Results for 'Chong Un Choe Smith'

946 found
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  1. Un'aporia nella costruzione della realtà sociale: Naturalismo e realismo in John R. Searle.Barry Smith - 2003 - In Paolo Di Lucia (ed.), Ontologia Sociale. Quodlibet. pp. 137-152.
    We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A (...)
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  2. La physique naïve: un essai d'ontologie.Barry Smith & Roberto Casati - 1993 - Intellectica 17 (2):173--197.
    The project of a naive physics has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as Kohler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit from a (...)
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  3. Klossowski's Reading of Nietzsche: Impulses, Phantasms, Simulacra, Stereotypes.Daniel W. Smith - 2005 - Diacritics 35 (1):8-21.
    In lieu of an abstract, here is a brief excerpt of the content:diacritics 35.1 (2005) 8-21MuseSearchJournalsThis JournalContents[Access article in PDF]Klossowski's Reading of Nietzsche Impulses, Phantasms, Simulacra, StereotypesDaniel W. SmithIn his writings on Nietzsche, Pierre Klossowski makes use of various concepts—such as intensities, phantasms, simulacra and stereotypes, resemblance and dissemblance, gregariousness and singularity—that have no place in Nietzsche's own oeuvre. These concepts are Klossowski's own creations, his own contributions to thought. Although Klossowski consistently refused to characterize himself as a philosopher ("Je (...)
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  4. Dalla metafisica classica all'informatica medica.Barry Smith - 2003 - In Smith Barry (ed.), Ontologia, , 154--158. Naples: Guida. pp. 154-159.
    In un articolo comparso sul Wall Street Journal del 13 novembre 2oi:n viene descritto il modo in cui i computer potrebbero essere utilizzati al fine di allertare i responsabili della salute pubblica in relazione ad eventuali problemi provocati dal bioterrorismo. L'autore nota come gli attacchi biologici sarebbero probabilmente contraddistinti da picchi statistici negli acquisti senza ricetta medica di rimedi per specifici disturbi di tipo comune e come i dati che riguardano tali acquisti possano essere resi disponibili immediatamente grazie agli inventari (...)
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  5. Verso una filosofia al servizio dell' industria: l'utilità dell' ontologia analitica per l'informatica medica.Barry Smith & Werner Ceusters - 2003 - Sistemi Intelligenti 15 (3):407-417.
    La ricerca medica è afflitta da un problema di comunicazione. Comunità distinte di ricercatori si servono di terminologie diverse e spesso incompatibili per esprimere i risultati del loro lavoro, generando in questo modo problemi di integrazione tra database ogniqualvolta si presenti la necessità di inserire i dati medici nei computer. In un primo momento i problemi di integrazione tra database venivano risolti caso per caso, in seguito si è fatta strada l’idea di realizzare un’unica tassonomia di riferimento in cui tradurre, (...)
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  6. Lógica y ontología formal.Barry Smith - 2004 - In . Grupo de Acción Filosófica (Gaf), Buenos Aires.
    La lógica es para Husserl una ciencia de la ciencia, una ciencia de lo que todas las ciencias tienen en común respecto de sus modos de validación. De este modo, la lógica trata por un lado con leyes universales relacionadas con la verdad, la deducción, la verificación y la falsación; y, por otro lado, con leyes relacionadas con la teoría como tal, y con lo que produce la unidad teorética. Ambos tipos de leyes se refieren por una parte a las (...)
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  7. La verità e il campo visivo.Barry Smith - 1999 - Paradigmi 17:49-62.
    L'articolo usa la teoria delle parti, del tutto e dei contomi per elaborare alcune relazioni cruciali tra la «psicologia ecologica» di J.J. Gibson e la fenomenologia di Husserl. Presenta, inoltre, una teoria ontologica dei contomi spaziali e delle entita spazialmente estese, applicandola al cam po visivo, qui concepito come un' entita spazialmente estesa dipendente dal soggetto che percepisce. Su questa base e possibile formulare un nuovo tipo di definizione teoretico-correspondentista della verita per gli enunciati del linguaggio naturale.
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  8. Die ganze Welt ist eine Bühne: Zur Ökologie und Ontologie menschlicher und tierischer Lebenswelt.Barry Smith - 2004 - Interdisziplinäre Phänomenologie / Interdisciplinary Phenomenology (Kyoto) 1:31-44.
    Die klassische bikategoriale Ontologie von Substanzen und Akzidentien ist für die Festlegung der Strukturen menschlichen und tierischen Verhaltens nicht hinreichend, da die Umwelten dieses Verhaltens sich nicht in dieses klassische System einfügen. Wir bieten dementsprechend den Grundriß einer Theorie der besonderen Gebilde, die die Alltagswelten menschlicher und tierischer Verhalten konstituieren. Die Ausgangsüberlegung ist die folgende, Wir sind alle (Schau)spieler, und diese brauchen eine Bühne. Unsere Bühne ist die jeweilige Umwelt, in der wir leben und handeln. Der Terminus ‘Umwelt’ wird hierbei (...)
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  9. La vérité et le champ visuel.Barry Smith - 2002 - In Jean-Michel Roy, Jean Francisco J. Varela & Bernard Pachoud (eds.), Naturaliser la phénoménologie: Husserlianisme et science cognitive. CNRS Editions. pp. 411-426.
    La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui (...)
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  10. Foucault sobre ética y subjetividad: ‘cuidado de sí’ y ‘estética de la existencia.Daniel J. Smith - 2017 - Dorsal. Revista de Estudios Foucaultianos 2:301-321.
    Este ensayo considera la estructura del sujeto ético que se encuentra en los últimos trabajos de Foucault sobre ética, y da cuenta de sus dos conceptos éticos fundamentales: “cuidado de sí” y “estética de la existencia”. El “cuidado de sí”, se argumenta, da a Foucault una manera de conceptualizar la ética que no depende de categorías jurídicas, y que no concibe al sujeto ético en el modelo de la sustancia. “El cuidado de sí” conlleva una comprensión del sujeto ético como (...)
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  11. Logica e ontologia formale nelle «Logische Untersuchungen» di Husserl.Barry Smith - 1991 - Rivista di Filosofia 83 (1):53-70.
    Per Husserl, come per Bolzano, la logica e una dottrina della sdenza. Husserl prende pero piu sul serio l'idea che le teorie scientifiche siano costituite dagli atti mentali di soggetti conoscenti. Quella che segue e un' esposizione della concezione husserliana della logica e della scienza, fondata appunto sugli atti; essa approdera a una delineazione dell'idea husserliana di «ontologia formale».
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  12. Logic and Existence.Daniel W. Smith - 2011 - Chiasmi International 13:361-377.
    Logique et existenceDeleuze à propos des « conditions du réel »Pour Deleuze, l’un des problèmes fondamentaux d’une théorie de la pensée est de savoir comment la pensée peut quitter la sphère du possible pour penser le réel, c’est-àdire pour penser l’existence elle-même. La position du réel semble être hors du concept. Des pré-kantiens comme Leibniz approchaient ce problème par le biais de la distinction entre vérités d’essence et vérités d’existence, alors que des post-kantiens comme Maimon l’approchaient par la distinction entre (...)
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  13. Die Struktur der Common-Sense Welt.Barry Smith - 1994 - Logos. Anales Del Seminario de Metafísica [Universidad Complutense de Madrid, España] 1:422-449.
    Die zeitgenössischen Philosophen haben zwar der Sprache, die wir verwenden, um die Welt der alltäglichen Erfahrung zu beschreiben oder um uns in dieser Welt zurechtzufinden, große Aufmerksamkeit geschenkt, sie haben sich jedoch – von einigen Ausnahmen abgesehen – geweigert, diese Welt selbst als passendes Objekt theoretischer Betrachtungen anzusehen. Im folgenden werde ich versuchen zu zeigen, wie es möglich ist, die Common-Sense-Welt als ontologisch eigenständiges Untersuchungsobjekt zu verstehen. Gleichzeitig werde ich mich bemühen, deutlich zu zeigen, wie eine solch eigenständige Behandlung uns (...)
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  14. Encounters with Deleuze.Constantin V. Boundas, Daniel W. Smith & Ada S. Jaarsma - 2020 - Symposium 24 (1):139-174.
    This interview, conducted over the span of several months, tracks the respective journeys of Constantin V. Boundas and Daniel W. Smith with the philosophy of Gilles Deleuze. Rather than “becoming Deleuzian,” which is neither desirable nor possible, these exchanges reflect an array of encounters with Deleuze. These include the initial discoveries of Deleuze’s writings by Boundas and Smith, in-person meetings between Boundas and Deleuze, and the wide-ranging and influential philosophical work on Deleuze’s concepts produced by both Boundas and (...)
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  15. Biomedizinische Ontologien für die Praxis.M. Brochhausen & Barry Smith - 2009 - European Journal for Biomedical Informatics 1.
    Hintergrund: Biomedizinische Ontologien existieren unter anderem zur Integration von klinischen und experimentellen Daten. Um dies zu erreichen ist es erforderlich, dass die fraglichen Ontologien von einer großen Zahl von Benutzern zur Annotation von Daten verwendet werden. Wie können Ontologien das erforderliche Maß an Benutzerfreundlichkeit, Zuverlässigkeit, Kosteneffektivität und Domänenabdeckung erreichen, um weitreichende Akzeptanz herbeizuführen? -/- Material und Methoden: Wir konzentrieren uns auf zwei unterschiedliche Strategien, die zurzeit hierbei verfolgt werden. Eine davon wird von SNOMED CT im Bereich der Medizin vertreten, die (...)
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  16. SIMPATÍA, RESENTIMIENTO Y PERDÓN: UN ANÁLISIS DEL ROL DEL RESENTIMIENTO EN LA TMS DE ADAM SMITH.Rodríguez Baños Jeyver & Jeyver Rodríguez Baños - 2017 - Universitas Philosophica (núm. 68):197-218.
    El artículo analiza el papel del resentimiento en la Teoría de los sentimientos morales de Adam Smith y su conexión con el proceso de la simpatía mutua por medio del cual el “espectador imparcial” asume plenamente el resentimiento de la víctima, al considerar que su pasión se rige por los principios de la propiedad y la justicia. Se sostiene que el resentimiento no solo cumple un rol central en la teoría del castigo de Adam Smith, en la medida (...)
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  17. Un Whig scettico? [REVIEW]Sergio Volodia Marcello Cremaschi - 1992 - L'Indice Dei Libri Del Mese 9 (October):49-50.
    A discussion of Donald Winch's 'Adam Smith's Politics'.
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  18.  56
    El estatuto antropológico de la amistad desde Leonardo Polo, en No somos islas.A. Romero-Iribas, Sara Barrena, Pablo Cobreros, Izaskun Martínez & Paloma Pérez-Ilzarbe (eds.) - 2023 - Pamplona: Eunsa.
    En la actualidad hay un renacer del interés académico por la amistad que se aborda desde múltiples disciplinas, tales como la Sociología (Spencer & Pahl, 2006), la Psicología (Hojjat & Moyer, 2017), la educación (Kristjánsson, 2022), la Política (Digeser, 2016) o las Relaciones Internacionales (Koschut & Oelsner, 2014). En filosofía, la amistad es un tema clásico que se ha abordado con interés variable en distintos momentos de la historia: para griegos y romanos fue relevante a nivel personal y político (Aristóteles, (...)
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  19. Jalousie.Frédéric Minner - 2018 - Encyclopédie Philosophique.
    On conçoit souvent la jalousie comme une émotion ayant pour objet les relations de proximité (amour, amitié, fratrie, etc.). Elle a généralement mauvaise presse et est typiquement envisagée comme une émotion moralement condamnable, voire comme un vice. Or, la jalousie ne porte pas uniquement sur les relations de proximité : elle peut également porter sur divers biens (prestige, richesses, biens matériels, privilèges, etc.). Par ailleurs, certains auteurs soutiennent que des cas de jalousie pourraient être moralement justifiés, voire que la jalousie (...)
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  20. Perception musicale et plaisir esthétique au siècle des Lumières.Thierry Côté - 2023 - Ithaque 1 (33):1–23.
    Cet article interroge les fondements théoriques de l’expérience musicale chez quatre penseurs des Lumières : Condillac, Rousseau, Chabanon, et Smith. On dégage d’abord les opérations qui, selon Condillac, permettent au spectateur d’actualiser les imitations visées par le musicien. Ce « régime empiriste de l’écoute » envisage l’expérience musicale dans une dualité entre plaisirs sensibles de pure « jouissance » et plaisirs d’imagination intellectualisés. Rousseau cherche à sortir de ce dualisme, en fondant l’émotion musicale dans une théorie de la communication (...)
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  21. La démocratie et la sélection: tirage au sort, élections et l'égalité.Annabelle Lever - 2023 - In La démocratie; une idée force. Paris: Mare et Martin.
    Devrions-nous remplacer les élections par des loteries ? Le célèbre livre de Bernard Manin sur le gouvernement représentatif a appris à beaucoup que les Grecs considéraient les élections comme un moyen aristocratique, et non démocratique, de sélectionner des personnes pour le pouvoir et l'autorité politique, en comparaison avec le tirage au sort, où chacun a une chance égale d'être sélectionné. (Manin 1997) Jusqu'à récemment, cependant, l'idée qu'un engagement envers la démocratie nécessite de remplacer les élections par le tirage au sort (...)
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  22. Le libéralisme, l’utilitarisme et l’économie politique classique dans l’interprétation d’Élie Halévy.Philippe Mongin - 1990 - la Revue du M.A.U.S.S 10:135-169.
    Élie HALÉVY (1870-1937), philosophe et historien des idées, fut professeur à l'École libre des sciences politiques, l'ancêtre de l'actuel Sciences Po. Comme son autre grand ouvrage, l'Histoire du peuple anglais au XIXe siècle, paru en six tomes de 1913 à 1932, les trois tomes de La formation du radicalisme philosophique, parus en 1901 pour les deux premiers et en 1904 pour le troisième, reflètent pour partie ses enseignements de l'Ecole libre consacrés à l'histoire britannique. Le premier tome, La jeunesse de (...)
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  23. Comportamento Sexual dos Animais Domésticos.Emanuel Isaque Cordeiro Da Silva -
    COMPORTAMENTO SEXUAL DOS ANIMAIS OBJETIVO O estudante explicará a conduta sexual de fêmeas e machos de diferentes espécies domésticas para detectar a fase de receptividade sexual, com a finalidade de programar de maneira adequada a monta ou a inseminação artificial. A observação da conduta sexual dos animais é indispensável para o sucesso da estação reprodutiva em uma determinada propriedade. Logo, o estudante obterá o alicerce necessário sobre os pontos teóricos e práticos a serem observados para a seleção dos animais aptos (...)
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  24. Vandalizing Tainted Commemorations.Chong-Ming Lim - 2020 - Philosophy and Public Affairs 48 (2):185-216.
    What should we do about “tainted” public commemorations? Recent events have highlighted the urgency of reaching a consensus on this question. However, existing discussions appear to be dominated by two naïve opposing views – to remove or preserve them. My aims in this essay are two-fold. First, I argue that the two views are not naïve, but undergirded by concerns with securing self-respect and with the character of our engagement with the past. Second, I offer a qualified defence of vandalising (...)
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  25. Biography of Barry Smith.Sandra Smith - 2017 - Cosmos + Taxis 4 (4):4-5.
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  26. Disabilities Are Also Legitimately Medically Interesting Constraints on Legitimate Interests.Chong-Ming Lim - 2018 - Mind 127 (508):977-1002.
    What is it for something to be a disability? Elizabeth Barnes, focusing on physical disabilities, argues that disability is a social category. It depends on the rules undergirding the judgements of the disability rights movement. Barnes’ account may strike many as implausible. I articulate the unease, in the form of three worries about Barnes’ account. It does not fully explain why the disability rights movement is constituted in such a way that it only picks out paradigmatic disability traits, nor why (...)
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  27. Reviewing resistances to reconceptualizing disability.Chong-Ming Lim - 2017 - Proceedings of the Aristotelian Society 117 (3):321-331.
    I attempt to adjudicate the disagreement between those who seek to reconceptualize disability as mere difference and their opponents. I do so by reviewing a central conviction motivating the resistance, concerning the relationship between disability and well-being. I argue that the conviction depends on further considerations about the costs and extent of change involved in accommodating individuals with a particular disability trait. I conclude by considering three pay-offs of this clarification.
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  28. The importance of getting the ethics right in a pandemic treaty.G. Owen Schaefer, Caesar A. Atuire, Sharon Kaur, Michael Parker, Govind Persad, Maxwell J. Smith, Ross Upshur & Ezekiel Emanuel - 2023 - The Lancet Infectious Diseases 23 (11):e489 - e496.
    The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...)
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  29. Clarifying the best interests standard: the elaborative and enumerative strategies in public policy-making.Chong Ming Lim, Michael C. Dunn & Jacqueline J. Chin - 2016 - Journal of Medical Ethics 42 (8):542-549.
    One recurring criticism of the best interests standard concerns its vagueness, and thus the inadequate guidance it offers to care providers. The lack of an agreed definition of ‘best interests’, together with the fact that several suggested considerations adopted in legislation or professional guidelines for doctors do not obviously apply across different groups of persons, result in decisions being made in murky waters. In response, bioethicists have attempted to specify the best interests standard, to reduce the indeterminacy surrounding medical decisions. (...)
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  30.  63
    Commemorative Artefactual Speech.Chong-Ming Lim - forthcoming - Ergo.
    Commemorative artefacts purportedly speak – they communicate messages to their audience, even if no words are uttered. Sometimes, such artefacts purportedly communicate demeaning or pejorative messages about some members of society. The characteristics of such speech are, however, under-examined. I present an account of the paradigmatic characteristics of the speech of commemorative artefacts (or, “commemorative artefactual speech”), as a distinct form of political speech. According to my account, commemorative artefactual speech paradigmatically involves the use of an artefact by an authorised (...)
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  31. Accommodating Autistics and Treating Autism: Can We Have Both?Chong-Ming Lim - 2015 - Bioethics 29 (8):564-572.
    One of the central claims of the neurodiversity movement is that society should accommodate the needs of autistics, rather than try to treat autism. People have variously tried to reject this accommodation thesis as applicable to all autistics. One instance is Pier Jaarsma and Stellan Welin, who argue that the thesis should apply to some but not all autistics. They do so via separating autistics into high- and low-functioning, on the basis of IQ and social effectiveness or functionings. I reject (...)
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  32. Effectiveness and Ecumenicity.Chong-Ming Lim - 2019 - Journal of Moral Philosophy 16 (5):590-612.
    Effective altruism is purportedly ecumenical towards different moral views, charitable causes, and evidentiary methods. I argue that effective altruists’ criticisms of purportedly less effective charities are inconsistent with their commitment to ecumenicity. Individuals may justifiably support charities other than those recommended by effective altruism. If effective altruists take their commitment to ecumenicity seriously, they will have to revise their criticisms of many of these charities.
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  33. Adam Smith's political philosophy: the invisible hand and spontaneous order.Craig Smith - 2006 - New York: Routledge.
    When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...)
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  34. Clarifying our duties to resist.Chong-Ming Lim - 2024 - Inquiry: An Interdisciplinary Journal of Philosophy 67 (9):3527-3546.
    According to a prominent argument, citizens in unjust societies have a duty to resist injustice. The moral and political principles that ground the duty to obey the law in just or nearly just conditions, also ground the duty to resist in unjust conditions. This argument is often applied to a variety of unjust conditions. In this essay, I critically examine this argument, focusing on conditions involving institutionally entrenched and socially normalised injustice. In such conditions, the issue of citizens’ duties to (...)
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  35. An Incomplete Inclusion of Non-cooperators into a Rawlsian Theory of Justice.Chong-Ming Lim - 2016 - Res Philosophica 93 (4):893-920.
    John Rawls’s use of the “fully cooperating assumption” has been criticized for hindering attempts to address the needs of disabled individuals, or non-cooperators. In response, philosophers sympathetic to Rawls’s project have extended his theory. I assess one such extension by Cynthia Stark, that proposes dropping Rawls’s assumption in the constitutional stage (of his four-stage sequence), and address the needs of non-cooperators via the social minimum. I defend Stark’s proposal against criticisms by Sophia Wong, Christie Hartley, and Elizabeth Edenberg and Marilyn (...)
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  36. Functions in Basic Formal Ontology.Andrew D. Spear, Werner Ceusters & Barry Smith - 2016 - Applied ontology 11 (2):103-128.
    The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...)
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  37. Toward an Ontological Treatment of Disease and Diagnosis.Richard H. Scheuermann, Werner Ceusters & Barry Smith - 2009 - In Richard H. Scheuermann, Werner Ceusters & Barry Smith (eds.), Toward an Ontological Treatment of Disease and Diagnosis. American Medical Informatics Association.
    Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the (...)
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  38. Measuring the Consequences of Rules: Holly M. Smith.Holly M. Smith - 2010 - Utilitas 22 (4):413-433.
    Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...)
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  39. How to model lexical priority.Martin Smith - forthcoming - Ergo: An Open Access Journal of Philosophy.
    A moral requirement R1 is said to be lexically prior to a moral requirement R2 just in case we are morally obliged to uphold R1 at the expense of R2 – no matter how many times R2 must be violated thereby. While lexical priority is a feature of many ethical theories, and arguably a part of common sense morality, attempts to model it within the framework of decision theory have led to a series of problems – a fact which is (...)
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  40. Publications by Barry Smith.Barry Smith - 2017 - Cosmos + Taxis 4 (4):67-104.
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  41. OHMI: The Ontology of Host-Microbiome Interactions.Yongqun He, Haihe Wang, Jie Zheng, Daniel P. Beiting, Anna Maria Masci, Hong Yu, Kaiyong Liu, Jianmin Wu, Jeffrey L. Curtis, Barry Smith, Alexander V. Alekseyenko & Jihad S. Obeid - 2019 - Journal of Biomedical Semantics 10 (1):1-14.
    Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...)
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  42. 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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  43. 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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  44. Ontologies as Integrative Tools for Plant Science.Ramona Walls, Balaji Athreya, Laurel Cooper, Justin Elser, Maria A. Gandolfo, Pankaj Jaiswal, Christopher J. Mungall, Justin Preece, Stefan Rensing, Barry Smith & Dennis W. Stevenson - 2012 - American Journal of Botany 99 (8):1263–1275.
    Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...)
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  45. The Neurological Disease Ontology.Mark Jensen, Alexander P. Cox, Naveed Chaudhry, Marcus Ng, Donat Sule, William Duncan, Patrick Ray, Bianca Weinstock-Guttman, Barry Smith, Alan Ruttenberg, Kinga Szigeti & Alexander D. Diehl - 2013 - Journal of Biomedical Semantics 4 (42):42.
    We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...)
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  46. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project.Chris F. Taylor, Dawn Field, Susanna-Assunta Sansone, Jan Aerts, Rolf Apweiler, Michael Ashburner, Catherine A. Ball, Pierre-Alain Binz, Molly Bogue, Tim Booth, Alvis Brazma, Ryan R. Brinkman, Adam Michael Clark, Eric W. Deutsch, Oliver Fiehn, Jennifer Fostel, Peter Ghazal, Frank Gibson, Tanya Gray, Graeme Grimes, John M. Hancock, Nigel W. Hardy, Henning Hermjakob, Randall K. Julian, Matthew Kane, Carsten Kettner, Christopher Kinsinger, Eugene Kolker, Martin Kuiper, Nicolas Le Novere, Jim Leebens-Mack, Suzanna E. Lewis, Phillip Lord, Ann-Marie Mallon, Nishanth Marthandan, Hiroshi Masuya, Ruth McNally, Alexander Mehrle, Norman Morrison, Sandra Orchard, John Quackenbush, James M. Reecy, Donald G. Robertson, Philippe Rocca-Serra, Henry Rodriguez, Heiko Rosenfelder, Javier Santoyo-Lopez, Richard H. Scheuermann, Daniel Schober, Barry Smith & Jason Snape - 2008 - Nature Biotechnology 26 (8):889-896.
    Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...)
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  47. Transmission Failure Explained.Martin Smith - 2009 - Philosophy and Phenomenological Research 79 (1):164-189.
    In this paper I draw attention to a peculiar epistemic feature exhibited by certain deductively valid inferences. Certain deductively valid inferences are unable to enhance the reliability of one's belief that the conclusion is true—in a sense that will be fully explained. As I shall show, this feature is demonstrably present in certain philosophically significant inferences—such as GE Moore's notorious 'proof' of the existence of the external world. I suggest that this peculiar epistemic feature might be correlated with the much (...)
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  48. A new theory of causation based on probability distribution determinism.Chong Liu - manuscript
    The concept of causation is essential for understanding relationships among various phenomena, yet its fundamental nature and the criteria for establishing it continue to be debated. This paper presents a new theory of causation through a quasi-axiomatic approach. The core of this framework is Probability Distribution Determinism (PDD), which updates traditional determinism by representing states of affairs as probability distributions, with the if-then function serving as its foundational definition. Based on PDD, by merely using appropriate naming strategies, it is possible (...)
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  49. The bridge between philosophy and information-driven science.Barry Smith - 2021 - Journal of Knowledge Structures and Systems 2 (2):47-55.
    This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.
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  50. The Environment Ontology: Contextualising biological and biomedical entities.Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis - 2013 - Journal of Biomedical Semantics 4 (43):1-9.
    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...)
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