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W. Doolittle
Dalhousie University
  1.  73
    Life and Life Only: A Radical Alternative to Life Definitionism.Carlos Mariscal & W. Ford Doolittle - 2020 - Synthese 197 (7):2975-2989.
    To date, no definition of life has been unequivocally accepted by the scientific community. In frustration, some authors advocate alternatives to standard definitions. These include using a list of characteristic features, focusing on life’s effects, or categorizing biospheres rather than life itself; treating life as a fuzzy category, a process or a cluster of contingent properties; or advocating a ‘wait-and-see’ approach until other examples of life are created or discovered. But these skeptical, operational, and pluralistic approaches have intensified the debate, (...)
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  2. It’s the Song, Not the Singer: An Exploration of Holobiosis and Evolutionary Theory.W. Ford Doolittle & Austin Booth - 2017 - Biology and Philosophy 32 (1):5-24.
    That holobionts are units of selection squares poorly with the observation that microbes are often recruited from the environment, not passed down vertically from parent to offspring, as required for collective reproduction. The taxonomic makeup of a holobiont’s microbial community may vary over its lifetime and differ from that of conspecifics. In contrast, biochemical functions of the microbiota and contributions to host biology are more conserved, with taxonomically variable but functionally similar microbes recurring across generations and hosts. To save what (...)
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  3. Making the Most of Clade Selection.W. Ford Doolittle - 2017 - Philosophy of Science 84 (2):275-295.
    Clade selection is unpopular with philosophers who otherwise accept multilevel selection theory. Clades cannot reproduce, and reproduction is widely thought necessary for evolution by natural selection, especially of complex adaptations. Using microbial evolutionary processes as heuristics, I argue contrariwise, that (1) clade growth (proliferation of contained species) substitutes for clade reproduction in the evolution of complex adaptation, (2) clade-level properties favoring persistence – species richness, dispersal, divergence, and possibly intraclade cooperation – are not collapsible into species-level traits, (3) such properties (...)
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  4.  47
    Speciation Without Species: A Final Word.W. Ford Doolittle - 2019 - Philosophy, Theory, and Practice in Biology 11.
    This paper, like many before it, aims to solve the “species problem” by declaring it a non-problem. It borrows its title from an earlier article by Jeff Lawrence and its philosophical concepts from Marc Ereshefsky, John Dupré, Peter Godfrey-Smith, Ken Waters, and Jody Hey. The emphasis is on bacteria, but my pragmatic species anti-realist conclusion may be a general one.
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  5. Natural Selection Through Survival Alone, and the Possibility of Gaia.W. Ford Doolittle - 2014 - Biology and Philosophy 29 (3):415-423.
    Here I advance two related evolutionary propositions. (1) Natural selection is most often considered to require competition between reproducing “individuals”, sometimes quite broadly conceived, as in cases of clonal, species or multispecies-community selection. But differential survival of non-competing and non-reproducing individuals will also result in increasing frequencies of survival-promoting “adaptations” among survivors, and thus is also a kind of natural selection. (2) Darwinists have challenged the view that the Earth’s biosphere is an evolved global homeostatic system. Since there is only (...)
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  6.  29
    Mutationism, Not Lamarckism, Captures the Novelty of CRISPR–Cas.Jeremy G. Wideman, S. Andrew Inkpen, W. Ford Doolittle & Rosemary J. Redfield - 2019 - Biology and Philosophy 34 (1):12.
    Koonin, in an article in this issue, claims that CRISPR–Cas systems are mechanisms for the inheritance of acquired adaptive characteristics, and that the operation of such systems comprises a “Lamarckian mode of evolution.” We argue that viewing the CRISPR–Cas mechanism as facilitating a form of “directed mutation” more accurately represents how the system behaves and the history of neoDarwinian thinking, and is to be preferred.
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  7.  37
    The Generality of Constructive Neutral Evolution.T. D. P. Brunet & W. Ford Doolittle - 2018 - Biology and Philosophy 33 (1-2):2.
    Constructive Neutral Evolution is an evolutionary mechanism that can explain much molecular inter-dependence and organismal complexity without assuming positive selection favoring such dependency or complexity, either directly or as a byproduct of adaptation. It differs from but complements other non-selective explanations for complexity, such as genetic drift and the Zero Force Evolutionary Law, by being ratchet-like in character. With CNE, purifying selection maintains dependencies or complexities that were neutrally evolved. Preliminary treatments use it to explain specific genetic and molecular structures (...)
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  8. Modern Synthesis is the Light of Microbial Genomics.Austin Booth, Carlos Mariscal & W. Ford Doolittle - 2016 - Annual Reviews of Microbiology 70 (1):279-297.
  9. Eukaryogenesis: How Special, Really?Austin Booth & W. Ford Doolittle - 2015 - Proceedings of the National Academy of Sciences of the United States of America:1-8.
    Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. First, the criteria by which we judge eukaryogenesis to have required a genuinely (...)
     
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  10.  26
    Microbial Neopleomorphism.W. Ford Doolittle - 2013 - Biology and Philosophy 28 (2):351-378.
    Our understanding of what microbes are and how they evolve has undergone many radical shifts since the late nineteenth century, when many still believed that bacteria could be spontaneously generated and most thought microbial “species” (if any) to be unstable and interchangeable in form and function (pleomorphic). By the late twentieth century, an ontology based on single cells and definable species with predictable properties, evolving like species of animals or plants, was widely accepted. Now, however, genomic and metagenomic data show (...)
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  11.  65
    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.
    Lateral gene transfer, the exchange of genetic information between lineages, not only makes construction of a universal Tree of Life difficult to achieve, but calls into question the utility and meaning of any result. Here I review the science of prokaryotic LGT, the philosophy of the TOL as it figured in Darwin’s formulation of the Theory of Evolution, and the politics of the current debate within the discipline over how threats to the TOL should be represented outside it. We could (...)
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  12.  6
    The Role of Purifying Selection in the Origin and Maintenance of Complex Function.Tyler D. P. Brunet, W. Ford Doolittle & Joseph P. Bielawski - 2021 - Studies in History and Philosophy of Science Part A 87:125-135.
  13.  22
    The Coupling of Taxonomy and Function in Microbiomes.S. Andrew Inkpen, Gavin M. Douglas, T. D. P. Brunet, Karl Leuschen, W. Ford Doolittle & Morgan G. I. Langille - 2017 - Biology and Philosophy 32 (6):1225-1243.
    Microbiologists are transitioning from the study and characterization of individual strains or species to the profiling of whole microbiomes and microbial ecology. Equipped with high-throughput methods for studying the taxonomic and functional characteristics of diverse samples, they are just beginning to encounter the conceptual, theoretical, and experimental problems of comparing taxonomy to function, and extracting useful measures from such comparisons. Although still unresolved, these problems are well studied in macro-ecology and are reiterated here as an historical precautionary for microbial ecologists. (...)
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  14.  61
    Eukaryotes First: How Could That Be? [REVIEW]Carlos Mariscal & W. Ford Doolittle - 2015 - Philosophical Transactions of the Royal Society B: Biological Sciences 370:1-10.
    In the half century since the formulation of the prokaryote : eukaryote dichotomy, many authors have proposed that the former evolved from something resembling the latter, in defiance of common (and possibly common sense) views. In such ‘eukaryotes first’ (EF) scenarios, the last universal common ancestor is imagined to have possessed significantly many of the complex characteristics of contemporary eukaryotes, as relics of an earlier ‘progenotic’ period or RNAworld. Bacteria and Archaea thus must have lost these complex features secondarily, through (...)
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  15.  11
    Horizontal Persistence and the Complexity Hypothesis.Aaron Novick & W. Ford Doolittle - 2020 - Biology and Philosophy 35 (1):2.
    This paper investigates the complexity hypothesis in microbial evolutionary genetics from a philosophical vantage. This hypothesis, in its current version, states that genes with high connectivity are likely to be resistant to being horizontally transferred. We defend four claims. There is an important distinction between two different ways in which a gene family can persist: vertically and horizontally. There is a trade-off between these two modes of persistence, such that a gene better at achieving one will be worse at achieving (...)
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  16.  11
    A Chemostat Model for Evolution by Persistence: Clade Selection and its Explanatory Autonomy.Celso Neto & W. Ford Doolittle - forthcoming - Philosophy of Science:1-47.
    Many contemporary biologists and philosophers of biology admit that selection occurs at any level of the biological hierarchy at which entities showing heritable variation in fitness are found, while insisting that fitness at any level entails differential reproduction, not differential persistence. Those who allow that persistence can be selected doubt that selection on non-reproducing entities can be reiterated, to produce “complex adaptations”. We present here a verbal model of sub-clones evolving in a simple idealized chemostat that calls into question these (...)
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  17.  33
    ‘Species’ Without Species.Aaron Novick & W. Ford Doolittle - 2021 - Studies in History and Philosophy of Science Part A 87:72-80.
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  18. Hierarchical Approaches to Genome Evolution.W. Ford Doolittle - 1988 - Canadian Journal of Philosophy, Supplementary Volume 14:101.
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  19.  21
    Adaptive Regeneration Across Scales: Replicators and Interactors From Limbs to Forests.S. Andrew Inkpen & W. Ford Doolittle - 2021 - Philosophy, Theory, and Practice in Biology 13:1-14.
    Here we endorse Hull’s replicator/interactor framework as providing the overarching understanding sought by MacCord and Maienschein. We suggest that difficulties in seeing the regeneration of limbs by salamanders and of forest ecosystems after fires as similar evolutionary processes can be overcome in this framework. In generalizing Dawkins’s “selfish gene” perspective, Hull defined natural selection as “a process in which the differential extinction and proliferation of interactors causes the differential perpetuation of the replicators that produced them”. Although genes and bacteria are (...)
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  20.  6
    Hierarchical Approaches to Genome Evolution.W. Ford Doolittle - 1988 - Canadian Journal of Philosophy 18 (sup1):101-133.
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  21.  10
    Adaptive Regeneration Across Scales: Replicators and Interactors From Limbs to Forests.S. Andrew Inkpen & W. Ford Doolittle - 2021 - Philosophy, Theory, and Practice in Biology 13.
    Diverse living systems possess the capacity for regeneration; that is, they can under some circumstances repair, re-produce, and maintain themselves in the face of disturbance or damage. Think of systems as diverse as forests, microbial biofilms, corals, salamanders, hydra, and human skin cells. This capacity is fundamental to life—without it, many biological systems would be too fragile to cope with stress and would frequently collapse—but because it is multiply realized in wildly different living systems at many scales, finding a common (...)
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  22.  36
    Comment on “Does Constructive Neutral Evolution Play an Important Role in the Origin of Cellular Complexity?”. [REVIEW]W. Ford Doolittle, Julius Lukeš, John M. Archibald, Patrick J. Keeling & Michael W. Gray - 2011 - Bioessays 33 (6):427-429.
  23.  33
    How Microbes "Jeopardize" the Modern Synthesis.Aaron Novick & W. Ford Doolittle - 2019 - PLOS Genetics 5 (15):e1008166.
    This editorial introduces a series of review articles concerning the ways in which recent work on microbial evolution has both deepened and challenged the modern synthesis. The authors develop a framework for thinking about theory change in biology.
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  24.  23
    Horizontal Persistence and the Complexity Hypothesis.Aaron Novick & W. Ford Doolittle - 2020 - Biology and Philosophy 35 (1):1-22.
    This paper investigates the complexity hypothesis in microbial evolutionary genetics from a philosophical vantage. This hypothesis, in its current version, states that genes with high connectivity are likely to be resistant to being horizontally transferred. We defend four claims. There is an important distinction between two different ways in which a gene family can persist: vertically and horizontally. There is a trade-off between these two modes of persistence, such that a gene better at achieving one will be worse at achieving (...)
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  25. Insights & Perspectives.W. Ford Doolittle, Julius Lukeš, John M. Archibald, Patrick J. Keeling & Michael W. Gray - unknown - Bioessays 33:427 - 429.
     
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  26.  1
    All about levels: transposable elements as selfish DNAs and drivers of evolution.W. Ford Doolittle - 2022 - Biology and Philosophy 37 (4):1-20.
    The origin and prevalence of transposable elements may best be understood as resulting from “selfish” evolutionary processes at the within-genome level, with relevant populations being all members of the same TE family or all potentially mobile DNAs in a species. But the maintenance of families of TEs as evolutionary drivers, if taken as a consequence of selection, might be better understood as a consequence of selection at the level of species or higher, with the relevant populations being species or ecosystems (...)
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  27.  16
    Archaebacterial Genomics: The Complete Genome Sequence of Methanococcus Jannaschii.David R. Edgell & W. Ford Doolittle - 1997 - Bioessays 19 (1):1-4.
  28.  9
    Some Broader Evolutionary Issues Which Emerge From Contemporary Molecular Biological Data.W. Ford Doolittle - 1984 - PSA: Proceedings of the Biennial Meeting of the Philosophy of Science Association 1984:129 - 144.
    The genome contains elements which are most easily understood as the products of selection operating at the level of the genome, without regard to phenotypic effect. The properties of such elements, and more general implications of molecular biological data, are discussed.
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