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 (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (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)

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)

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)

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)

© 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: journals.permissions@oup.comThe 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)

Two recent novels, Ian McEwan’s Atonement and Margaret Atwood’s The Blind Assassin, are philosophically instructive. These books are interesting, I argue, because they reveal something about understanding and appreciating narrative. They show us that audience’s participation in narrative is much more subtle and complex than philosophers generally acknowledge. An analysis of these books reveals that narrative imagining is not static or unified, but dynamic and multipolar. I argue that once the complexity of narrative engagement is better understood, some prominent philosophical (...) problems and debates concerning narrative dissolve. (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)

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)

Some films scare us; some make us cry; some thrill us. Some of the most interesting films, however, leave us suspended between feelings – both joyous and sad, or angry and serene. This paper attempts to explain how this can happen and why it is important. I look closely at one film that creates and exploits these conflicted responses. I argue that cases of conflict in film illuminate a pair of vexing questions about emotion in film: (1) To what extent (...) are emotional responses rational, or in need of rationalization?; and (2) What relationship is there between emotional response and value (moral, filmic, or otherwise)? Conflict, I argue, can be revealing, and can help us better understand emotional responses to narrative film1 in general. The paper is divided into four sections. First, I sketch a theory of emotional engagement that makes sense of the notion of a “conflicted emotional response” to a film. Second, I turn to a particular case of a film that produces this sort of conflict, Fritz Lang’s M (1931), and show that the conflict engendered by that film is both more significant and less unusual than it may appear. In the final two sections, I argue that there is no need to rationalize or make consistent such mixed emotional responses, and that there is real moral, aesthetic, and cognitive value to be had from such conflict. (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)

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)

Psychopaths are the bugbears of moral philosophy. They are often used as examples of perfectly rational people who are nonetheless willing to do great moral wrong without regret; hence the disorder has received the epithet “moral insanity” (Pritchard 1835). But whereas philosophers have had a great deal to say about psychopaths’ glaring and often horrifying lack of moral conscience, their aesthetic capacities have received hardly any attention, and are generally assumed to be intact or even enhanced. Popular culture often portrays (...) psychopaths in ways that suggest a great gap between their amorality and their aesthetic sensitivity. In The Silence of the Lambs (Jonathan Demme, 1991), Hannibal Lecter appreciates fine art, fashion, and wine, while he eats his way through his enemies. His real-life counterparts, however, do not demonstrate the same sensitivities. There is no evidence that psychopaths are capable of real aesthetic appreciation, and some evidence that they are not. In this paper, we set out the limited evidence for the psychopath’s deficient aesthetic sensitivity. The best explanations of what the psychopath lacks turn out to implicate abilities that are also thought to be central to moral thought and action: an impaired capacity for empathizing with others and deficient ability to take a disinterested attitude towards things (socalled distance). We endorse the latter explanation. Thinking about what underlies the psychopath’s deficient aesthetic understanding turns out to throw light on a difficult problem: the connection between ethics and aesthetics. (shrink)

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)

Discerning the decisionmaking of Kim Jong-Un and the North Korean regime on issues of peaceful engagement and warlike actions endures as a mighty challenge for U.S. intelligence analysts and policymakers. In this report, we seek to inform analysis of Democratic People’s Republic of Korea (DPRK) leadership decisionmaking. To do so, we use three discussion papers that were written to facilitate discussion of an interagency working group. The three papers are assembled here in a single report. The first discussion paper describes (...) decisionmaking among different authoritarian regimes, including North Korea, and the opening up of those economies to outside engagement. The second paper outlines two different scenarios that might occur when conventional deterrence on the Korean Peninsula breaks down and the resulting decisions that North Korea’s leadership could face. The third paper assesses DPRK decisionmaking about nuclear weapon use. The report concludes with some observations, drawn from the issues covered in these three discussion papers, about DPRK decisionmaking and stability on the Korean Peninsula. (shrink)

This volume, a lightly-edited version of Professor Samuel Scolnicov’s 1974 Ph.D. thesis, is a fitting tribute to his impressive career. It will perhaps be most useful for those interested in better understanding Scolnicov’s work and his views on Plato as a whole, not least for the comprehensive list of his publications that requires a full twelve pages of print. Scholars with an interest in Plato’s method of hypothesis will also find some useful remarks on key passages in the Meno, Phaedo, (...) and Republic as well as on Greek mathematical analysis.Illuminating other aspects of Scolnicov’s work is clearly part of the intention behind enabling broader access to this study. As Harold Tarrant notes in his introduction... (shrink)

This essay interrogates the philosophy of Pinter through analyses of his language, religious understanding of life and through passing references to Buddhism.

Today's academia is obsessed about writing and speaking gobbledygook. At least most of the time. It has little time in sitting still and actually reading fiction, poetry and say, Wittgenstein. One pretends to say fancy things about these authors but one does not actually read books anymore. COVID 19 Lockdown prompted this author to answer queries from students and peers about a reading list. So prepare a wide ranging list he did which covers everything from the version of Mahabharata one (...) ought to read to novels on celibacy. But then he chose to publish at Prabuddha Bharata over all other platforms because the Ramakrishna Mission has the finances to keep this list alive 200 years hence. This was written during COVID 19 Lockdown in India at the end of April, 2020. Nirad C Chaudhuri insisted on making a good bibliography in his magnum opus. This author follows Nirad C Chaudhuri in quietly speaking about how Harold Bloom plagiarised the Late Professor John Senior's reading list. The list also comments on Romanticism and the art of writing itself. The list on Hinduism is truly contrarian. One hopes that this list survives when GoodReads and other Listopias are no longer. -/- Today's academia is obsessed about writing and speaking gobbledygook. At least most of the time. It has little time in sitting still and actually reading fiction, poetry and say, Wittgenstein. One pretends to say fancy things about these authors but one does not actually read books anymore. COVID 19 Lockdown prompted this author to answer queries from students and peers about a reading list. So prepare a wide ranging list he did which covers everything from the version of Mahabharata one ought to read to novels on celibacy. But then he chose to publish at Prabuddha Bharata over all other platforms because the Ramakrishna Mission has the finances to keep this list alive 200 years hence. This was written during COVID 19 Lockdown in India at the end of April, 2020. Nirad C Chaudhuri insisted on making a good bibliography in his magnum opus. This author follows Nirad C Chaudhuri in quietly speaking about how Harold Bloom plagiarised the Late Professor John Senior's reading list. The list also comments on Romanticism and the art of writing itself. The list on Hinduism is truly contrarian. One hopes that this list survives when GoodReads and other Listopias are no longer. -/- These COVID 19 days, while the First world is mooning over syllabi for their kids and third and fourth world folks like me are tackling Umphan; I chose to prepare a new kind of syllabus. A syllabus which is not merely a list. In these days of incessant and meaningless webinars which my students can only spread memes about and only the poor and doctors will actually travel to white nations which are killing their own; here's a list which ends with Hindu classics which are contrarian. Nirad C Chaudhuri, a much maligned man in India and a forgotten polyglot in white privileged academia said we must first prepare a bibliography. So, Figure it out. I used some of the Hindu resources on recognition mentioned here and tried to work on Stephen King; a privileged white tenure track person from Trumpland just snowballed me. Now, this list is syllabi and also just a list of a bunch of books to read during Lockdowns which will be more common in the future because COVID 19, as Dr Fauci tells us; is here to stay. Even if one COVID 19 person is there; then along with Ebola, my white privileged tenure track fiends; off you go to gagaland. We in India already know these diseases. Go figure it out. (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)

The meta-problem of consciousness is the problem of explaining why we have the intuition that there is a hard problem of consciousness. David Chalmers briefly notes that my phenomenal powers view may be able to answer to this challenge in a way that avoids problems (having to do with avoiding coincidence) facing other realist views. In this response, I will briefly outline the phenomenal powers view and my main arguments for it and—drawing in part on a similar view developed by (...) Harold Langsam—discuss how more precisely its answer to the challenge would go. (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)

This paper examines Harold Garfinkel's notion of the natural attitude about sex and his claim that it is fundamentally moral in nature. The author looks beneath the natural attitude in order to explain its peculiar resilience and oppressive force. There she reveals a moral order grounded in the dichotomously sexed bodies so constituted through boundaries governing privacy and decency. In particular, naked bodies are sex-differentiated within a system of genital representation through gender presentation—a system that helps constitute the very (...) boundaries between the public and private. (shrink)

Divers (2014) 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.

At the centre of the monograph (1984, first edition) lies a detailed interpretation and critique of the idea of the Good in the Republic. The main thesis of the interpretation runs as follows: The idea of the Good functions as a third item between thinking and being. The main purpose of the monograph is to introduce the systematic problem of the third item via the historical problem of the idea of the Good. The second, enlarged edition (1989) gives a new (...) reconstruction of an "exasperatingly difficult but ever fascinating topic" (H. Cherniss), that is, of the platonic theory of the ideal numbers and the two principles that were contained in the “so-called unwritten doctrines” (Aristotle). The final chapter gives new information on the reception of Plato's idea of the Good in P. Natorp and M. Heidegger. It also includes an updated bibliography. The third edition (2015) is a reprint of the second edition of 1989. Further remarks and an updated bibliography to 2005 are to be found in: - Ferber, Rafael (2005). Ist die Idee des Guten nicht transzendent oder ist sie es doch? Nochmals Platons ΕΠΕΚΕΙΝΑ ΤΗΣ ΟΥΣΙΑΣ. In: Barbaric Damir: Platon über das Gute und die Gerechtigkeit / Plato on Goodness and Justice / Platone sul Bene e sulla Giustizia. Würzburg, 149-174.:www.zora.uzh.ch/34098/ - Ferber, Rafael / Damschen, Gregor (2015). Is the Idea of the Good Beyond Being? Plato's "epekeinea tês ousias" Revisted (Republic, 6, 509b8-10). In: Nails, Debra; Harold, Tarrant; Kajava, Mika; Salmenkivi, Eero. Second Sailing: Alternative Perspectives on Plato. Espoo, 197-203: http://www.zora.uzh.ch/116007/. (shrink)

In his book The Things We Mean, Stephen Schiffer advances a subtle defence of what he calls the ‘face-value’ analysis of attributions of belief and reports of speech. Under this analysis, ‘Harold believes that there is life on Venus’ expresses a relation between Harold and a certain abstract object, the proposition that there is life on Venus. The present essay first proposes an improvement to Schiffer’s ‘pleonastic’ theory of propositions. It then challenges the face-value analysis. There will be (...) such things as propositions only if they possess conditions of identity and distinctness. By analyzing Frege’s theory of propositions (Gedanken), I argue that such conditions may be found for the special case of beliefs and sayings advanced as premises and conclusions of deductive arguments. These conditions, however, are not applicable to most ordinary beliefs and sayings. Ordinary attributions and reports, then, do not place thinkers and speakers in relations to propositions. A bonus is exposure of the fallacy in the Putnam-Taschek objection to Frege’s theory of sense and reference. (shrink)

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)

Physicians in Islamic countries might be requested to participate in the Islamic legal code of qiṣāṣ, in which the victim or family has the right to an eye-for-an-eye retaliation. Qiṣāṣ is only used as a punishment in the case of murder or intentional physical injury. In situations such as throwing acid, the national legal system of some Islamic countries asks for assistance from physicians, because the punishment should be identical to the crime. The perpetrator could not be punished without a (...) physician’s participation, because there is no way to guarantee that the sentence would be carried out without inflicting more injury than the initial victim had suffered. By examining two cases of acid throwing, this paper discusses issues related to physicians’ participation in qiṣāṣ from the perspective of medical ethics and Islamic Shari’a law. From the standpoint of medical ethics, physicians’ participation in qiṣāṣ is not appropriate. First, qiṣāṣ is in sharp contrast to the Hippocratic Oath and other codes of medical ethics. Second, by physicians’ participation in qiṣāṣ, medical practices are being used improperly to carry out government mandates. Third, physician participation in activities that cause intentional harm to people destroys the trust between patients and physicians and may adversely affect the patient–physician relationship more generally. From the standpoint of Shari’a, there is no consensus among Muslim scholars whether qiṣāṣ should be performed on every occasion. We argue that disallowing physician involvement in qiṣāṣ is necessary from the perspectives of both medical ethics and Shari’a law. (shrink)

Wittgenstein's lack of sympathy for Shakespeare's works has been well noted by George Steiner and Harold Bloom among others. Wittgenstein writes in 1950, for instance: "It seems to me as though his pieces are, as it were, enormous sketches, not paintings; as though they were dashed off by someone who could permit himself anything, so to speak. And I understand how someone may admire this & call it supreme art, but I don't like it." Of course, the animosity of (...) one great mind for another has its own interest. But the interest here is increased by two factors: (1) Wittgenstein's brief but specific critique of Shakespeare's similes, of interest particularly since he identifies his own philosophical strength half-deprecatingly but still seriously as one of crafting beautiful similes; and (2) Wittgenstein's and Shakespeare's shared concern, as revealed in Stanley Cavell's writings, with the human impulse to skepticism. The present paper considers the importance of these two factors in weighing Wittgenstein's judgment. It suggests that Wittgenstein's frequent charge that Shakespeare is "completely unrealistic" is not a misunderstanding of the Bard (Wittgenstein distinguishes his "failure to understand" from others' willingness to misunderstand Shakespeare) but rather an expression of Wittgenstein's anxiety over Shakespeare's wholly original use of language to represent the sound of the raw motives to skepticism. (shrink)

This essay develops standards for grading religions including various forms of spiritualism. First, I examine the standards proposed by William James, John Hick, Paul Knitter, Dan Cohn-Sherbok, and Harold Netland. Most of them are useful in grading religions with or without conditions. However, those standards are not enough for refined and piercing evaluation. Thus, I introduce standards used in spiritualism. Although those standards are for grading spirits and their teachings, they are useful in refined and piercing evaluation of religious (...) phenomena. The spiritual standards complement James's, Hick's, Knitter's, and Netland's standards. Although most of the spiritual standards are rationally unjustifiable, they have practical value. (shrink)

Harold Noonan has recently argued (2003) that one of Lewis’s (1983: 76– 77) arguments for the view that objects persist by perduring is flawed. Lewis’s argument can be divided into two main sections, the first of which attempts to show that it is possible that there exists a world of temporal parts or stages, and the second, which attempts to show that our world is such a world. Noonan claims that there is a flaw in each of these two (...) stages.We argue to the contrary. (shrink)

Respect for victims requires that we have social systems for punishing and condemning (reproving) serious crimes. But, the conditions of social marginalization and political subordination of the communities from which an overwhelming number of prisoners in the United States come place serious barriers in the face of effective reprobation. Mass incarceration makes this problem worse by disrupting and disrespecting entire communities. While humanities education in the prisons is far from a total solution, it is one way to make reprobation meaningful, (...) so long as the prison classroom is a place where the educators’ values are also put at risk. (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.

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)

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)

In a recent article, Harold Noonan argues that application conditions and criteria of identity are not distinct from one another. This seems to threaten the standard approach to distinguishing sortals from adjectival terms. I propose that his observation, while correct, does not have this consequence. I present a simple scheme for distinguishing sortals from adjectival terms. I also propose an amended version of the standard canonical form of criteria of identity.

This article examines the influence of the Persian mystic poet Hafi z on western poets. Interest in Hafiz started in England in the eighteenth century with the translations of Sir William Jones. In the nineteenth century, the German translation of Baron von HammerPurgstall inspired Goethe to create his masterpiece Westöstliche Divan (West-Eastern Divan). The poetry of Hafiz evoked such passion in Goethe that he referred to him as ‘Saint Hafiz’ and ‘Celestial Friend’. Inspired by Westöstliche Divan, a number of German (...) poets including Rückert and Platen composed volumes of poetry on the model of ghazal, the popular poetic form perfected by Hafi z in Persian literature. Prominent among the German thinkers influenced and fascinated by Hafiz was Friedrich Nietzsche who repeatedly mentioned him in his works. The influence of Hafiz stretched to America in 1838 when Ralph Waldo Emerson read Goethe’s West-Eastern Divan. In Hafiz, Emerson found a man who derived pleasure in the very elements which others found mean. Under the influence of Hafiz’s Saki-nameh or the Book of Wine, he created his finest poem Bacchus which, according to Harold Bloom, set the terms for the dialectic of American poetry. (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 central claim of the Parfitian psychological approach to personal identity is that the fact about personal identity is underpinned by a non-branching psychological continuity relation. Hence, for the advocates of the Parfitian view, it is important to understand what it is for a relation to take or not take a branching form. Nonetheless, very few attempts have been made in the literature of personal identity to define the non-branching clause. This paper undertakes this task. Drawing upon a recent debate (...) between Anthony Brueckner and Harold Noonan on the issue, I present three candidates for the non-branching clause. (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.

Harold Hodes in [1] introduces an extension of first-order modal logic featuring a backtracking operator, and provides a possible worlds semantics, according to which the operator is a kind of device for ‘world travel’; he does not provide a proof theory. In this paper, I provide a natural deduction system for modal logic featuring this operator, and argue that the system can be motivated in terms of a reading of the backtracking operator whereby it serves to indicate modal scope. (...) I prove soundness and completeness theorems with respect to Hodes’ semantics, as well as semantics with fewer restrictions on the accessibility relation. (shrink)

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.