Results for 'Chris Mungall'

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  1. CARO: The Common Anatomy Reference Ontology.Haendel Melissa, A. Neuhaus, Fabian Osumi-Sutherland, David Mabee, M. Paula, L. V. MejinoJosé, Mungall Chris, J. Smith & Barry - 2008 - In Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer. pp. 327--349.
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  2. An improved ontological representation of dendritic cells as a paradigm for all cell types.Masci Anna Maria, N. Arighi Cecilia, D. Diehl Alexander, E. Lieberman Anne, Mungall Chris, H. Scheuermann Richard, Barry Smith & G. Cowell Lindsay - 2009 - BMC Bioinformatics 10 (1):70.
    The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...)
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  3. The Plant Ontology: A common reference ontology for plants.L. Walls Ramona, D. Cooper Laurel, Elser Justin, W. Stevenson Dennis, Barry Smith, Mungall Chris, A. Gandolfo Maria & Jaiswal Pankaj - 2010 - In Walls Ramona L., Cooper Laurel D., Justin Elser, Stevenson Dennis W., Smith Barry, Chris Mungall, Gandolfo Maria A. & Pankaj Jaiswal (eds.), Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010.
    The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...)
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  4. Proceedings of the Workshop on Bio-Ontologies, ISMB, Boston, July, 2010.L. Walls Ramona, D. Cooper Laurel, Justin Elser, W. Stevenson Dennis, Smith Barry, Chris Mungall, A. Gandolfo Maria & Pankaj Jaiswal - 2010
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  5. Relations in Biomedical Ontologies.Barry Smith, Werner Ceusters, Bert Klagges, Jacob Köhler, Anand Kuma, Jane Lomax, Chris Mungall, , Fabian Neuhaus, Alan Rector & Cornelius Rosse - 2005 - Genome Biology 6 (5):R46.
    To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.
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  6. CARO: The Common Anatomy Reference Ontology.Melissa Haendel, Fabian Neuhaus, David Osumi-Sutherland, Paula M. Mabee, José L. V. Mejino Jr, Chris J. Mungall & Barry Smith - 2008 - In Anatomy Ontologies for Bioinformatics: Principles and Practice. Springer. pp. 327-349.
    The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...)
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  7. VO: Vaccine Ontology.Yongqun He, Lindsay Cowell, Alexander D. Diehl, H. L. Mobley, Bjoern Peters, Alan Ruttenberg, Richard H. Scheuermann, Ryan R. Brinkman, Melanie Courtot, Chris Mungall, Barry Smith & Others - 2009 - In Barry Smith (ed.), ICBO 2009: Proceedings of the First International Conference on Biomedical Ontology. Buffalo: NCOR.
    Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...)
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  8. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics.Laurel Cooper, Austin Meier, Marie-Angélique Laporte, Justin L. Elser, Chris Mungall, Brandon T. Sinn, Dario Cavaliere, Seth Carbon, Nathan A. Dunn, Barry Smith, Botong Qu, Justin Preece, Eugene Zhang, Sinisa Todorovic, Georgios Gkoutos, John H. Doonan, Dennis W. Stevenson, Elizabeth Arnaud & Pankaj Jaiswal - 2018 - Nucleic Acids Research 46 (D1):D1168–D1180.
    The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...)
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  9. Survey-based naming conventions for use in OBO Foundry ontology development.Schober Daniel, Barry Smith, Lewis Suzanna, E. Kusnierczyk, Waclaw Lomax, Jane Mungall, Chris Taylor, F. Chris, Rocca-Serra Philippe & Sansone Susanna-Assunta - 2009 - BMC Bioinformatics 10 (1):125.
    A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...)
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  10. National Center for Biomedical Ontology: Advancing biomedicine through structured organization of scientific knowledge.Daniel L. Rubin, Suzanna E. Lewis, Chris J. Mungall, Misra Sima, Westerfield Monte, Ashburner Michael, Christopher G. Chute, Ida Sim, Harold Solbrig, M. A. Storey, Barry Smith, John D. Richter, Natasha Noy & Mark A. Musen - 2006 - Omics: A Journal of Integrative Biology 10 (2):185-198.
    The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...)
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  11.  36
    The RNA Ontology (RNAO): an ontology for integrating RNA sequence and structure data.Robert Hoehndorf, Colin Batchelor, Thomas Bittner, Michel Dumontier, Karen Eilbeck, Rob Knight, Chris J. Mungall, Jane S. Richardson, Jesse Stombaugh & Eric Westhof - 2011 - Applied ontology 6 (1):53-89.
  12. An improved ontological representation of dendritic cells as a paradigm for all cell types.Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Liebermann, Chris Mungall, Richard H. Scheuermann, Barry Smith & Lindsay Cowell - 2009 - BMC Bioinformatics 10 (1):70.
  13. How to Explain Miscomputation.Chris Tucker - 2018 - Philosophers' Imprint 18:1-17.
    Just as theory of representation is deficient if it can’t explain how misrepresentation is possible, a theory of computation is deficient if it can’t explain how miscomputation is possible. Nonetheless, philosophers have generally ignored miscomputation. My primary goal in this paper is to clarify both what miscomputation is and how to adequately explain it. Miscomputation is a special kind of malfunction: a system miscomputes when it computes in a way that it shouldn’t. To explain miscomputation, you must provide accounts of (...)
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  14. When Transmission Fails.Chris Tucker - 2010 - Philosophical Review 119 (4):497-529.
    The Neo-Moorean Deduction (I have a hand, so I am not a brain-in-a-vat) and the Zebra Deduction (the creature is a zebra, so isn’t a cleverly disguised mule) are notorious. Crispin Wright, Martin Davies, Fred Dretske, and Brian McLaughlin, among others, argue that these deductions are instances of transmission failure. That is, they argue that these deductions cannot transmit justification to their conclusions. I contend, however, that the notoriety of these deductions is undeserved. My strategy is to clarify, attack, defend, (...)
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  15. Luck, Propositional Perception, and the Entailment Thesis.Chris Ranalli - 2014 - Synthese 191 (6):1223-1247.
    Looking out the window, I see that it's raining outside. Do I know that it’s raining outside? According to proponents of the Entailment Thesis, I do. If I see that p, I know that p. In general, the Entailment Thesis is the thesis that if S perceives that p, S knows that p. But recently, some philosophers (McDowell 2002, Turri 2010, Pritchard 2011, 2012) have argued that the Entailment Thesis is false. On their view, we can see p and not (...)
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  16. The dual scale model of weighing reasons.Chris Tucker - 2021 - Noûs 56 (2):366-392.
    The metaphor of weighing reasons brings to mind a single (double-pan balance) scale. The reasons for φ go in one pan and the reasons for ~φ go in the other. The relative weights, as indicated by the relative heights of the two pans of the scale, determine the deontic status of φ. This model is simple and intuitive, but it cannot capture what it is to weigh reasons correctly. A reason pushes the φ pan down toward permissibility (has justifying weight) (...)
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  17.  78
    Do States Have the Right to Exclude Immigrations?Chris Bertram - 2018 - Cambridge, UK ; Medford, MA: Polity.
    States claim the right to choose who can come to their country. They put up barriers and expose migrants to deadly journeys. Those who survive are labelled ‘illegal’ and find themselves vulnerable and unrepresented. The international state system advantages the lucky few born in rich countries and locks others into poor and often repressive ones. In this book, Christopher Bertram skilfully weaves a lucid exposition of the debates in political philosophy with original insights to argue that migration controls must be (...)
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  18. Epistemic Competence and Agency in Sosa and Xunzi.Chris Fraser - 2022 - In Yong Huang (ed.), Ernest Sosa encountering Chinese philosophy: a cross-cultural approach to virtue epistemology. New York: Bloomsbury Academic. pp. 39-50.
     
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  19.  43
    Ecology and socialism: [solutions to capitalist ecological crisis].Chris Williams - 2010 - Chicago: Haymarket Books.
    A timely, well-grounded analysis that reveals an inconvenient truth: we can't save capitalism and save the planet.
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  20.  11
    Oxford Handbook of International Political Theory.Chris Brown & Robyn Eckersley (eds.) - 2018 - Oxford University Press.
    International Political Theory focuses on the point where two fields of study meet - International Relations and Political Theory. It takes from the former a central concern with the 'international' broadly defined; from the latter it takes a broadly normative identity. IPT studies the 'ought' questions that have been ignored or side-lined by the modern study of International Relations and the 'international' dimension that Political Theory has in the past neglected. A central proposition of IPT is that the 'domestic' and (...)
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  21. Natural kinds.Chris Daly - 1998 - In Edward Craig (ed.), Routledge Encyclopedia of Philosophy: Genealogy to Iqbal. Routledge. pp. 682-5.
     
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  22. Philosophy of the Physical Sciences.Chris Smeenk & Hoefer Carl - 2016 - In Paul Humphreys (ed.), The Oxford Handbook of Philosophy of Science. Oxford University Press USA.
    The authors survey some debates about the nature and structure of physical theories and about the connections between our physical theories and naturalized metaphysics. The discussion is organized around an “ideal view” of physical theories and criticisms that can be raised against it. This view includes controversial commitments regarding the best analysis of physical modalities and intertheory relations. The authors consider the case in favor of taking laws as the primary modal notion, discussing objections related to alleged violations of the (...)
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  23. The dynamics of vagueness.Chris Barker - 2002 - Linguistics and Philosophy 25 (1):1-36.
  24. Scepticism about Grounding.Chris Daly - 2012 - In Fabrice Correia & Benjamin Schnieder (eds.), Metaphysical Grounding: Understanding the Structure of Reality. Cambridge University Press. pp. 81.
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  25.  93
    Action understanding as inverse planning.Chris L. Baker, Rebecca Saxe & Joshua B. Tenenbaum - 2009 - Cognition 113 (3):329-349.
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  26. Feminism, theory, and the politics of difference.Chris Weedon - 1999 - Malden, Mass.: Blackwell.
    "Feminism, Theory and the Politics of Difference" looks at the question of difference across the full spectrum of feminist theory from liberal, radical, lesbian ...
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  27. Dignity-enhancing nursing care.Chris Gastmans - 2013 - Nursing Ethics 20 (2):142-149.
    Starting from two observations regarding nursing ethics research in the past two decades, namely, the dominant influence of both the empirical methods and the principles approach, we present the cornerstones of a foundational argument-based nursing ethics framework. First, we briefly outline the general philosophical–ethical background from which we develop our framework. This is based on three aspects: lived experience, interpretative dialogue, and normative standard. Against this background, we identify and explore three key concepts—vulnerability, care, and dignity—that must be observed in (...)
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  28. Philosophy of Psychedelics.Chris Letheby - 2021 - Oxford, UK: Oxford University Press.
    Recent clinical trials show that psychedelics such as LSD and psilocybin can be given safely in controlled conditions, and can cause lasting psychological benefits with one or two administrations. Supervised psychedelic sessions can reduce symptoms of anxiety, depression, and addiction, and improve well-being in healthy volunteers, for months or even years. But these benefits seem to be mediated by "mystical" experiences of cosmic consciousness, which prompts a philosophical concern: do psychedelics cause psychological benefits by inducing false or implausible beliefs about (...)
  29.  26
    Ethics gets in the way: A reply to David Bastow: Chris Gudmunsen.Chris Gudmunsen - 1972 - Religious Studies 8 (4):311-318.
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  30. Negotiating Taste.Chris Barker - 2013 - Inquiry: An Interdisciplinary Journal of Philosophy 56 (2-3):240-257.
    Using a vague predicate can make commitments about the appropriate use of that predicate in the remaining part of the discourse. For instance, if I assert that some particular pig is fat, I am committed to judging any fatter pig to be fat as well. We can model this update effect by recognizing that truth depends both on the state of the world and on the state of the discourse: the truth conditions of ‘This pig is fat’ rule out evaluation (...)
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  31. Justice and Attachment to Natural Resources.Chris Armstrong - 2013 - Journal of Political Philosophy 22 (1):48-65.
  32.  24
    Intrusive images in psychological disorders: Characteristics, neural mechanisms, and treatment implications.Chris R. Brewin, James D. Gregory, Michelle Lipton & Neil Burgess - 2010 - Psychological Review 117 (1):210-232.
  33. What is Deep Disagreement?Chris Ranalli - 2018 - Topoi 40 (5):983-998.
    What is the nature of deep disagreement? In this paper, I consider two similar albeit seemingly rival answers to this question: the Wittgensteinian theory, according to which deep disagreements are disagreements over hinge propositions, and the fundamental epistemic principle theory, according to which deep disagreements are disagreements over fundamental epistemic principles. I assess these theories against a set of desiderata for a satisfactory theory of deep disagreement, and argue that while the fundamental epistemic principle theory does better than the Wittgensteinian (...)
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  34. Self unbound: ego dissolution in psychedelic experience.Chris Letheby & Philip Gerrans - 2017 - Neuroscience of Consciousness 3:1-11.
    Users of psychedelic drugs often report that their sense of being a self or ‘I’ distinct from the rest of the world has diminished or altogether dissolved. Neuroscientific study of such ‘ego dissolution’ experiences offers a window onto the nature of self-awareness. We argue that ego dissolution is best explained by an account that explains self-awareness as resulting from the integrated functioning of hierarchical predictive models which posit the existence of a stable and unchanging entity to which representations are bound. (...)
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  35.  24
    Continuations and Natural Language.Chris Barker & Chung-Chieh Shan - 2014 - Oxford University Press.
    This book takes concepts developed by researchers in theoretical computer science and adapts and applies them to the study of natural language meaning. Summarizing over a decade of research, Chris Barker and Chung-chieh Shan put forward the Continuation Hypothesis: that the meaning of a natural language expression can depend on its own continuation.
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  36. Are Ableist Insults Secretly Slurs?Chris Cousens - 2020 - Language Sciences 77.
    Philosophers often treat racist and sexist slurs as a special sort of puzzle. What is the difference between a slur and its correlates? In attempting to answer this question, a second distinction has been overlooked: that between slurs and insults. What makes a term count as a slur? This is not an unnecessary taxonomical question as long as ableist terms such as ‘moron’ are dismissed as mere insults. Attempts to resolve the insult/slur distinction by considering the communicative content of slurs (...)
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  37. Fairness, Free-Riding and Rainforest Protection.Chris Armstrong - 2016 - Political Theory 44 (1):106-130.
    If dangerous climate change is to be avoided, it is vital that carbon sinks such as tropical rainforests are protected. But protecting them has costs. These include opportunity costs: the potential economic benefits which those who currently control rainforests have to give up when they are protected. But who should bear those costs? Should countries which happen to have rainforests within their territories sacrifice their own economic development, because of our broader global interests in protecting key carbon sinks? This essay (...)
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  38.  40
    Justice and Natural Resources: An Egalitarian Theory.Chris Armstrong - 2017 - Oxford: Oxford University Press.
    Struggles over precious resources such as oil, water, and land are increasingly evident in the contemporary world. States, indigenous groups, and corporations vie to control access to those resources, and the benefits they provide. These conflicts are rapidly spilling over into new arenas, such as the deep oceans and the Polar regions. How should these precious resources be governed, and how should the benefits and burdens they generate be shared? Justice and Natural Resources provides a systematic theory of natural resource (...)
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  39. Deep disagreement and hinge epistemology.Chris Ranalli - 2018 - Synthese:1-33.
    This paper explores the application of hinge epistemology to deep disagreement. Hinge epistemology holds that there is a class of commitments—hinge commitments—which play a fundamental role in the structure of belief and rational evaluation: they are the most basic general ‘presuppositions’ of our world views which make it possible for us to evaluate certain beliefs or doubts as rational. Deep disagreements seem to crucially involve disagreements over such fundamental commitments. In this paper, I consider pessimism about deep disagreement, the thesis (...)
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  40.  76
    An Introduction to Philosophical Methods.Chris Daly - 2010 - Peterborough, CA: Broadview Press.
    An Introduction to Philosophical Methods is the first book to survey the various methods that philosophers use to support their views. Rigorous yet accessible, the book introduces and illustrates the methodological considerations that are involved in current philosophical debates. Where there is controversy, the book presents the case for each side, but highlights where the key difficulties with them lie. While eminently student-friendly, the book makes an important contribution to the debate regarding the acceptability of the various philosophical methods, and (...)
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  41.  55
    Deep disagreement and hinge epistemology.Chris Ranalli - 2020 - Synthese 197 (11):4975-5007.
    This paper explores the application of hinge epistemology to deep disagreement. Hinge epistemology holds that there is a class of commitments—hinge commitments—which play a fundamental role in the structure of belief and rational evaluation: they are the most basic general ‘presuppositions’ of our world views which make it possible for us to evaluate certain beliefs or doubts as rational. Deep disagreements seem to crucially involve disagreements over such fundamental commitments. In this paper, I consider pessimism about deep disagreement, the thesis (...)
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  42. Truth in Pre-Han Thought.Chris Fraser - 2020 - In Yiu-Ming Fung (ed.), Dao Companion to Chinese Philosophy of Logic. Dordrecht: Springer.
     
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  43. So where's the explanation?Chris Daly - 2005 - In Helen Beebee & Julian Dodd (eds.), Truthmakers: The Contemporary Debate. Clarendon Press. pp. 85.
  44.  62
    Deep Disagreement (Part 1): Theories of Deep Disagreement.Chris Ranalli & Thirza Lagewaard - 2022 - Philosophy Compass 17 (12):e12886.
    Some disagreements concern our most fundamental beliefs, principles, values, or worldviews, such as those about the existence of God, society and politics, or the trustworthiness of science. These are ‘deep disagreements’. But what exactly are deep disagreements? This paper critically overviews theories of deep disagreement. It does three things. First, it explains the differences between deep and other kinds of disagreement, including peer, persistent, and widespread disagreement. Second, it critically overviews two mainstream theories of deep disagreement, the Wittgensteinian account and (...)
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  45. South asian philosophies.Chris Bartley - 1999 - In Ninian Smart (ed.), World philosophies. New York: Routledge.
     
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  46. Southeast Asia-sacred forests and human-environment relations.Nikolas Århem Chris Coggins, Hoan Thi Phan Agni Klintuni Boedhihartono & Ekoningtyas Margu Wardani Ha Van Le - 2022 - In Chris Coggins & Bixia Chen (eds.), Sacred forests of Asia: spiritual ecology and the politics of nature conservation. New York: Routledge.
     
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  47.  28
    The sociological ambition: elementary forms of social and moral life.Chris Shilling - 2001 - Thousand Oaks: SAGE. Edited by Philip A. Mellor.
    In a comprehensive and innovative reassessment of the discipline, this book argues that classical and contemporary social theories must be studied in relation to the ambition that shaped and established sociology: the ambition to comprehend the relationship between social and moral life. Surveying a range of sociological analyses from Comte to feminism, postmodernism and rational choice theory, this book examines the various attempts that have been made to reconstruct the discipline over the last century, and the challenges facing it today. (...)
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  48.  15
    Doing ethics in media: theories and practical applications.Chris Roberts - 2022 - New York, NY: Routledge. Edited by Jay Black.
    The second edition of Doing Ethics in Media continues its mission of providing an accessible but comprehensive introduction to media ethics, with a theoretical grounding in moral philosophy, to help students think clearly and systematically about dilemmas in the rapidly changing media environment. Each chapter highlights specific considerations, cases, and practical applications for the fields of journalism, advertising, digital media, entertainment, public relations, and social media. Six fundamental decision-making questions - the "5Ws and H" around which the book is organized (...)
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  49. A Role for Mathematics in the Physical Sciences.Chris Pincock - 2007 - Noûs 41 (2):253-275.
    Conflicting accounts of the role of mathematics in our physical theories can be traced to two principles. Mathematics appears to be both (1) theoretically indispensable, as we have no acceptable non-mathematical versions of our theories, and (2) metaphysically dispensable, as mathematical entities, if they existed, would lack a relevant causal role in the physical world. I offer a new account of a role for mathematics in the physical sciences that emphasizes the epistemic benefits of having mathematics around when we do (...)
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    Deep Disagreement (Part 1): Theories of Deep Disagreement.Chris Ranalli & Thirza Lagewaard - 2022 - Philosophy Compass 17 (12):e12886.
    Some disagreements concern our most fundamental beliefs, principles, values, or worldviews, such as those about the existence of God, society and politics, or the trustworthiness of science. These are ‘deep disagreements’. But what exactly are deep disagreements? This paper critically overviews theories of deep disagreement. It does three things. First, it explains the differences between deep and other kinds of disagreement, including peer, persistent, and widespread disagreement. Second, it critically overviews two mainstream theories of deep disagreement, the Wittgensteinian account and (...)
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