Results for 'Harold N. Bryant'

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  1. 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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  2. 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 Proceedings of the 2nd International Conference on Biomedical Ontology. Buffalo, NY: NCOR. 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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  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 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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  5. Godel, Escherian Staircase and Possibility of Quantum Wormhole With Liquid Crystalline Phase of Iced-Water - Part I: Theoretical Underpinning.Victor Christianto, T. Daniel Chandra & Florentin Smarandache - 2023 - Bulletin of Pure and Applied Sciences 42 (2):70-75.
    As a senior physicist colleague and our friend, Robert N. Boyd, wrote in a journal (JCFA, Vol. 1,. 2, 2022), Our universe is but one page in a large book [4]. For example, things and Beings can travel between Universes, intentionally or unintentionally. In this short remark, we revisit and offer short remark to Neil’s ideas and trying to connect them with geometrization of musical chords as presented by D. Tymoczko and others, then to Escher staircase and then to Jacob’s (...)
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  6. Godel, Escherian Staircase and Possibility of Quantum Wormhole With Liquid Crystalline Phase of Iced-Water - Part II: Experiment Description.Victor Christianto, T. Daniel Chandra & Florentin Smarandache - 2023 - Bulletin of Pure and Applied Sciences 42 (2):85-100.
    The present article was partly inspired by G. Pollack’s book, and also Dadoloff, Saxena & Jensen (2010). As a senior physicist colleague and our friend, Robert N. Boyd, wrote in a journal (JCFA, Vol. 1, No. 2, 2022), for example, things and Beings can travel between Universes, intentionally or unintentionally [4]. In this short remark, we revisit and offer short remark to Neil Boyd’s ideas and trying to connect them with geometry of musical chords as presented by D. Tymoczko and (...)
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  7. Joint Doctrine Ontology: A Benchmark for Military Information Systems Interoperability.Peter Morosoff, Ron Rudnicki, Jason Bryant, Robert Farrell & Barry Smith - 2015 - In Semantic Technology for Intelligence, Defense and Security (STIDS). CEUR vol. 1325. pp. 2-9.
    When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...)
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  8. Keep the chickens cooped: the epistemic inadequacy of free range metaphysics.Amanda Bryant - 2020 - Synthese 197 (5):1867-1887.
    This paper aims to better motivate the naturalization of metaphysics by identifying and criticizing a class of theories I call ’free range metaphysics’. I argue that free range metaphysics is epistemically inadequate because the constraints on its content—consistency, simplicity, intuitive plausibility, and explanatory power—are insufficiently robust and justificatory. However, since free range metaphysics yields clarity-conducive techniques, incubates science, and produces conceptual and formal tools useful for scientifically engaged philosophy, I do not recommend its discontinuation. I do recommend, however, ending the (...)
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  9. 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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  10. Logicism and the ontological commitments of arithmetic.Harold T. Hodes - 1984 - Journal of Philosophy 81 (3):123-149.
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  11. Axioms for actuality.Harold T. Hodes - 1984 - Journal of Philosophical Logic 13 (1):27 - 34.
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  12. Epistemic Infrastructure for a Scientific Metaphysics.Amanda Bryant - 2021 - Grazer Philosophische Studien 98 (1):27-49.
    A naturalistic impulse has taken speculative analytic metaphysics in its critical sights. Importantly, the claim that it is desirable or requisite to give metaphysics scientific moorings rests on underlying epistemological assumptions or principles. If the naturalistic impulse toward metaphysics is to be well-founded and its prescriptions to have normative force, those assumptions or principles should be spelled out and justified. In short, advocates of naturalized or scientific metaphysics require epistemic infrastructure. This paper begins to supply it. The author first sketches (...)
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  13. 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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  14. Grounding interventionism: Conceptual and epistemological challenges.Amanda Bryant - 2022 - Metaphilosophy 53 (2-3):322-343.
    Philosophers have recently highlighted substantial affinities between causation and grounding, which has inclined some to import the conceptual and formal resources of causal interventionism into the metaphysics of grounding. The prospect of grounding interventionism raises two important questions: exactly what are grounding interventions, and why should we think they enable knowledge of grounding? This paper will approach these questions by examining how causal interventionists have addressed (or might address) analogous questions and then comparing the available options for grounding interventionism. I (...)
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  15. Medical Models of Addiction.Harold Kincaid & Jacqueline Anne Sullivan - 2010 - In Kincaid Ross (ed.), What is Addiction?
    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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  16. 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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  17.  89
    Deleuze'ün Spinoza'sı: Yaratıcı Felsefi Tarih ve Spinozacılığın Pratik Sonuçları.İbrahim Okan Akkın - 2023 - In Eylem Yolsal Murteza (ed.), Filozofların Filozofları. İstanbul: Pinhan Yayıncılık. pp. 163-188.
    Deleuze’ün Spinozacı yaşam tahayyülünde ‘ne yapmalıyız?’ sorusuna normatif, ahlaki ya da siyasi bir yanıt bulamıyoruz ama varoluşu düşünmenin içkin bir olanağını keşfediyoruz. Düşünmeye 'dışarıdan' yani dünyadan başlamak insani (kurgusal) bir dünyaya değil, içinde yaşadığımız gerçek dünyaya inanmak demektir. İçkinliğin politik anlamı düşünceyi dünyaya getirmektir.
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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. On modal logics which enrich first-order S5.Harold T. Hodes - 1984 - Journal of Philosophical Logic 13 (4):423 - 454.
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  20. Naturalizing grounding: How theories of ground can engage science.Amanda Bryant - 2018 - Philosophy Compass 13 (5):e12489.
    This paper surveys some of the grounding literature searching for points of contact between theories of ground and science. I find that there are some places where a would-be naturalistic grounding theorist can draw inspiration. I synthesize a list of recommendations for how science may be put to use in theories of ground. I conclude that the prospects for naturalizing the metaphysics of ground are bright.
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  21. 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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  22. 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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  23. Where Do the Cardinal Numbers Come From?Harold T. Hodes - 1990 - Synthese 84 (3):347-407.
    This paper presents a model-theoretic semantics for discourse "about" natural numbers, one that captures what I call "the mathematical-object picture", but avoids what I can "the mathematical-object theory".
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  24. Naturalisms.Amanda Bryant - 2020 - Think 19 (56):35-50.
    The word ‘naturalism’ has a bewildering array of uses in philosophy. Roughly speaking, it connotes pro-scientific attitudes and approaches. This article introduces the subject of naturalism by sketching a history of pro-scientific attitudes and approaches in philosophy, from their origins in the early modern period through to the present day. It then distinguishes a number of distinct families of naturalism: metaphysical, logico-linguistic, epistemological, and methodological. The resulting taxonomy encompasses a plurality of loosely related views rather than a number of variations (...)
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  25. The composition of Fregean thoughts.Harold T. Hodes - 1982 - Philosophical Studies 41 (2):161 - 178.
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  26. Physicalism.Amanda Bryant - 2020 - In Michael J. Raven (ed.), The Routledge Handbook of Metaphysical Grounding. New York: Routledge. pp. 484-500.
    This chapter considers potential applications of grounding to the formulation of physicalism. I begin with an overview of competing conceptions of the physical and of physicalism. I then consider whether grounding physicalism overcomes well-known and seemingly fatal problems with supervenience physicalism. I conclude that while grounding physicalism improves upon supervenience physicalism in certain respects, it arguably falls victim to some of the same difficulties.
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  27. Skeptik Teizm ve Kötülük: Peter van Inwagen'ın "Minimum-Yok İddiası".Atilla Akalın - 2021 - Theosophia 3 (3):77-90.
    Skeptical theists are seeking for some reasonable solutions to the evidential problem of evil. One of the most fundamental responses of skeptical theism is that the concept of “gratuitous evil”, which cannot be a proof of the absence of God. Therefore, it is not the existence of God that skeptical theism suspects. Instead, skeptical theism contemplates whether the evil in the world really has a “gratuitous” basis. This paper focuses on Peter van Inwagen's “no-minimum claim”. No-minimum claim” stands in opposition (...)
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  28. Cardinality logics, part I: inclusions between languages based on ‘exactly’.Harold Hodes - 1988 - Annals of Pure and Applied Logic 39 (3):199-238.
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  29. The Supposed Spectre of Scientism.Amanda Bryant - 2022 - In Moti Mizrahi Mizrahi (ed.), For and Against Scientism: Science, Methodology, and the Future of Philosophy. Lanham: Rowman & Littlefield Publishers. pp. 47-74.
    This chapter considers the assumptions required to make scientisms of different forms genuinely threatening to philosophers, where a genuine threat would consist of a concrete risk to their statuses, the value of their teaching and research, their livelihoods, their preferred research methods, or the health of the discipline. I will find that strong and weak forms of scientism alike require substantive assumptions to make them threatening in those regards. In particular, they require sometimes heavy-handed circumscriptions of philosophy and science, as (...)
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  30. 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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  31. Verbal irony in the wild.Gregory A. Bryant - 2011 - Pragmatics and Cognition 19 (2):291-309.
    Verbal irony constitutes a rough class of indirect intentional communication involving a complex interaction of language-specific and communication-general phenomena. Conversationalists use verbal irony in conjunction with paralinguistic signals such as speech prosody. Researchers examining acoustic features of speech communication usually focus on how prosodic information relates to the surface structure of utterances, and often ignore prosodic phenomena associated with implied meaning. In the case of verbal irony, there exists some debate concerning how these prosodic features manifest themselves in conversation. A (...)
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  32. 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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  33. 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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  34. 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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  35. 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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  36. Moderate monism, persistence and sortal concepts.Harold Noonan - manuscript
    Coincidence comes in two varieties – permanent and temporary. Moderate monism is the position that permanent coincidence, but not temporary coincidence, entails identity. Extreme monism is the position that even temporary coincidence entails identity. Pluralists are opponents of monism tout court. The intuitively obvious, commonsensical position is moderate monism. It is therefore important to see if it can be sustained.
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  37. 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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  38. Putting philosophy of political science on the map.Harold Kincaid & Jeroen Van Bouwel - 2023 - 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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  39. 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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  40. 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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  41. Corrections to "where do sets come from?".Harold T. Hodes - 1991 - Journal of Symbolic Logic 56 (4):1486.
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  42. In Defence of the Letter of Fictionalism.Harold Noonan - 1994 - Analysis 54 (3):133-139.
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  43. 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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  44.  77
    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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  45.  85
    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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  46. 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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  47. Cardinality logics. Part II: Definability in languages based on `exactly'.Harold Hodes - 1988 - Journal of Symbolic Logic 53 (3):765-784.
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  48. 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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  49. 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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  50. 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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