Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

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 (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

In this volume, leading philosophers of psychiatry examine psychiatric classification systems, including the Diagnostic and Statistical Manual of Mental Disorders, asking whether current systems are sufficient for effective diagnosis, treatment, and research. Doing so, they take up the question of whether mental disorders are natural kinds, grounded in something in the outside world. Psychiatric categories based on natural kinds should group phenomena in such a way that they are subject to the same type of causal explanations and respond similarly to (...) the same type of causal interventions. When these categories do not evince such groupings, there is reason to revise existing classifications. The contributors all question current psychiatric classifications systems and the assumptions on which they are based. They differ, however, as to why and to what extent the categories are inadequate and how to address the problem. Topics discussed include taxometric methods for identifying natural kinds, the error and bias inherent in DSM categories, and the complexities involved in classifying such specific mental disorders as "oppositional defiance disorder" and pathological gambling. -/- Contributors George Graham, Nick Haslam, Allan Horwitz, Harold Kincaid, Dominic Murphy, Jeffrey Poland, Nancy Nyquist Potter, Don Ross, Dan Stein, Jacqueline Sullivan, Serife Tekin, Peter Zachar. (shrink)

This article tackles the sole surviving ancient commentary on what was perhaps the second most important Platonic work, with special interest for the manner in which the ancients tackled the setting of Plato's dialogues, Socratic ignorance, Socratic eros, the central myth-like Palinode, and the question of oral as against written teaching.

This paper considers two reasons that might support Russell’s choice of a ramified-type theory over a simple-type theory. The first reason is the existence of purported paradoxes that can be formulated in any simple-type language, including an argument that Russell considered in 1903. These arguments depend on certain converse-compositional principles. When we take account of Russell’s doctrine that a propositional function is not a constituent of its values, these principles turn out to be too implausible to make these arguments troubling. (...) The second reason is conditional on a substitutional interpretation of quantification over types other than that of individuals. This reason stands up to investigation: a simple-type language will not sustain such an interpretation, but a ramified-type language will. And there is evidence that Russell was tacitly inclined towards such an interpretation. A strong construal of that interpretation opens a way to make sense of Russell’s simultaneous repudiation of propositions and his willingness to quantify over them. But that way runs into trouble with Russell’s commitment to the finitude of human understanding. (shrink)

A model-theoretic approach to the semantics of set-theoretic discourse.

What responsibilities do audiences have in engaging with artworks? Certain audience responses seem quite clear: for example, audiences should not vandalize or destroy artworks; they should not disrupt performances. This paper examines other kinds of resisting responses that audiences sometimes engage in, including petitioning the artist to change their works, altering copies of artworks, and creating new artworks in another artist’s fictional world. I argue for five claims: (1) while these actions can sometimes infringe on the rights of artists, the (...) rights of artists are not absolute; (2) the fact that such actions are based on mistaken interpretations of the artworks has no normative weight; (3) there can be reason to object to additions and alterations whose conception of the artwork is morally worse than the original (and so, there can be reason to support additions and alterations whose conception is morally better); (4) petitioning raises special moral problems; and, most important, (5) some of these actions are valuable because they involve creative and aesthetic activity. Those acts of audience resistance that are creative, morally improve on the original work, and that minimize the infringement of the artists’ rights are good, and should be encouraged. (shrink)

This paper has three aims: to define autonomism clearly and charitably, to offer a positive argument in its favour, and to defend a larger view about what is at stake in the debate between autonomism and its critics. Autonomism is here understood as the claim that a valuer does not make an error in failing to bring her moral and aesthetic judgements together, unless she herself values doing so. The paper goes on to argue that reason does not require the (...) valuer to make coherent her aesthetic and moral evaluations. Finally, the paper shows that the denial of autonomism has realist commitments that autonomism does not have, and concludes that issues of value realism and irrealism are relevant to the debates about autonomism in ways that have not hitherto been recognized. (shrink)

Relative to any reasonable frame, satisfiability of modal quantificational formulae in which “= ” is the sole predicate is undecidable; but if we restrict attention to satisfiability in structures with the expanding domain property, satisfiability relative to the familiar frames (K, K4, T, S4, B, S5) is decidable. Furthermore, relative to any reasonable frame, satisfiability for modal quantificational formulae with a single monadic predicate is undecidable ; this improves the result of Kripke concerning formulae with two monadic predicates.

This article explores problems with several definitions of Originalism proposed by Justice Scalia in "Reading Law: The Interpretation of Legal Texts." It begins by looking at Justice Scalia's citation of a possible statement by Queen Anne that Justice Scalia claims in itself justifies Originalism. Queen Anne may have told Sir Christopher Wren that St. Paul's Cathedral was "awful, artificial, and amusing" at a time when those words meant "awe-inspiring, highly artistic, and thought-provoking." Conceding that one must understand how Queen Anne (...) meant these terms, this article shows how this example actually undermines Originalism when applied to on-going rules. It also explores inconsistencies and problems with several definitions of Originalism including Justice Scalia's arbitrary exclusion of technology from the constraints of "original meaning." It further disputes his claim that Originalism ". . .will narrow the range of acceptable judicial decision-making and acceptable argumentation [and that it] will curb -- even reverse -- the tendency of judges to imbue authoritative texts with their own policy preferences." This article maintains that Originalism has the opposite effect. -/- Keywords: originalism, original meaning, Scalia, interpretation, meaning. (shrink)

Immoralists hold that in at least some cases, moral fl aws in artworks can increase their aesthetic value. They deny what I call the valence constraint: the view that any effect that an artwork’s moral value has on its aesthetic merit must have the same valence. The immoralist offers three arguments against the valence constraint. In this paper I argue that these arguments fail, and that this failure reveals something deep and interesting about the relationship between cognitive and moral value. (...) In the fi nal section I offer a positive argument for the valence constraint. (shrink)

Divers presents a set of de re modal truths which, he claims, are inconvenient for Lewisean modal realism. We argue that there is no inconvenience for Lewis.

Ancient Chinese and Greek thinkers alike were preoccupied with the moral value of music; they distinguished between good and bad music by looking at the music’s effect on moral character. The idea can be understood in terms of two closely related questions. Does music have the power to affect the ethical character of either listener or performer? If it does, is it better as music for doing so? I argue that an affirmative answers to both questions are more plausible than (...) it might seem at first. (shrink)

Logicism is, roughly speaking, the doctrine that mathematics is fancy logic. So getting clear about the nature of logic is a necessary step in an assessment of logicism. Logic is the study of logical concepts, how they are expressed in languages, their semantic values, and the relationships between these things and the rest of our concepts, linguistic expressions, and their semantic values. A logical concept is what can be expressed by a logical constant in a language. So the question “What (...) is logic?” drives us to the question “What is a logical constant?” Though what follows contains some argument, limitations of space constrain me in large part to express my Credo on this topic with the broad brush of bold assertion and some promissory gestures. (shrink)

31 chapters covering the Old Academy to Late Antiquity. See attached TOC.

Aesthetic internalism claims a link between judgement and motivation: aesthetic judgements bring with them motivations to act in characteristic ways. Critics object that there is a difference between merely liking something and judging it to be aesthetically good, and that it is our likings, not our aesthetic judgements, that motivate us. This paper develops a version of aesthetic internalism that can respond to this criticism. Wholehearted aesthetic judgements are characterized by stability, attention, and motivation. Making such judgements is an important (...) part of a good life, and so at least some aesthetic judgements are motivating. So we have reason to think that this version of aesthetic internalism is true. This paper defends wholehearted aesthetic internalism against objections, and assesses an argument from aesthetic internalism to aesthetic non-cognitivism. While wholehearted aesthetic internalism can only offer qualified support to non-cognitivism, it nonetheless offers a number of fruitful avenues for further work. (shrink)

Discourse carries thin commitment to objects of a certain sort iff it says or implies that there are such objects. It carries a thick commitment to such objects iff an account of what determines truth-values for its sentences say or implies that there are such objects. This paper presents two model-theoretic semantics for mathematical discourse, one reflecting thick commitment to mathematical objects, the other reflecting only a thin commitment to them. According to the latter view, for example, the semantic role (...) of number-words is not designation but rather the encoding of cardinality-quantifiers. I also present some reasons for preferring this view. (shrink)

The topic of this essay is how non-realistic novels challenge our philosophical understanding of the moral significance of literature. I consider just one case: Joseph Heller’s Catch-22. I argue that standard philosophical views, based as they are on realistic models of literature, fail to capture the moral significance of this work. I show that Catch-22 succeeds morally because of the ways it resists using standard realistic techniques, and suggest that philosophical discussion of ethics and literature must be pluralistic if it (...) is to include all morally salient literature, and not just novels in the “Great Tradition” and their ilk. (shrink)

This paper and its sequel “look under the hood” of the usual sorts of proof-theoretic systems for certain well-known intuitionistic and classical propositional modal logics. Section 1 is preliminary. Of most importance: a marked formula will be the result of prefixing a formula in a propositional modal language with a step-marker, for this paper either 0 or 1. Think of 1 as indicating the taking of “one step away from 0.” Deductions will be constructed using marked formulas. Section 2 presents (...) the model-theoretic concepts, based on those in [7], that guide the rest of this paper. Section 3 presents Natural Deduction systems IK and CK, formalizations of intuitionistic and classical one-step versions of K. In these systems, occurrences of step-markers allow deductions to display deductive structure that is covered over in familiar “no step” proof-theoretic systems for such logics. Box and Diamond are governed by Introduction and Elimination rules; the familiar K rule and Necessitation are derived (i.e. admissible) rules. CK will be the result of adding the 0-version of the Rule of Excluded Middle to the rules which generate IK. Note: IK is the result of merely dropping that rule from those generating CK, without addition of further rules or axioms (as was needed in [7]). These proof-theoretic systems yield intuitionistic and classical consequence relations by the obvious definition. Section 4 provides some examples of what can be deduced in IK. Section 5 defines some proof-theoretic concepts that are used in Section 6 to prove the soundness of the consequence relation for IK (relative to the class of models defined in Section 2.) Section 7 proves its completeness (relative to that class). Section 8 extends these results to the consequence relation for CK. (Looking ahead: Part 2 will investigate one-step proof-theoretic systems formalizing intuitionistic and classical one-step versions of some familiar logics stronger than K.). (shrink)

© British Society of Aesthetics 2018. Published by Oxford University Press on behalf of the British Society of Aesthetics. All rights reserved. For Permissions, please email: [email protected] adaptation of literary works into films has been almost completely neglected as a philosophical topic. I discuss two questions about this phenomenon:What do we mean when we say that a film is faithful to its source?Is being faithful to its source a merit in a film adaptation?In response to, I set out two distinct (...) senses of fidelity: story fidelity and thematic fidelity. I then argue, in response to, that thematic fidelity, but not story fidelity, is an aesthetic merit in a film adaptation. The key steps in this argument involve showing that merely preserving the story from one medium to another does not typically involve an aesthetically... (shrink)

I explore the claim that “fictive imagining” – imagining what it is like to be a character – can be morally dangerous. In particular, I consider the controversy over William Styron’s imagining the revolutionary protagonist in his Confessions of Nat Turner. I employ Ted Cohen’s model of fictive imagining to argue, following a generally Kantian line of thought, that fictive imagining can be dangerous if one has the wrong motives. After considering several possible motives, I argue that only internally directed (...) motives can satisfy the moral concern. Finally, I suggest that when one has the right motives, fictive imagining is morally praiseworthy since it improves one’s ability to imagine the lives of others. (shrink)

This article briefly addresses the following questions: Why should we study narrative? Does narrative have a basic overarching form or forms? How does framing drive narrative? How do concepts drive narrative? What can we do when we lack the necessary concepts for the narrative we need to tell? Are there basic storylines that repeat? Are there basic character types that we reuse? Can narrative drive the results of a Supreme Court case? Can narrative drive transactional practice? How does narrative's importance (...) underscore the importance of an education in the humanities? (shrink)

One important but infrequently discussed difficulty with expressivism is the attitude type individuation problem.1 Expressivist theories purport to provide a unified account of normative states. Judgments of moral goodness, beauty, humor, prudence, and the like, are all explicated in the same way: as expressions of attitudes, what Allan Gibbard calls “states of norm-acceptance”. However, expressivism also needs to explain the difference between these different sorts of attitude. It is possible to judge that a thing is both aesthetically good and morally (...) bad. While the realist can explain the difference by suggesting that each judgment makes reference to a different property (or set of properties), the expressivist cannot. She must show that what is expressed by the speaker is different in each case. This has proven to be difficult to do. (shrink)

In recent years it has become more and more difficult to distinguish between metaethical cognitivism and non-cognitivism. For example, proponents of the minimalist theory of truth hold that moral claims need not express beliefs in order to be (minimally) truth-apt, and yet some of these proponents still reject the traditional cognitivist analysis of moral language and thought. Thus, the dispute in metaethics between cognitivists and non-cognitivists has come to be seen as a dispute over the correct way to characterize our (...) psychology: are moral judgments beliefs, or a kind of pro-attitude? In this paper, I argue that this distinction, too, is difficult to maintain in the light of a reasonable skepticism about folk psychology. I conclude by suggesting some new possibilities for the analysis of moral language that look beyond this distinction. I begin by briefly reviewing some contemporary positions in metaethics on cognitivism and non-cognitivism, that are intended to emphasize the supposed psychological differences between the two views. I show that the appearance of a clear difference between these views depends on one's having a very strong commitment to the context-independence and completeness of certain concepts of folk psychology. I then argue for a moderate skepticism about folk psychology. I conclude that folk concepts like ?belief? are not sufficiently well-defined to settle this metaethical dispute. (shrink)

Where $\underline{a}$ is a Turing degree and ξ is an ordinal $ , the result of performing ξ jumps on $\underline{a},\underline{a}^{(\xi)}$ , is defined set-theoretically, using Jensen's fine-structure results. This operation appears to be the natural extension through $(\aleph_1)^{L^\underline{a}}$ of the ordinary jump operations. We describe this operation in more degree-theoretic terms, examine how much of it could be defined in degree-theoretic terms and compare it to the single jump operation.

The paper discusses the arguments for and against animalism and concludes that a pluralist position which rejects animalism and embraces a multiplicity of thinkers is the best option.

Biomedical science has been remarkably successful in explaining illness by categorizing diseases and then by identifying localizable lesions such as a virus and neoplasm in the body that cause those diseases. Not surprisingly, researchers have aspired to apply this powerful paradigm to addiction. So, for example, in a review of the neuroscience of addiction literature, Hyman and Malenka (2001, p. 695) acknowledge a general consensus among addiction researchers that “[a]ddiction can appropriately be considered as a chronic medical illness.” Like other (...) diseases, “Once addiction has taken hold, it tends to follow a chronic course.” (Koob and La Moal 2006, p. ?). Working from this perspective, much effort has gone into characterizing the symptomology of addiction and the brain changes that underlie them. Evidence for involvement of dopamine transmission changes in the ventral tegmental area (VTA) and nucleus accumbens (NAc) have received the greatest attention. Kauer and Malenka (2007, p. 844) put it well: “drugs of abuse can co-opt synaptic plasticity mechanisms in brain circuits involved in reinforcement and reward processing”. Our goal in this chapter to provide an explicit description of the assumptions of medical models, the different forms they may take, and the challenges they face in providing explanations with solid evidence of addiction. <br>. (shrink)

Coincidence comes in two varieties – permanent and temporary. Moderate monism is the position that permanent coincidence, but not temporary coincidence, entails identity. Extreme monism is the position that even temporary coincidence entails identity. Pluralists are opponents of monism tout court. The intuitively obvious, commonsensical position is moderate monism. It is therefore important to see if it can be sustained.

In this essay I argue that if Kantian and consequentialist ethical theories are vulnerable to the so-called “problem of alienation,” a virtue ethics based on Xunzi’s ethical writings will also be vulnerable to this problem. I outline the problem of alienation, and then show that the role of ritual ( li ) in Xunzi’s theory renders his view susceptible to the problem as it has been traditionally understood. I consider some replies on Xunzi’s behalf, and also discuss whether the problem (...) affects other Confucian and eudaimonian approaches to virtue ethics. I close by considering some solutions to the problem and the affect that this result has on the argumentative dialectic between the three major ethical traditions. (shrink)

Contrary to economics or history, for example, there does not exist an organized field dedicated to the philosophy of political science. Given that the philosophical issues raised by political science research are just as pressing and vibrant as those raised in these more organized fields, fostering a field that labels itself Philosophy of Political Science (PoPS) is important. PoPS is advanced here as a fruitful meeting place where both philosophers and practicing political scientists contribute and discuss—with philosophical discussions that are (...) close to and informed by actual developments in political science, making philosophy of science continuous with the sciences in line with contemporary naturalist philosophy of science. The topics scrutinized in the different chapters of the Handbook will figure prominently in PoPS, as we lay out in this chapter. (shrink)

In this chapter, which is purely exegetical, I suggest that close attention to the legacy of Anscombe’s mentor Wittgenstein can shed some unaccustomed light both on the idiosyncratic form of inquiry in her book Intention and on some of the particular conclusions found in that book. In the first part, I point to a methodological parallel between Wittgenstein’s post-1945 investigations into the nature of everyday psychological concepts and Anscombe’s treatment of the concept of intention. In the second part, the Wittgensteinian (...) provenance of Anscombe’s logical category ‘knowledge without observation’ is exhibited, and her extension of what falls under this form of knowledge (from Wittgenstein’s case of knowing the arrangement of one’s limbs, to matters concerning intention as well) is outlined. This extension will require a twist in how the intentional form of such knowledge is regarded as corrigible. Finally, I identify the odd form of knowledge just explicated with ‘practical knowledge’ as Anscombe sees it, and try to show that some puzzles revolving around her invocation of Theophrastus’ principle and Aquinas’ view of the causal power of practical knowledge may be resolved thereby. (shrink)