Results for 'Drabkin Harold'

123 found
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  1. The representation of protein complexes in the Protein Ontology.Carol Bult, Harold Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D’Eustachio, Barry Smith, Judith Blake & Cathy Wu - 2011 - BMC Bioinformatics 12 (371):1-11.
    Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...)
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  2. 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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  3. Protein Ontology: A controlled structured network of protein entities.A. Natale Darren, N. Arighi Cecilia, A. Blake Judith, J. Bult Carol, R. Christie Karen, Cowart Julie, D’Eustachio Peter, D. Diehl Alexander, J. Drabkin Harold, Helfer Olivia, Barry Smith & Others - 2013 - Nucleic Acids Research 42 (1):D415-21..
    The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...)
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  4. Protein-centric connection of biomedical knowledge: Protein Ontology research and annotation tools.Cecilia N. Arighi, Darren A. Natale, Judith A. Blake, Carol J. Bult, Michael Caudy, Alexander D. Diehl, Harold J. Drabkin, Peter D'Eustachio, Alexei Evsikov, Hongzhan Huang, Barry Smith & Others - 2011 - In Landgrebe Jobst & Smith Barry (eds.), Proceedings of the 2nd International Conference on Biomedical Ontology. CEUR, vol. 833. pp. 285-287.
    The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
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  5. Protein Ontology: Enhancing and scaling up the representation of protein entities.Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan, Hongzhan Huang, Jia Ren, Karen Ross & Alan Ruttenberg - 2017 - Nucleic Acids Research 45 (D1):D339-D346.
    The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...)
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  6. TGF-beta signaling proteins and the Protein Ontology.Arighi Cecilia, Liu Hongfang, Natale Darren, Barker Winona, Drabkin Harold, Blake Judith, Barry Smith & Wu Cathy - 2009 - BMC Bioinformatics 10 (Suppl 5):S3.
    The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...)
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  7. On Resisting Art.James Harold - 2023 - Journal of Aesthetics and Art Criticism 81 (1):35-45.
    What responsibilities do audiences have in engaging with artworks? Certain audience responses seem quite clear: for example, audiences should not vandalize or destroy artworks; they should not disrupt performances. This paper examines other kinds of resisting responses that audiences sometimes engage in, including petitioning the artist to change their works, altering copies of artworks, and creating new artworks in another artist’s fictional world. I argue for five claims: (1) while these actions can sometimes infringe on the rights of artists, the (...)
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  8. Classifying Psychopathology: Mental Kinds and Natural Kinds.Harold Kincaid & Jacqueline Anne Sullivan - 2014 - In Harold Kincaid & Jacqueline Anne Sullivan (eds.), Classifying Psychopathology: Mental Kinds and Natural Kinds. MIT Press. pp. 1-10.
    In this volume, leading philosophers of psychiatry examine psychiatric classification systems, including the Diagnostic and Statistical Manual of Mental Disorders, asking whether current systems are sufficient for effective diagnosis, treatment, and research. Doing so, they take up the question of whether mental disorders are natural kinds, grounded in something in the outside world. Psychiatric categories based on natural kinds should group phenomena in such a way that they are subject to the same type of causal explanations and respond similarly to (...)
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  9. Logicism and the ontological commitments of arithmetic.Harold T. Hodes - 1984 - Journal of Philosophy 81 (3):123-149.
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  10. Defending Aesthetic Internalism: Liking, Loving, and Wholeheartedness.James Harold - forthcoming - Philosophical Quarterly.
    Aesthetic internalism claims a link between judgement and motivation: aesthetic judgements bring with them motivations to act in characteristic ways. Critics object that there is a difference between merely liking something and judging it to be aesthetically good, and that it is our likings, not our aesthetic judgements, that motivate us. This paper develops a version of aesthetic internalism that can respond to this criticism. Wholehearted aesthetic judgements are characterized by stability, attention, and motivation. Making such judgements is an important (...)
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  11. Why Ramify?Harold T. Hodes - 2015 - Notre Dame Journal of Formal Logic 56 (2):379-415.
    This paper considers two reasons that might support Russell’s choice of a ramified-type theory over a simple-type theory. The first reason is the existence of purported paradoxes that can be formulated in any simple-type language, including an argument that Russell considered in 1903. These arguments depend on certain converse-compositional principles. When we take account of Russell’s doctrine that a propositional function is not a constituent of its values, these principles turn out to be too implausible to make these arguments troubling. (...)
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  12. Cut-conditions on sets of multiple-alternative inferences.Harold T. Hodes - 2022 - Mathematical Logic Quarterly 68 (1):95 - 106.
    I prove that the Boolean Prime Ideal Theorem is equivalent, under some weak set-theoretic assumptions, to what I will call the Cut-for-Formulas to Cut-for-Sets Theorem: for a set F and a binary relation |- on Power(F), if |- is finitary, monotonic, and satisfies cut for formulas, then it also satisfies cut for sets. I deduce the CF/CS Theorem from the Ultrafilter Theorem twice; each proof uses a different order-theoretic variant of the Tukey- Teichmüller Lemma. I then discuss relationships between various (...)
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  13. Hermias: On Plato's Phaedrus.Harold A. S. Tarrant & Dirk Baltzly - 2017 - In Harold Tarrant, Danielle A. Layne, Dirk Baltzly & François Renaud (eds.), Brill’s Companion to the Reception of Plato in Antiquity. Leiden: Brill.
    This article tackles the sole surviving ancient commentary on what was perhaps the second most important Platonic work, with special interest for the manner in which the ancients tackled the setting of Plato's dialogues, Socratic ignorance, Socratic eros, the central myth-like Palinode, and the question of oral as against written teaching.
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  14. One-step Modal Logics, Intuitionistic and Classical, Part 1.Harold T. Hodes - 2021 - Journal of Philosophical Logic 50 (5):837-872.
    This paper and its sequel “look under the hood” of the usual sorts of proof-theoretic systems for certain well-known intuitionistic and classical propositional modal logics. Section 1 is preliminary. Of most importance: a marked formula will be the result of prefixing a formula in a propositional modal language with a step-marker, for this paper either 0 or 1. Think of 1 as indicating the taking of “one step away from 0.” Deductions will be constructed using marked formulas. Section 2 presents (...)
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  15. Audiences’ Role in Generating Moral Understanding: Screen Stories as Sites for Interpretative Communities.James Harold - 2023 - In Carl Plantinga (ed.), Screen Stories and Moral Understanding: Interdisciplinary Perspectives. New York, New York: Oxford University Press. pp. 197-211.
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  16. Immoralism and the Valence Constraint.James Harold - 2008 - British Journal of Aesthetics 48 (1):45-64.
    Immoralists hold that in at least some cases, moral fl aws in artworks can increase their aesthetic value. They deny what I call the valence constraint: the view that any effect that an artwork’s moral value has on its aesthetic merit must have the same valence. The immoralist offers three arguments against the valence constraint. In this paper I argue that these arguments fail, and that this failure reveals something deep and interesting about the relationship between cognitive and moral value. (...)
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  17. On modal logics which enrich first-order S5.Harold T. Hodes - 1984 - Journal of Philosophical Logic 13 (4):423 - 454.
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  18. Some theorems on the expressive limitations of modal languages.Harold T. Hodes - 1984 - Journal of Philosophical Logic 13 (1):13 - 26.
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  19. Axioms for actuality.Harold T. Hodes - 1984 - Journal of Philosophical Logic 13 (1):27 - 34.
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  20. Finite level borel games and a problem concerning the jump hierarchy.Harold T. Hodes - 1984 - Journal of Symbolic Logic 49 (4):1301-1318.
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  21. The Value of Fidelity in Adaptation.James Harold - 2018 - British Journal of Aesthetics 58 (1):89-100.
    © British Society of Aesthetics 2018. Published by Oxford University Press on behalf of the British Society of Aesthetics. All rights reserved. For Permissions, please email: [email protected] adaptation of literary works into films has been almost completely neglected as a philosophical topic. I discuss two questions about this phenomenon:What do we mean when we say that a film is faithful to its source?Is being faithful to its source a merit in a film adaptation?In response to, I set out two distinct (...)
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  22. The composition of Fregean thoughts.Harold T. Hodes - 1982 - Philosophical Studies 41 (2):161 - 178.
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  23. Autonomism Reconsidered.James Harold - 2011 - British Journal of Aesthetics 51 (2):137-147.
    This paper has three aims: to define autonomism clearly and charitably, to offer a positive argument in its favour, and to defend a larger view about what is at stake in the debate between autonomism and its critics. Autonomism is here understood as the claim that a valuer does not make an error in failing to bring her moral and aesthetic judgements together, unless she herself values doing so. The paper goes on to argue that reason does not require the (...)
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  24. On The Sense and Reference of A Logical Constant.Harold Hodes - 2004 - Philosophical Quarterly 54 (214):134-165.
    Logicism is, roughly speaking, the doctrine that mathematics is fancy logic. So getting clear about the nature of logic is a necessary step in an assessment of logicism. Logic is the study of logical concepts, how they are expressed in languages, their semantic values, and the relationships between these things and the rest of our concepts, linguistic expressions, and their semantic values. A logical concept is what can be expressed by a logical constant in a language. So the question “What (...)
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  25. Ontological Commitments, Thick and Thin.Harold T. Hodes - 1990 - In George Boolos (ed.), Method, Reason and Language: Essays in Honor of Hilary Putnam. Cambridge University Press. pp. 235-260.
    Discourse carries thin commitment to objects of a certain sort iff it says or implies that there are such objects. It carries a thick commitment to such objects iff an account of what determines truth-values for its sentences say or implies that there are such objects. This paper presents two model-theoretic semantics for mathematical discourse, one reflecting thick commitment to mathematical objects, the other reflecting only a thin commitment to them. According to the latter view, for example, the semantic role (...)
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  26. In Defence of the Letter of Fictionalism.Harold Noonan - 1994 - Analysis 54 (3):133-139.
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  27. Putting philosophy of political science on the map.Harold Kincaid & Jeroen Van Bouwel - 2022 - In Harold Kincaid & Jeroen van Bouwel (eds.), The Oxford Handbook of Philosophy of Political Science. New York: Oxford University Press. pp. 1-14.
    Contrary to economics or history, for example, there does not exist an organized field dedicated to the philosophy of political science. Given that the philosophical issues raised by political science research are just as pressing and vibrant as those raised in these more organized fields, fostering a field that labels itself Philosophy of Political Science (PoPS) is important. PoPS is advanced here as a fruitful meeting place where both philosophers and practicing political scientists contribute and discuss—with philosophical discussions that are (...)
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  28. Langdell and the Eclipse of Character.Harold Anthony Lloyd - forthcoming - University of Pittsburgh Law Review.
    Christopher Columbus Langdell has not only damaged the study of law with his three follies: his legal formalism, his redacted appellate case method, and his notion that legal practice taints the professor of law. His three follies have also impaired character development critical for legal actors. This Article focuses on four such critical character traits and virtues impaired by Langdell: (i) imagination, (ii) empathy, (ii) balance, and (iv) integrity. -/- This Article also calls out potential character issues with two professor (...)
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  29. The Ethics of Non-Realist Fiction: Morality’s Catch-22.James Harold - 2007 - Philosophia 35 (2):145-159.
    The topic of this essay is how non-realistic novels challenge our philosophical understanding of the moral significance of literature. I consider just one case: Joseph Heller’s Catch-22. I argue that standard philosophical views, based as they are on realistic models of literature, fail to capture the moral significance of this work. I show that Catch-22 succeeds morally because of the ways it resists using standard realistic techniques, and suggest that philosophical discussion of ethics and literature must be pluralistic if it (...)
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  30. One-Step Modal Logics, Intuitionistic and Classical, Part 2.Harold T. Hodes - 2021 - Journal of Philosophical Logic 50 (5):873-910.
    Part 1 [Hodes, 2021] “looked under the hood” of the familiar versions of the classical propositional modal logic K and its intuitionistic counterpart. This paper continues that project, addressing some familiar classical strengthenings of K and GL), and their intuitionistic counterparts. Section 9 associates two intuitionistic one-step proof-theoretic systems to each of the just mentioned intuitionistic logics, this by adding for each a new rule to those which generated IK in Part 1. For the systems associated with the intuitionistic counterparts (...)
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  31. Three Value Logics: An Introduction, A Comparison of Various Logical Lexica and Some Philosophical Remarks.Harold Hodes - 1989 - Annals of Pure and Applied Logic 43 (2):99-145.
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  32. Literary Cognitivism.James Harold - 2015 - In Noël Carroll & John Gibson (eds.), The Routledge Companion to Philosophy of Literature. New York: Routledge.
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  33. On the Ancient Idea that Music Shapes Character.James Harold - 2016 - Dao: A Journal of Comparative Philosophy 15 (3):341-354.
    Ancient Chinese and Greek thinkers alike were preoccupied with the moral value of music; they distinguished between good and bad music by looking at the music’s effect on moral character. The idea can be understood in terms of two closely related questions. Does music have the power to affect the ethical character of either listener or performer? If it does, is it better as music for doing so? I argue that an affirmative answers to both questions are more plausible than (...)
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  34. Flexing the imagination.James Harold - 2003 - Journal of Aesthetics and Art Criticism 61 (3):247–258.
    I explore the claim that “fictive imagining” – imagining what it is like to be a character – can be morally dangerous. In particular, I consider the controversy over William Styron’s imagining the revolutionary protagonist in his Confessions of Nat Turner. I employ Ted Cohen’s model of fictive imagining to argue, following a generally Kantian line of thought, that fictive imagining can be dangerous if one has the wrong motives. After considering several possible motives, I argue that only internally directed (...)
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  35. Where do sets come from?Harold T. Hodes - 1991 - Journal of Symbolic Logic 56 (1):150-175.
    A model-theoretic approach to the semantics of set-theoretic discourse.
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  36. Individual-actualism and three-valued modal logics, part 1: Model-theoretic semantics.Harold T. Hodes - 1986 - Journal of Philosophical Logic 15 (4):369 - 401.
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  37. Can Expressivists Tell the Difference Between Beauty and Moral Goodness?James Harold - 2008 - American Philosophical Quarterly 45 (3):289-300.
    One important but infrequently discussed difficulty with expressivism is the attitude type individuation problem.1 Expressivist theories purport to provide a unified account of normative states. Judgments of moral goodness, beauty, humor, prudence, and the like, are all explicated in the same way: as expressions of attitudes, what Allan Gibbard calls “states of norm-acceptance”. However, expressivism also needs to explain the difference between these different sorts of attitude. It is possible to judge that a thing is both aesthetically good and morally (...)
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  38. Reflections on Putnam, Wright and brains in vats.Harold W. Noonan - 1998 - Analysis 58 (1):59-62.
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  39. Modal realism, still at your convenience.Harold Noonan & Mark Jago - 2017 - Analysis 77 (2):299-303.
    Divers presents a set of de re modal truths which, he claims, are inconvenient for Lewisean modal realism. We argue that there is no inconvenience for Lewis.
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  40. Plenitude, Pluralism, and Neo-Lockean Persons.Harold Noonan - 2015 - Journal of Consciousness Studies 22 (11-12):108-131.
    The paper discusses the arguments for and against animalism and concludes that a pluralist position which rejects animalism and embraces a multiplicity of thinkers is the best option.
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  41. Jumping through the transfinite: The master code hierarchy of Turing degrees.Harold T. Hodes - 1980 - Journal of Symbolic Logic 45 (2):204-220.
    Where $\underline{a}$ is a Turing degree and ξ is an ordinal $ , the result of performing ξ jumps on $\underline{a},\underline{a}^{(\xi)}$ , is defined set-theoretically, using Jensen's fine-structure results. This operation appears to be the natural extension through $(\aleph_1)^{L^\underline{a}}$ of the ordinary jump operations. We describe this operation in more degree-theoretic terms, examine how much of it could be defined in degree-theoretic terms and compare it to the single jump operation.
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  42. The Modal Theory Of Pure Identity And Some Related Decision Problems.Harold T. Hodes - 1984 - Mathematical Logic Quarterly 30 (26-29):415-423.
    Relative to any reasonable frame, satisfiability of modal quantificational formulae in which “= ” is the sole predicate is undecidable; but if we restrict attention to satisfiability in structures with the expanding domain property, satisfiability relative to the familiar frames (K, K4, T, S4, B, S5) is decidable. Furthermore, relative to any reasonable frame, satisfiability for modal quantificational formulae with a single monadic predicate is undecidable ; this improves the result of Kripke concerning formulae with two monadic predicates.
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  43. An Exact Pair for the Arithmetic Degrees Whose Join is Not a Weak Uniform Upper Bound.Harold T. Hodes - 1982 - Recursive Function Theory-Newsletters 28.
    Proof uses forcing on perfect trees for 2-quantifier sentences in the language of arithmetic. The result extends to exact pairs for the hyperarithmetic degrees.
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  44. Uniform Upper Bounds on Ideals of Turing Degrees.Harold T. Hodes - 1978 - Journal of Symbolic Logic 43 (3):601-612.
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  45. Balancing Freedom and Restraint: The Role of Virtue in Legal Analysis.Harold Anthony Lloyd - 2023 - Southern California Interdisciplinary Law Journal 32:315-353.
    Even if one sees the law as “a self-contained system of legal reasoning” from which we deduce “neutral,” non-political conclusions from “general principles and analogies among cases and doctrines” (including formalist claims that judges simply call “balls and strikes” like umpires in a baseball game), one should still consider certain characteristics of the party making such deductions or calling such “balls and strikes.” [Relevant citations to quoted language are in the Article.] If such decision maker has questionable motivations, lacks proper (...)
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  46. Brill’s Companion to the Reception of Plato in Antiquity.Harold Tarrant, Danielle A. Layne, Dirk Baltzly & François Renaud (eds.) - 2017 - Leiden: Brill.
    31 chapters covering the Old Academy to Late Antiquity. See attached TOC.
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    Identity eliminated.Harold W. Noonan - 2007 - Analysis 67 (2):122-127.
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  48. Cognitivism, non-cognitivism, and skepticism about folk psychology.James Harold - 2012 - Philosophical Psychology 25 (2):165 - 185.
    In recent years it has become more and more difficult to distinguish between metaethical cognitivism and non-cognitivism. For example, proponents of the minimalist theory of truth hold that moral claims need not express beliefs in order to be (minimally) truth-apt, and yet some of these proponents still reject the traditional cognitivist analysis of moral language and thought. Thus, the dispute in metaethics between cognitivists and non-cognitivists has come to be seen as a dispute over the correct way to characterize our (...)
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  49. Medical Models of Addiction.Harold Kincaid & Jacqueline Anne Sullivan - 2010 - In Don Ross, Harold Kincaid & David Spurrett (eds.), What Is Addiction? The MIT Press.
    Biomedical science has been remarkably successful in explaining illness by categorizing diseases and then by identifying localizable lesions such as a virus and neoplasm in the body that cause those diseases. Not surprisingly, researchers have aspired to apply this powerful paradigm to addiction. So, for example, in a review of the neuroscience of addiction literature, Hyman and Malenka (2001, p. 695) acknowledge a general consensus among addiction researchers that “[a]ddiction can appropriately be considered as a chronic medical illness.” Like other (...)
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  50. Narrative engagement with Atonement and The Blind Assasin.James Harold - 2005 - Philosophy and Literature 29 (1):130-145.
    Two recent novels, Ian McEwan’s Atonement and Margaret Atwood’s The Blind Assassin, are philosophically instructive. These books are interesting, I argue, because they reveal something about understanding and appreciating narrative. They show us that audience’s participation in narrative is much more subtle and complex than philosophers generally acknowledge. An analysis of these books reveals that narrative imagining is not static or unified, but dynamic and multipolar. I argue that once the complexity of narrative engagement is better understood, some prominent philosophical (...)
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