: Towards a More Inclusive Philosophy of Biology. [REVIEW]Maureen A. O’Malley & John Dupré - 2007 - 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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  • The Hegemony of Molecular Biology.Philip Kitcher - 1999 - Biology and Philosophy 14 (2):195-210.
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  • Natural Taxonomy in Light of Horizontal Gene Transfer.Cheryl P. Andam, David Williams & J. Peter Gogarten - 2010 - Biology and Philosophy 25 (4):589-602.
    We discuss the impact of horizontal gene transfer (HGT) on phylogenetic reconstruction and taxonomy. We review the power of HGT as a creative force in assembling new metabolic pathways, and we discuss the impact that HGT has on phylogenetic reconstruction. On one hand, shared derived characters are created through transferred genes that persist in the recipient lineage, either because they were adaptive in the recipient lineage or because they resulted in a functional replacement. On the other hand, taxonomic patterns in (...)
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  • Symbiosis, Lateral Function Transfer and the (Many) Saplings of Life.Frédéric Bouchard - 2010 - Biology and Philosophy 25 (4):623-641.
    One of intuitions driving the acceptance of a neat structured tree of life is the assumption that organisms and the lineages they form have somewhat stable spatial and temporal boundaries. The phenomenon of symbiosis shows us that such ‘fixist’ assumptions does not correspond to how the natural world actually works. The implications of lateral gene transfer (LGT) have been discussed elsewhere; I wish to stress a related point. I will focus on lateral function transfer (LFT) and will argue, using examples (...)
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  • Gene Sharing and Genome Evolution: Networks in Trees and Trees in Networks.Robert G. Beiko - 2010 - Biology and Philosophy 25 (4):659-673.
    Frequent lateral genetic transfer undermines the existence of a unique “tree of life” that relates all organisms. Vertical inheritance is nonetheless of vital interest in the study of microbial evolution, and knowing the “tree of cells” can yield insights into ecological continuity, the rates of change of different cellular characters, and the evolutionary plasticity of genomes. Notwithstanding within-species recombination, the relationships most frequently recovered from genomic data at shallow to moderate taxonomic depths are likely to reflect cellular inheritance. At the (...)
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  • On the Need for Integrative Phylogenomics, and Some Steps Toward its Creation.Eric Bapteste & Richard M. Burian - 2010 - Biology and Philosophy 25 (4):711-736.
    Recently improved understanding of evolutionary processes suggests that tree-based phylogenetic analyses of evolutionary change cannot adequately explain the divergent evolutionary histories of a great many genes and gene complexes. In particular, genetic diversity in the genomes of prokaryotes, phages, and plasmids cannot be fit into classic tree-like models of evolution. These findings entail the need for fundamental reform of our understanding of molecular evolution and the need to devise alternative apparatus for integrated analysis of these genomes. We advocate the development (...)
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  • Depth: An Account of Scientific Explanation.Michael Strevens - 2008 - Harvard University Press.
    Approaches to explanation -- Causal and explanatory relevance -- The kairetic account of /D making -- The kairetic account of explanation -- Extending the kairetic account -- Event explanation and causal claims -- Regularity explanation -- Abstraction in regularity explanation -- Approaches to probabilistic explanation -- Kairetic explanation of frequencies -- Kairetic explanation of single outcomes -- Looking outward -- Looking inward.
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  • The Devil in the Details: Asymptotic Reasoning in Explanation, Reduction, and Emergence.Robert W. Batterman - 2001 - Oxford University Press.
    Robert Batterman examines a form of scientific reasoning called asymptotic reasoning, arguing that it has important consequences for our understanding of the scientific process as a whole. He maintains that asymptotic reasoning is essential for explaining what physicists call universal behavior. With clarity and rigor, he simplifies complex questions about universal behavior, demonstrating a profound understanding of the underlying structures that ground them. This book introduces a valuable new method that is certain to fill explanatory gaps across disciplines.
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  • Genes and the Agents of Life: The Individual in the Fragile Sciences Biology.Robert A. Wilson - 2005 - New York, NY, USA: Cambridge University Press.
    Genes and the Agents of Life undertakes to rethink the place of the individual in the biological sciences, drawing parallels with the cognitive and social sciences. Genes, organisms, and species are all agents of life but how are each of these conceptualized within genetics, developmental biology, evolutionary biology, and systematics? The book includes highly accessible discussions of genetic encoding, species and natural kinds, and pluralism above the levels of selection, drawing on work from across the biological sciences. The book is (...)
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  • Bacteria, Sex, and Systematics.L. R. Franklin - 2007 - Philosophy of Science 74 (1):69-95.
    Philosophical discussions of species have focused on multicellular, sexual animals and have often neglected to consider unicellular organisms like bacteria. This article begins to fill this gap by considering what species concepts, if any, apply neatly to the bacterial world. First, I argue that the biological species concept cannot be applied to bacteria because of the variable rates of genetic transfer between populations, depending in part on which gene type is prioritized. Second, I present a critique of phylogenetic bacterial species, (...)
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  • The Philosophy of Science.Stephen Edelston Toulmin - 1953 - New York: Hutchinson's University Library.
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  • Darwinian Populations and Natural Selection.Peter Godfrey-Smith - 2009 - Oxford University Press.
    The book presents a new way of understanding Darwinism and evolution by natural selection, combining work in biology, philosophy, and other fields.
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  • The Cytoplasmic Structure Hypothesis for Ribosome Assembly, Vertical Inheritance, and Phylogeny.David S. Thaler - 2009 - Bioessays 31 (7):774-783.
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  • Wonderful Life; The Burgess Shale and the Nature of History.Stephen Jay Gould - 1992 - Journal for General Philosophy of Science / Zeitschrift für Allgemeine Wissenschaftstheorie 23 (2):359-360.
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  • Revisiting the Concept of Lineage in Prokaryotes: A Phylogenetic Perspective.Yan Boucher & Eric Bapteste - 2009 - Bioessays 31 (5):526-536.
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  • Science, Truth, and Democracy.Philip Kitcher - 2003 - Mind 112 (448):746-749.
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  • Science, Truth, and Democracy.Philip Kitcher - 2001 - Oxford University Press.
    Striving to boldly redirect the philosophy of science, this book by renowned philosopher Philip Kitcher examines the heated debate surrounding the role of science in shaping our lives. Kitcher explores the sharp divide between those who believe that the pursuit of scientific knowledge is always valuable and necessary--the purists--and those who believe that it invariably serves the interests of people in positions of power. In a daring turn, he rejects both perspectives, working out a more realistic image of the sciences--one (...)
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  • Biological Individuality: The Identity and Persistence of Living Entities.Jack Wilson - 1999 - Cambridge University Press.
    What makes a biological entity an individual? Jack Wilson shows that past philosophers have failed to explicate the conditions an entity must satisfy to be a living individual. He explores the reason for this failure and explains why we should limit ourselves to examples involving real organisms rather than thought experiments. This book explores and resolves paradoxes that arise when one applies past notions of individuality to biological examples beyond the conventional range and presents an analysis of identity and persistence. (...)
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  • Biological Individuality: The Identity and Persistence of Living Entities.Jack Wilson - 2001 - Philosophical Quarterly 51 (203):264-266.
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  • Naturalist.Edward O. Wilson - 1996 - Journal of the History of Biology 29 (1):145-147.
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  • The Origin of Species by Means of Natural Selection.Charles Darwin - 1978 - Franklin Library.
    ORIGIN OF SPECIES. INTRODUCTION. When on board HMS 'Beagle,' as naturalist, I was ranch struck with certain facts in the distribution of the organic beings ...
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  • The Sciences of the Artificial.Herbert A. Simon - 1969 - [Cambridge, M.I.T. Press.
    Continuing his exploration of the organization of complexity and the science of design, this new edition of Herbert Simon's classic work on artificial ...
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