Results for 'Katharine Barker'

74 found
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  1. Grounding and the Myth of Ontological Innocence.Jonathan Barker - 2021 - Australasian Journal of Philosophy 99 (2):303-318.
    According to the Ontological Innocence Thesis (OIT), grounded entities are ontologically innocent relative to their full grounds. I argue that OIT entails a contradiction, and therefore must be discarded. My argument turns on the notion of “groundmates,” two or more numerically distinct entities that share at least one of their full grounds. I argue that, if OIT is true, then it is both the case that there are groundmates and that there are no groundmates. Therefore, so I conclude, OIT is (...)
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  2. Against Purity.Jonathan Barker - 2023 - Ergo: An Open Access Journal of Philosophy 9.
    A fundamental fact is “pure” just in case it has no grounded entities—ex. Tokyo, President Biden, the River Nile, {Socrates}, etc.—among its constituents. Purity is the thesis that every fundamental fact is pure. I argue that Purity is false. My argument begins with a familiar conditional: if Purity is true, then there are no fundamental “grounding facts” or facts about what grounds what. This conditional is accepted by virtually all of Purity’s defenders. However, I argue that it is also the (...)
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  3. Genealogical Defeat and Ontological Sparsity.Jonathan Barker - 2023 - Midwest Studies in Philosophy 47:1-23.
    When and why does awareness of a belief's genealogy render it irrational to continue holding that belief? According to explanationism, awareness of a belief’s genealogy gives rise to an epistemic defeater when and because it reveals that the belief is not explanatorily connected to the relevant worldly facts. I argue that an influential recent version of explanationism, due to Korman and Locke, incorrectly implies that it is not rationally permissible to adopt a “sparse” ontology of worldly facts or states of (...)
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  4. Disability, Impairment, and Marginalised Functioning.Katharine Jenkins & Aness Kim Webster - 2021 - Australasian Journal of Philosophy 99 (4):730-747.
    One challenge in providing an adequate definition of physical disability is unifying the heterogeneous bodily conditions that count as disabilities. We examine recent proposals by Elizabeth Barnes (2016), and Dana Howard and Sean Aas (2018), and show how this debate has reached an impasse. Barnes’ account struggles to deliver principled unification of the category of disability, whilst Howard and Aas’ account risks inappropriately sidelining the body. We argue that this impasse can be broken using a novel concept: marginalised functioning. Marginalised (...)
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  5. Knowing how and being able.Beth Barker - 2024 - Synthese 204 (76):1-20.
    Intellectualists about know-how tend to deny that knowing how to ϕ requires the corresponding ability to ϕ. So, it’s supposed to be an attractive feature of intellectualism that it can explain cases of knowing how without ability, while anti-intellectualism—roughly, the view that knowing how is a kind of ability—cannot. I show that intellectualism fails to explain the very cases that are supposed to showcase this feature of the view. Despite appearances, this does not amount to an objection to intellectualism per (...)
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  6. The Emperor's New Metaphysics of Powers.Stephen Barker - 2013 - Mind 122 (487):605-653.
    This paper argues that the new metaphysics of powers, also known as dispositional essentialism or causal structuralism, is an illusory metaphysics. I argue for this in the following way. I begin by distinguishing three fundamental ways of seeing how facts of physical modality — facts about physical necessitation and possibility, causation, disposition, and chance — are grounded in the world. The first way, call it the first degree, is that the actual world or all worlds, in their entirety, are the (...)
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  7. Debunking Arguments and Metaphysical Laws.Jonathan Barker - 2020 - Philosophical Studies 177 (7):1829-1855.
    I argue that one’s views about which “metaphysical laws” obtain—including laws about what is identical with what, about what is reducible to what, and about what grounds what—can be used to deflect or neutralize the threat posed by a debunking explanation. I use a well-known debunking argument in the metaphysics of material objects as a case study. Then, after defending the proposed strategy from the charge of question-begging, I close by showing how the proposed strategy can be used by certain (...)
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  8. We are Nearly Ready to Begin the Species Problem.Matthew J. Barker - 2022 - In John S. Wilkins, Igor Pavlinov & Frank Zachos (eds.), Species Problems and Beyond: Contemporary Issues in Philosophy and Practice. Boca Raton: CRC Press. pp. 3-38.
    This paper isolates a hard, long-standing species problem: developing a comprehensive and exacting theory about the constitutive conditions of the species category, one that is accurate for most of the living world, and which vindicates the widespread view that the species category is of more theoretical import than categories such as genus, sub-species, paradivision, and stirp. The paper then uncovers flaws in several views that imply we have either already solved that hard species problem or dissolved it altogether – so-called (...)
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  9. The Ultimate Argument Against Dispositional Monist Accounts of Laws.Stephen Barker & Benjamin Smart - 2012 - Analysis 72 (4):714-722.
    Bird argues that Armstrong’s necessitarian conception of physical modality and laws of nature generates a vicious regress with respect to necessitation. We show that precisely the same regress afflicts Bird’s dispositional-monist theory, and indeed, related views, such as that of Mumford & Anjum. We argue that dispositional monism is basically Armstrongian necessitarianism modified to allow for a thesis about property identity.
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  10. Well-being, Disability, and Choosing Children.Matthew J. Barker & Robert A. Wilson - 2019 - Mind 128 (510):305-328.
    The view that it is better for life to be created free of disability is pervasive in both common sense and philosophy. We cast doubt on this view by focusing on an influential line of thinking that manifests it. That thinking begins with a widely-discussed principle, Procreative Beneficence, and draws conclusions about parental choice and disability. After reconstructing two versions of this argument, we critique the first by exploring the relationship between different understandings of well-being and disability, and the second (...)
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  11. Misrelating values and empirical matters in conservation: A problem and solutions.Matthew J. Barker & Dylan J. Fraser - 2023 - Biological Conservation 281.
    We uncover a largely unnoticed and unaddressed problem in conservation research: arguments built within studies are sometimes defective in more fundamental and specific ways than appreciated, because they misrelate values and empirical matters. We call this the unraveled rope problem because just as strands of rope must be properly and intricately wound with each other so the rope supports its load, empirical aspects and value aspects of an argument must be related intricately and properly if the argument is to objectively (...)
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  12. Material Objects and Essential Bundle Theory.Stephen Barker & Mark Jago - 2018 - Philosophical Studies 175 (12):2969-2986.
    In this paper we present a new metaphysical theory of material objects. On our theory, objects are bundles of property instances, where those properties give the nature or essence of that object. We call the theory essential bundle theory. Property possession is not analysed as bundle-membership, as in traditional bundle theories, since accidental properties are not included in the object’s bundle. We have a different story to tell about accidental property possession. This move reaps many benefits. Essential bundle theory delivers (...)
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  13. Diverse Environments, Diverse People.Matthew J. Barker - 2019 - In C. Tyler DesRoches, Frank Jankunis & Byron Williston (eds.), Canadian Environmental Philosophy. Mcgill-Queen's University Press. pp. 99-122.
    This paper is about both an application of virtue ethics, and about virtue ethics itself. A popular application of neo-Aristotelian virtue ethics to environmental issues is called interpersonal extensionism. It argues that we should view the normative range of traditional interpersonal virtues, such as compassion and humility, as extending beyond our interactions with people to also include our interactions with non-human environments. This paper uncovers an unaddressed problem for this view, then proposes a solution by revising how we understand neo-Aristotelian (...)
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  14. What You Don't Know Won't Hurt You?John A. Barker - 1976 - American Philosophical Quarterly 13 (4):303 - 308.
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  15. Disembodiment: The phenomenology of the body in medical examinations.Katharine Young - 1989 - Semiotica 73 (1-2):43-66.
    In order to conduct medical examinations, physicians transform patients from social subjects into medical objects. The routines associated with conducting medical examinations constitute rituals for effecting this transformation: moving from public space to private space; changing into ritual costumes; taking up ritual positions in an examination room; conducting ritual verbal and physical examinations. The transformations endow participants with a different ontological status from the one they hold in everyday life. They address the phenomenological problem of how a self is inserted (...)
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  16. Pure versus Hybrid Expressivism and the Enigma of Conventional Implicature.Stephen Barker - 2014 - In Guy Fletcher & Michael Ridge (eds.), Having It Both Ways: Hybrid Theories and Modern Metaethics. New York: Oxford University Press. pp. 199-222.
    Can hybridism about moral claims be made to work? I argue it can if we accept the conventional implicature approach developed in Barker (Analysis 2000). However, this kind of hybrid expressivism is only acceptable if we can make sense of conventional implicature, the kind of meaning carried by operators like ‘even’, ‘but’, etc. Conventional implictures are a form of pragmatic presupposition, which involves an unsaid mode of delivery of content. I argue that we can make sense of conventional implicatures, (...)
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  17. (1 other version)Monism and Material Constitution.Stephen Barker & Mark Jago - 2014 - Pacific Philosophical Quarterly 95 (1):189-204.
    Are the sculpture and the mass of gold which permanently makes it up one object or two? In this article, we argue that the monist, who answers ‘one object’, cannot accommodate the asymmetry of material constitution. To say ‘the mass of gold materially constitutes the sculpture, whereas the sculpture does not materially constitute the mass of gold’, the monist must treat ‘materially constitutes’ as an Abelardian predicate, whose denotation is sensitive to the linguistic context in which it appears. We motivate (...)
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  18. Gestures and the phenomenology of emotion in narrative.Katharine Young - 2000 - Semiotica 131 (1-2):79-112.
    Stories evoke emotions in their hearers. Do they evoke emotions in their tellers as well? Tellers can tell stories from the inside as if they were characters in the world of the tale or they can tell stories from the outside as if they were perceiving the taleworld from elsewhere. From the outside, the teller can represent the emotion a character feels; from the inside, the teller can express the emotion the character feels. In either instance, tellers can be moved (...)
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  19. Harms and Wrongs in Epistemic Practice.Simon Barker, Charlie Crerar & Trystan S. Goetze - 2018 - Royal Institute of Philosophy Supplement 84:1-21.
    This volume has its roots in two recent developments within mainstream analytic epistemology: a growing recognition over the past two or three decades of the active and social nature of our epistemic lives; and, more recently still, the increasing appreciation of the various ways in which the epistemic practices of individuals and societies can, and often do, go wrong. The theoretical analysis of these breakdowns in epistemic practice, along with the various harms and wrongs that follow as a consequence, constitutes (...)
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  20. Cohesion, Gene flow, and the Nature of Species.Matthew J. Barker & Robert A. Wilson - 2010 - Journal of Philosophy 107 (2):59-77.
    A far-reaching and influential view in evolutionary biology claims that species are cohesive units held together by gene flow. Biologists have recognized empirical problems facing this view; after sharpening the expression of the view, we present novel conceptual problems for it. At the heart of these problems is a distinction between two importantly different concepts of cohesion, what we call integrative and response cohesion. Acknowledging the distinction problematizes both the explanandum of species cohesion and the explanans of gene flow that (...)
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  21. Epistemic Injustice and Performing Know-how.Beth Barker - 2021 - Social Epistemology 35 (6):608-620.
    In this paper, I expand our framework for epistemic injustice by shifting focus from epistemic evaluations of individuals in information exchange to epistemic evaluations of individuals engaging their know-how in performance. I call the injustice to individuals qua knowers-how performative injustice, and I argue that performative injustice has distinct features worth understanding apart from varieties of epistemic injustice devoted to information exchange. I develop an account of the performative authority that is unfairly evaluated in cases of performative injustice and show (...)
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  22. Irony and the dogma of force and sense.Stephen J. Barker & Mihaela Popa-Wyatt - 2015 - Analysis 75 (1):9-16.
    Frege’s distinction between force and sense is a central pillar of modern thinking about meaning. This is the idea that a self-standing utterance of a sentence S can be divided into two components. One is the proposition P that S’s linguistic meaning and context associates with it. The other is S’s illocutionary force. The force/sense distinction is associated with another thesis, the embedding principle, that implies that the only content that embeds in compound sentences is propositional content. We argue that (...)
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  23. Linguistic Interventions and Transformative Communicative Disruption.Rachel Katharine Sterken - 2019 - In Alexis Burgess, Herman Cappelen & David Plunkett (eds.), Conceptual Engineering and Conceptual Ethics. New York, USA: Oxford University Press. pp. 417-434.
    What words we use, and what meanings they have, is important. We shouldn't use slurs; we should use 'rape' to include spousal rape (for centuries we didn’t); we should have a word which picks out the sexual harassment suffered by people in the workplace and elsewhere (for centuries we didn’t). Sometimes we need to change the word-meaning pairs in circulation, either by getting rid of the pair completely (slurs), changing the meaning (as we did with 'rape'), or adding brand new (...)
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  24. Expressivism About Making and Truth-Making.Stephen Barker - 2012 - In Fabrice Correia & Benjamin Schnieder (eds.), Metaphysical grounding: understanding the structure of reality. Cambridge: Cambridge University Press. pp. 272-293.
    My goal is to illuminate truth-making by way of illuminating the relation of making. My strategy is not to ask what making is, in the hope of a metaphysical theory about is nature. It's rather to look first to the language of making. The metaphor behind making refers to agency. It would be absurd to suggest that claims about making are claims about agency. It is not absurd, however, to propose that the concept of making somehow emerges from some feature (...)
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  25. Can Counterfactuals Really Be about Possible Worlds?Stephen Barker - 2011 - Noûs 45 (3):557-576.
    The standard view about counterfactuals is that a counterfactual (A > C) is true if and only if the A-worlds most similar to the actual world @ are C-worlds. I argue that the worlds conception of counterfactuals is wrong. I assume that counterfactuals have non-trivial truth-values under physical determinism. I show that the possible-worlds approach cannot explain many embeddings of the form (P > (Q > R)), which intuitively are perfectly assertable, and which must be true if the contingent falsity (...)
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  26. Epistemic Closure and Skepticism.John A. Barker & Fred Adams - 2010 - Logos and Episteme 1 (2):221-246.
    Closure is the epistemological thesis that if S knows that P and knows that P implies Q, then if S infers that Q, S knows that Q. Fred Dretske acknowledges that closure is plausible but contends that it should be rejected because it conflicts with the plausible thesis: Conclusive reasons (CR): S knows that P only if S believes P on the basis of conclusive reasons, i.e., reasons S wouldn‘t have if it weren‘t the case that P. Dretske develops an (...)
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  27. Semantic Paradox and Alethic Undecidability.Stephen Barker - 2014 - Analysis 74 (2):201-209.
    I use the principle of truth-maker maximalism to provide a new solution to the semantic paradoxes. According to the solution, AUS, its undecidable whether paradoxical sentences are grounded or ungrounded. From this it follows that their alethic status is undecidable. We cannot assert, in principle, whether paradoxical sentences are true, false, either true or false, neither true nor false, both true and false, and so on. AUS involves no ad hoc modification of logic, denial of the T-schema's validity, or obvious (...)
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  28. Essentialism.Matthew J. Barker - 2013 - In Byron Kaldis (ed.), Encyclopedia of Philosophy and the Social Sciences. Los Angeles: Sage Publications.
    This ~4000 word essay introduces topics of essentialism, as they arise in social sciences. It distinguishes empirical (e.g., psychological) from philosophical studies of essentialisms, and both metaphysical and scientific essentialisms within philosophy. Essentialism issues in social science are shown to be more subtle and complex than often presumed.
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  29. Science and Values.Matthew J. Barker - 2015 - Eugenics Archive.
    This short paper, written for a wide audience, introduces "science and values" topics as they have arisen in the context of eugenics. The paper especially focuses on the context of 20th century eugenics in western Canada, where eugenic legislation in two provinces was not repealed until the 1970s and thousands of people were sterilized without their consent. A framework for understanding science-value relationships within this context is discussed, and so too is recent relevant work in philosophy of science.
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  30. Semantics without the distinction between sense and force.Stephen J. Barker - 2007 - In Savas L. Tsohatzidis (ed.), John Searle's Philosophy of Language: Force, Meaning and Mind. Cambridge University Press. pp. 190-210.
    At the heart of semantics in the 20th century is Frege’s distinction between sense and force. This is the idea that the content of a self-standing utterance of a sentence S can be divided into two components. One part, the sense, is the proposition that S’s linguistic meaning and context associates with it as its semantic interpretation. The second component is S’s illocutionary force. Illocutionary forces correspond to the three basic kinds of sentential speech acts: assertions, orders, and questions. Forces (...)
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  31. Generics and the Metaphysics of Kinds.David Liebesman & Rachel Katharine Sterken - 2021 - Philosophy Compass (7):1-14.
    Recent years have seen renewed interest in the semantics of generics. And a relatively mainstream view in this work is that the semantics of generics must appeal to kinds. But what are kinds? Can we learn anything about their nature by looking at how semantic theories of generics appeal to them? In this article, we overview recent work on the semantics of generics and consider their consequences for our understanding of the metaphysics of kinds.
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  32. Being Positive About Negative Facts.Mark Jago & Stephen Barker - 2012 - Philosophy and Phenomenological Research 85 (1):117-138.
    Negative facts get a bad press. One reason for this is that it is not clear what negative facts are. We provide a theory of negative facts on which they are no stranger than positive atomic facts. We show that none of the usual arguments hold water against this account. Negative facts exist in the usual sense of existence and conform to an acceptable Eleatic principle. Furthermore, there are good reasons to want them around, including their roles in causation, chance-making (...)
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  33. Truth-Bearers and the Unsaid.Stephen Barker - 2011 - In Ken Turner (ed.), Making Semantics Pragmatic. Emerald Group Publishing.
    I argue that conventional implicatures embed in logical compounds, and are non-truth-conditional contributors to sentence meaning. This, I argue has significant implications for how we understand truth, truth-conditional content, and truth-bearers.
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  34. Counterfactual analyses of causation: The problem of effects and epiphenomena revisited.Stephen Barker - 2003 - Noûs 37 (1):133–150.
    I argue that Lewis's counterfactual theory of causation, given his treatment of counterfactuals in terms of world-comparative similarity faces insuperable problems in the form of the problem of effects and the problem of epiphenomena.
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  35. Biological explanations, realism, ontology, and categories.Matthew J. Barker - 2013 - Studies in History and Philosophy of Science Part C: Studies in History and Philosophy of Biological and Biomedical Sciences 44 (4):617-622.
    This is an extended review of John Dupré's _Processes of Life_, a collection of essays. It clarifies Dupré's concepts of reductionism and anti-reductionism, and critically examines his associated discussions of downward causation, and both the context sensitivity and multiple realization of categories. It reviews his naturalistic monism, and critically distinguishes between his realism about categories and constructivism about classification. Challenges to his process ontology are presented, as are arguments for his pluralism about scientific categories. None of his main conclusions are (...)
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  36. Expressivism About Reference and Quantification Over the Non-existent Without Meinongian Metaphysics.Stephen Barker - 2015 - Erkenntnis 80 (S2):215-234.
    Can we believe that there are non-existent entities without commitment to the Meinongian metaphysics? This paper argues we can. What leads us from quantification over non-existent beings to Meinongianism is a general metaphysical assumption about reality at large, and not merely quantification over the non-existent. Broadly speaking, the assumption is that every being we talk about must have a real definition. It’s this assumption that drives us to enquire into the nature of beings like Pegasus, and what our relationship as (...)
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  37. The Island Has Its Reasons: Moral Subjectivism in Fiction.Kasandra Barker - 2016 - Dialogue 55 (2):121-124.
    Tamar Gendler takes on “explaining our comparative difficulty in imagining fictional worlds that we take to be morally deviant” (56), otherwise known as the puzzle of imaginative resistance. Generally speaking, readers have no trouble believing untrue factual claims such as in Alice in Wonderland or The Adventures of Huckleberry Finn, but we resist claims which advocate praise or approval of immoral acts such as murder. Gendler submits that the implied author aims to persuade the reader to change his or her (...)
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  38. Kant on Modality.Colin Marshall & Aaron Barker - 2024 - In Andrew Stephenson & Anil Gomes (eds.), Oxford Handbook of Kant. Oxford, UK: Oxford University Press.
    This chapter analyzes several key themes in Kant’s views about modality. We begin with the pre-critical Only Possible Argument in Support of a Demonstration of the Existence of God, in which Kant distinguishes between formal and material elements of possibility, claims that all possibility requires an actual ground, and argues for the existence of a single necessary being. We then briefly consider how Kant’s views change in his mature period, especially concerning the role of form and thought in defining modality. (...)
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  39. Presupposition and entailment.John A. Barker - 1976 - Notre Dame Journal of Formal Logic 17 (2):272-278.
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  40. (1 other version)Computer modeling and the fate of folk psychology.John A. Barker - 2002 - Metaphilosophy 33 (1-2):30-48.
    Although Paul Churchland and Jerry Fodor both subscribe to the so-called theory-theory– the theory that folk psychology (FP) is an empirical theory of behavior – they disagree strongly about FP’s fate. Churchland contends that FP is a fundamentally flawed view analogous to folk biology, and he argues that recent advances in computational neuroscience and connectionist AI point toward development of a scientifically respectable replacement theory that will give rise to a new common-sense psychology. Fodor, however, wagers that FP will be (...)
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  41. When Traditional Essentialism Fails: Biological Natural Kinds.Robert A. Wilson, Matthew J. Barker & Ingo Brigandt - 2007 - Philosophical Topics 35 (1-2):189-215.
    Essentialism is widely regarded as a mistaken view of biological kinds, such as species. After recounting why (sections 2-3), we provide a brief survey of the chief responses to the “death of essentialism” in the philosophy of biology (section 4). We then develop one of these responses, the claim that biological kinds are homeostatic property clusters (sections 5-6) illustrating this view with several novel examples (section 7). Although this view was first expressed 20 years ago, and has received recent discussion (...)
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  42. Knowledge as Fact-Tracking True Belief.Fred Adams, John A. Barker & Murray Clarke - 2017 - Manuscrito 40 (4):1-30.
    ABSTRACT Drawing inspiration from Fred Dretske, L. S. Carrier, John A. Barker, and Robert Nozick, we develop a tracking analysis of knowing according to which a true belief constitutes knowledge if and only if it is based on reasons that are sensitive to the fact that makes it true, that is, reasons that wouldn’t obtain if the belief weren’t true. We show that our sensitivity analysis handles numerous Gettier-type cases and lottery problems, blocks pathways leading to skepticism, and validates (...)
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  43. Biological Individuals.Robert A. Wilson & Matthew J. Barker - 2024 - Stanford Encyclopedia of Philosophy.
    The impressive variation amongst biological individuals generates many complexities in addressing the simple-sounding question what is a biological individual? A distinction between evolutionary and physiological individuals is useful in thinking about biological individuals, as is attention to the kinds of groups, such as superorganisms and species, that have sometimes been thought of as biological individuals. More fully understanding the conceptual space that biological individuals occupy also involves considering a range of other concepts, such as life, reproduction, and agency. There has (...)
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  44. Letter Regarding Canada's Bill C-7, Medical Assistance in Dying (MAID) and Disability.Robert A. Wilson & Matthew J. Barker - manuscript
    This letter was submitted to the Senate Standing Committee on Legal and Constitutional Affairs, Government of Canada, on 29th January, 2021, as final debate over Bill C-7 was being undertaken in the Senate regarding MAiD and the strong opposition to the legislation expressed across the Canadian disability community. It draws on our individual and joint work on eugenics, well-being, and disability.
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  45. Beat the (Backward) Clock.Fred Adams, John A. Barker & Murray Clarke - 2016 - Logos and Episteme 7 (3):353-361.
    In a recent very interesting and important challenge to tracking theories of knowledge, Williams & Sinhababu claim to have devised a counter-example to tracking theories of knowledge of a sort that escapes the defense of those theories by Adams & Clarke. In this paper we will explain why this is not true. Tracking theories are not undermined by the example of the backward clock, as interesting as the case is.
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  46. Methods Matter: Beating the Backward Clock.Murray Clarke, Fred Adams & John A. Barker - 2017 - Logos and Episteme 8 (1):99-112.
    In “Beat the (Backward) Clock,” we argued that John Williams and Neil Sinhababu’s Backward Clock Case fails to be a counterexample to Robert Nozick’s or Fred Dretske’s Theories of Knowledge. Williams’ reply to our paper, “There’s Nothing to Beat a Backward Clock: A Rejoinder to Adams, Barker and Clarke,” is a further attempt to defend their counterexample against a range of objections. In this paper, we argue that, despite the number and length of footnotes, Williams is still wrong.
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  47. Cognitive Expressivism, Faultless Disagreement, and Absolute but Non-Objective Truth.Stephen Barker - 2010 - Proceedings of the Aristotelian Society 110 (2):183-199.
    I offer a new theory of faultless disagreement, according to which truth is absolute (non-relative) but can still be non-objective. What's relative is truth-aptness: a sentence like ‘Vegemite is tasty’ (V) can be truth-accessible and bivalent in one context but not in another. Within a context in which V fails to be bivalent, we can affirm that there is no issue of truth or falsity about V, still disputants, affirming and denying V, were not at fault, since, in their context (...)
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  48. Framework for a protein ontology.Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith & Cathy H. Wu - 2007 - BMC Bioinformatics 8 (Suppl 9):S1.
    Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...)
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  49. The Protein Ontology: A structured representation of protein forms and complexes.Darren Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Carol J. Bult, Michael Caudy, Harold J. Drabkin, Peter D’Eustachio, Alexei V. Evsikov, Hongzhan Huang, Jules Nchoutmboube, Natalia V. Roberts, Barry Smith, Jian Zhang & Cathy H. Wu - 2011 - Nucleic Acids Research 39 (1):D539-D545.
    The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...)
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  50. Functional diversity: An epistemic roadmap.Christophe Malaterre, Antoine C. Dussault, Sophia Rousseau-Mermans, Gillian Barker, Beatrix E. Beisner, Frédéric Bouchard, Eric Desjardins, Tanya I. Handa, Steven W. Kembel, Geneviève Lajoie, Virginie Maris, Alison D. Munson, Jay Odenbaugh, Timothée Poisot, B. Jesse Shapiro & Curtis A. Suttle - 2019 - BioScience 10 (69):800-811.
    Functional diversity holds the promise of understanding ecosystems in ways unattainable by taxonomic diversity studies. Underlying this promise is the intuition that investigating the diversity of what organisms actually do—i.e. their functional traits—within ecosystems will generate more reliable insights into the ways these ecosystems behave, compared to considering only species diversity. But this promise also rests on several conceptual and methodological—i.e. epistemic—assumptions that cut across various theories and domains of ecology. These assumptions should be clearly addressed, notably for the sake (...)
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