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. 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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  10. 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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  11.  38
    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. 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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  14. 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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  15. 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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  16. Inconsistent mathematics.Chris Mortensen - 2008 - Studia Logica.
  17. 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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  18.  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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  19. Propositions and Parthood: The Universe and Anti-Symmetry.Chris Tillman & Gregory Fowler - 2012 - Australasian Journal of Philosophy 90 (3):525 - 539.
    It is plausible that the universe exists: a thing such that absolutely everything is a part of it. It is also plausible that singular, structured propositions exist: propositions that literally have individuals as parts. Furthermore, it is plausible that for each thing, there is a singular, structured proposition that has it as a part. Finally, it is plausible that parthood is a partial ordering: reflexive, transitive, and anti-symmetric. These plausible claims cannot all be correct. We canvass some costs of denying (...)
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  20. 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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  21.  4
    Fidelity to Life ∼ Hospitable Biopolitics.Chris Hall - 2024 - Angelaki 29 (1):9-19.
    While fidelity is a crucial aspect of Jacques Derrida’s thinking as it pertains to issues of faith, ethics, and responsibility, this key position in deconstructionist discourse has hardly yet been brought to light. Less still have the biopolitical resonances of Derrida’s work, with its careful attention to the terms and stakes of life particularly in his later writing, been considered as a deconstructionist practice of fidelity and infidelity in its own right. In pursuing these threads, this essay argues that thinking (...)
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  22. Experience as evidence.Chris Tucker - 2019 - In Maria Lasonen-Aarnio & Clayton Littlejohn (eds.), The Routledge Handbook of the Philosophy of Evidence. Routledge.
    This chapter explores whether and when experience can be evidence. It argues that experiences can be evidence, and that this claim is compatible with just about any epistemological theory. It evaluates the most promising argument for the conclusion that certain experiences (e.g., seeming to see) are always evidence for believing what the experiences represent. While the argument is very promising, one premise needs further defense. The argument also depends on a certain connection between reasonable belief and the first person perspective.
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  23.  10
    Awareness: what it is, what it does.Chris Nunn - 1995 - New York: Routledge.
    Annotation Up-to-date and accessible examination of scientific thinking about the nature of consciousness. Chris Nunn sets out the most exciting theoretical and experimental advances in this fast developing and controversial area.
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  24. The Self-Field: Mind, Body and Environment.Chris Abel - 2021 - Oxford: Routledge.
    In this incisive study of the biological and cultural origins of the human self, the author challenges readers to re-think ideas about the self and consciousness as being exclusive to humans. In their place, he expounds a metatheoretical approach to the self as a purposeful system of extended cognition common to animal life: the invisible medium maintaining mind, body and environment as an integrated 'field of being'. Supported by recent research in evolutionary and developmental studies together with related discoveries in (...)
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  25. Reciprocal integrity.Chris Argyris & Donald A. Schön - 1988 - In Suresh Srivastva (ed.), Executive integrity: the search for high human values in organizational life. San Francisco: Jossey-Bass.
     
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  26. 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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  27.  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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  28. Natural kinds.Chris Daly - 1998 - In Edward Craig (ed.), Routledge Encyclopedia of Philosophy: Genealogy to Iqbal. Routledge. pp. 682-5.
     
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  29. 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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  30.  44
    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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  31. Parity, Pluralism, and Permissible Partiality.Chris Tucker - forthcoming - In Eric Siverman & Chris Tweed (eds.), Virtuous and Vicious Partiality. Routledge.
    We can often permissibly choose a worse self-interested option over a better altruistic alternative. For example, it is permissible to eat out rather than donate the money to feed five hungry children for a single meal. If we eat out, we do something permissibly partial toward ourselves. If we donate, we go beyond the call of moral duty and do something supererogatory. Such phenomena aren’t easy to explain, and they rule out otherwise promising moral theories. Incommensurability and Ruth Chang’s notion (...)
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  32. 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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  33. Solving the Authority Problem: Why We Won’t Debate You, Bro.Chris Cousens - 2023 - Topoi 42 (2):469-480.
    Public arguments can be good or bad not only as a matter of logic, but also in the sense that speakers can do good or bad things with arguments. For example, hate speakers use public arguments to contribute to the subordination of their targets. But how can ordinary speakers acquire the authority to perform subordinating speech acts? This is the ‘Authority Problem’. This paper defends a solution inspired by McGowan’s (Australas J Philos 87:389–407, 2009) analysis of oppressive speech, including against (...)
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  34. The dynamics of vagueness.Chris Barker - 2002 - Linguistics and Philosophy 25 (1):1-36.
  35.  13
    Action Research: A Methodology for Change and Development.Chris Kyriacou - 2007 - British Journal of Educational Studies 55 (4):468-469.
  36. 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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  37. Metaphysics and Agency in Guo Xiang's Commentary on the Zhuangzi.Chris Fraser - forthcoming - In David Chai (ed.), Dao Companion to Xuanxue.
     
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  38.  95
    Action understanding as inverse planning.Chris L. Baker, Rebecca Saxe & Joshua B. Tenenbaum - 2009 - Cognition 113 (3):329-349.
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  39. An Ethics of Philosophical Belief: The case for personal commitments.Chris Ranalli - forthcoming - In Sandy Goldberg & Mark Walker (eds.), Attitude in Philosophy. Oxford University Press.
    What should we do when faced with powerful theoretical arguments that support a severe change in our personal beliefs and commitments? For example, what should new parents do when confronted by unanswered anti-natalist arguments, or two lovers vexed by social theory that apparently undermines love? On the one hand, it would be irrational to ignore theory just because it’s theory; good theory is evidence, after all. On the other hand, factoring in theory can be objectifying, or risks unraveling one's life, (...)
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  40. 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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  41.  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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  42. 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 (...)
  43. 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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  44. Is Radical Doubt Morally Wrong?Chris Ranalli - forthcoming - Erkenntnis.
    Is radical skepticism ethically problematic? This paper argues that it is. Radical skepticism’s strong regulation of our doxastic economy results in us having to forego doxastic commitments that we owe to others. Whatever skepticism’s epistemic defects, it is ethically defective. In turn, I defend Moralism, the view that the kind of extreme doubt characteristic of radical skepticism is a serious moral and eudaimonic weakness of radical skeptical epistemology. Whether this means that skepticism is false or incorrect, however, is a further (...)
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  45. Justice and Attachment to Natural Resources.Chris Armstrong - 2013 - Journal of Political Philosophy 22 (1):48-65.
  46.  6
    Time to treat the climate and nature crisis as one indivisible global health emergency.Chris Zielinski - 2024 - Journal of Medical Ethics 50 (3):2-2.
    Over 200 health journals call on the United Nations (UN), political leaders and health professionals to recognise that climate change and biodiversity loss are one indivisible crisis and must be tackled together to preserve health and avoid catastrophe. This overall environmental crisis is now so severe as to be a global health emergency. The world is currently responding to the climate crisis and the nature crisis as if they were separate challenges. This is a dangerous mistake. The 28th Conference of (...)
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  47. Finding a Way Together: Interpersonal Ethics in Zhuangzi.Chris Fraser - forthcoming - In Dao Companion to Zhuangzi.
     
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  48.  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.
  49. 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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  50. 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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