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.

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; 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)

Augustine′s conversion to Christianity in A.D. 386 is a pivotal moment not only in his own life, but in Christian and world history, for the theology of Augustine set the course of theological and cultural development in the western Christian church. But to what exactly was Augustine converted? Scholars have long debated whether he really converted to Christianity in 386, whether he was a Platonist, and, if he adhered to both Platonism and Christianity, which dominated his thought. The debate of (...) the last thirteen decades spans an immense body of literature in multiple languages. In this literature, four major views on Augustine′s conversion may be discerned. The first view is associated with Gaston Boissier and Adolph von Harnack, and was famously championed by Prosper Alfaric: that Augustine in 386 converted to neo-Platonism but not to Christianity. Second, there is the view recently promoted by Catherine Conybeare: that Augustine in 386 converted to Christianity and rejected neo-Platonism. Third, there is the view that he converted to Christianity and was also a neo-Platonist; the most famous adherents of this view are Robert J. O′Connell and Pierre Courcelle. Finally, there is the view recently promoted by Carol Harrison: that Augustine committed to Christianity in 386, yet did not utterly reject neo-Platonism; rather, he aimed to develop a Christian faith that was informed by neo-Platonic insight. In this article, I first explain and distinguish these four general views, and then I explain why I prefer the fourth view. -/- More Info: This is the pre-peer reviewed version of Boone, Mark, "The Role of Platonism in Augustine's 386 Conversion to Christianity," Religion Compass 9.5 (May 2015), 151-61. This article has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/rec3.12149/abstract. (shrink)

J. L. Schellenberg’s Philosophy of Religion argues for a specific brand of sceptical religion that takes ‘Ultimism’ – the proposition that there is a metaphysically, axiologically, and soteriologically ultimate reality – to be the object to which the sceptical religionist should assent. In this article I shall argue that Ietsism – the proposition that there is merely something transcendental worth committing ourselves to religiously – is a preferable object of assent. This is for two primary reasons. First, Ietsism is far (...) more modest than Ultimism; Ietsism, in fact, is open to the truth of Ultimism, while the converse does not hold. Second, Ietsism can fulfil the same criteria that compel Schellenberg to argue for Ultimism. (shrink)

In Heidegger’s Being and Time certain concepts are discussed which are central to the ontological constitution of Dasein. This paper demonstrates the interesting manner in which some of these concepts can be used in a reading of T.S. Eliot’s The Love Song of J. Alfred Prufrock. A comparative analysis is performed, explicating the relevant Heideggerian terms and then relating them to Eliot’s poem. In this way strong parallels are revealed between the two men’s respective thoughts and distinct modernist sensibilities. Prufrock, (...) the protagonist of the poem, and the world he inhabits illustrate poetically concepts such as authenticity, inauthenticity, the ‘they’, idle talk and angst, which Heidegger develops in Being and Time. (shrink)

This paper is a detailed examination of some parts of J. P. Moreland's book on "the argument from consciousness". (There is a companion article that discusses the parts of the book not taken up in this critical notice.).

Review of Craig And Mroeland: *Naturalism: A Critical Analysis*.

J.M. Coetzee’s book, 'Elizabeth Costello' is one of the stranger works to appear in recent years. Yet if we focus our attention on the book’s two chapters dealing with animals, two preoccupations emerge. The first sees Coetzee use animals to evoke a particular conception of ethics, one similar to that of the philosopher Mary Midgley. Coetzee’s second theme connects animals to the phenomena of scapegoating, as it has been characterized by the philosophical anthropologist René Girard. While both themes involve human (...) interactions with animals, each transcends application to that particular issue and raises deeper questions, respectively concerning the foundations of morality and the therapeutic allure of political violence. Making explicit these two preoccupations enhances our understanding of Coetzee’s fiction, particularly Disgrace. However, when Coetzee’s two philosophical strands are analyzed in their own terms, the ethics of sympathy is shown to be a more coherent notion than the understanding of politics he takes over from Girard. (shrink)

In the 20th century among the greatest philosophers and literates there was an ample, ideal, wide ranging forum on the question of Europe to which, following a run already started by F. Nietzsche, M. Heidegger, E. Husserl, P. Valéry, Ortega y Gasset, Nikolaj Berdjaev, and after the second world war G. Gadamer, J. Habermas, J. Derrida and others offered meaningful contributions. The questions were: What will be of the spirit of Europe? What will be of Europe? Europe: quo vadis? The (...) aim of this paper is to articulate the meaningful stages of this historical forum through some essays of mentioned philosophers and literates. The first essay is the conference "Europa und die deutsche Philosophie”, delivered by Heidegger in Rome 1936 at the Kaiser-Wilhelm-Institut, the same year of the publication of Husserl’s Krisis. Thereafter, with the purpose of marking a clear discontinuity between the debate of the first half of the century and the second, I comment on Gadamer’s essay “Europa und die oikoumene”, published half a century after the conference of Heidegger, then the Gadamer’s essay "Das Erbe Europas”, 1989, in which Gadamer deduces on the existential condition of Europeans, today. At the end, I analyze Derrida’s pamphlet "L'autre cap suivi de la démocratie ajournie", English version “The Other Heading: Reflection on Today’s Europe”, that opens with the provocative and heretical Derridean gesture: To which concept, to what real individual, to what entity can we confer today the name of Europe? (shrink)

A brief life sketch of Dr A P J Abdul Kalam.

La metafísica después de ser ignorada por años ha regresado al centro de la escena en la filosofía contemporánea. Tomás de Aquino ha vivido una historia muy parecida, lo que dio nacimiento al tomismo analítico. A pesar de los trabajos desarrollados en esta línea de investigación, la metafísica del Aquinate ha sido fuertemente ignorada. Sin embargo, la metafísica de Tomás de Aquino tiene una ventaja, poco discutida entre los tomistas y tomasinos, y es la de ser una metafísica esencialista. Así, (...) en armonía con el trabajo del metafísico E. J. Lowe, quien presenta su metafísica como “esencialista seria”, se quiere mostrar que la metafísica del Aquinate tiene las mismas virtudes del “esencialismo serio”, lo que permite postularla como una posición válida y plausible para la metafísica contemporánea. (shrink)

F.W.J. Schelling worked on mythological issues through his entire lifetime and it had great influence on his philosophy. Unfortunately, there are very few who make a reference to Schelling while dealing with this matter, and even if they do, they mention only philosophy of revelation, which was developed in the last period of Schelling’s work. Mythological issues appear in Schelling’s works in reference to philosophy of nature, philosophy of identity, as well as to his historiosophy, theory of art, and theological (...) issues. The paper aims at showing that in all those areas myth was not just a minor addition to the Schelling’s theory, but it played an important, often crucial role. (shrink)

Scottish and French Enlightenment J. Mackintosh and the revolution controversy in Great Britain -/- Author / Authors : Dr. Eleni Xilakis Page no. 79-88 Discipline : Political Science/Polity/ Democratic studies Script/language : Roman/English Category : Research paper Keywords: Scottish and French Enlightenment, J. Mackintosh, the revolution controversy in Great Britain.

Rita Widmaier and Malte-Ludolf Babin have done a valuable scholarly service for studies of the early modern European reception of China in collecting letters from Leibniz's extensive correspondence concerning China and translating them from the original Latin and French into German. This multi-lingual and chronologically organized edition gathers letters to and from Leibniz as well as supplementary texts composed between the years 1694 and 1716. It incorporates helpful clarificatory notes as well as an informative and lucid introduction.This edition focuses on (...) the exchanges between Leibniz and the Jesuit theologian and philosopher Barthélemy Des Bosses S.J. and other Jesuits in Europe who were in... (shrink)

Alice Crary has recently developed a radical reading of J. L. Austin's philosophy of language. The central contention of Crary's reading is that Austin gives convincing reasons to reject the idea that sentences have context-invariant literal meaning. While I am in sympathy with Crary about the continuing importance of Austin's work, and I think Crary's reading is deep and interesting, I do not think literal sentence meaning is one of Austin's targets, and the arguments that Crary attributes to Austin or (...) finds Austinian in spirit do not provide convincing reasons to reject literal sentence meaning. In this paper, I challenge Crary's reading of Austin and defend the idea of literal sentence meaning. (shrink)

Book review of 'More Kinds of Being: A Further Study of Individuation, Identity, and the Logic of Sortal Terms'. By E. J. LOWE.

This is a critical review of J. B. Schneewind's Essays on the History of Moral Philosophy which both praises and raises worries about some of the main claims found in select articles in the volume. It engages with Schneewind's remarks on the historiography of moral philosophy.

In recent metaethics, moral realists have advanced a companions-in-guilt argument against moral nihilism. Proponents of this argument hold that the conclusion that there are no categorical normative reasons implies that there are no epistemic reasons. However, if there are no epistemic reasons, there are no epistemic reasons to believe nihilism. Therefore, nihilism is false or no one has epistemic reasons to believe it. While this argument is normally presented as a reply to Mackie, who introduced the term “companions-in-guilt” in his (...) Ethics: Inventing Right and Wrong of 1977, Herbert J. Phillips presented a form of this argument in Ethics in 1940. In this paper, I will discuss Phillips’ version of the companions-in-guilt argument, demonstrate how recent epistemology bears out an important premise of the argument, and compare Phillips’ argument to Derek Parfit’s recent work. (shrink)

On 6 January 1795, the twenty-year-old Schelling—still a student at the Tübinger Stift—wrote to his friend and former roommate, Hegel: “Now I am working on an Ethics à la Spinoza. It is designed to establish the highest principles of all philosophy, in which theoretical and practical reason are united”. A month later, he announced in another letter to Hegel: “I have become a Spinozist! Don’t be astonished. You will soon hear how”. At this period in his philosophical development, Schelling had (...) been deeply under the spell of Fichte’s new philosophy and the Wissenschaftslehre. The text Schelling was writing at the time was the early Vom Ich als Prinzip der Philosophie, though his characterization of this text would much better fit the somewhat later work which is the focus of the current paper: Schelling’s 1801 Darstellung meines System der Philosophie (hereafter: Presentation). The Presentation is a text written more geometrico, following the style of Spinoza’s Ethics. While Spinoza’s influence and inspiration is stated explicitly and unmistakably in Schelling’s preface, the content of this composition might seem quite foreign to Spinoza’s philosophy, so much so, in fact, that Michael Vater—the astute translator and editor of the recent English translation of the text—has contended that “despite the formal similarities between Spinoza’s geometrical method and Schelling’s numbered mathematical-geometrical constructions, Schelling’s direct debts to Spinoza are few”. The Presentation is an extremely dense and difficult text, and while I agree that at first glance Schelling’s engagement with the concept of reason (Vernunft) and the identity formula ‘A=A’ seems to have little if anything to do with Spinoza (especially since Spinoza’s key terminology of ‘God’, ‘causa sui’, ‘substance’, ‘attribute’, and ‘mode’ is barely mentioned in the Presentation), I suspect that at a deeper level Schelling is attempting to transform Spinoza’s system by replacing God, Spinoza’s ultimate reality, with reason. Though this might at first seem bizarre, I believe it can be profitably motivated and explained upon further reflection. It is this transformation of Spinoza’s God into (the early) Schelling’s reason that is the primary subject of this study. I develop this paper in the following order. In the first part I provide a very brief overview of Schelling’s lifelong engagement with Spinoza’s philosophy, which will prepare us for my study of the 1801 Presentation. In the second part, I consider the formal structure and rhetoric of the Presentation against the background of Spinoza’s Ethics, and show how Schelling regularly imitates Spinoza’s tiniest rhetorical gestures. In the third and final part I turn to the opening of the Presentation, and argue that Schelling attempts there to distance himself from Fichte by developing a conception of reason as the absolute, or the identity of the subject and object, just as the thinking substance and the extended substance are identified in Spinoza’s God. (shrink)

This is the review in Polish of the book by J. Barnes "Arystoteles".

Perhaps no other novel has received as much attention from moral philosophers as South African writer J. M. Coetzee’s Disgrace . The novel is ethically compelling and yet no moral theory explains its force. Despite clear Kantian moments, neither rationalism nor self-respect can account for the strange ethical task that the protagonist sets for himself. Calling himself the dog man, like the ancient Cynics, this shamelessly cynical protagonist takes his cues for ethics not from humans but from animals. He does (...) not however claim much in the way of empathy or understanding of animals, and his own odd motives remain a puzzle throughout the stages of his ethical transformation. Many scholars approach Coetzee’s text through an ethics of alterity, and even argue that Disgrace is exemplary in this regard. Kristeva’s rendition of alterity ethics brings us close to the novel’s vision, and yet the novel points towards a more primordial basis for ethics in the search for meaning through the human encounter with other animal species. (shrink)

Wittgenstein’s concepts shed light on the phenomenon of schizophrenia in at least three different ways: with a view to empathy, scientific explanation, or philosophical clarification. I consider two different “positive” wittgensteinian accounts―Campbell’s idea that delusions involve a mechanism of which different framework propositions are parts, Sass’ proposal that the schizophrenic patient can be described as a solipsist, and a Rhodes’ and Gipp’s account, where epistemic aspects of schizophrenia are explained as failures in the ordinary background of certainties. I argue that (...) none of them amounts to empathic-phenomenological understanding, but they provide examples of how philosophical concepts can contribute to scientific explanation, and to philosophical clarification respectively. (shrink)

J. J. OʼDonnell is one those scholars whose learning is assumed rather than displayed. As a result, his brief approach to the long-terms effects of the computer revolution onreading and higher education feels like a bracing, sophisticated exchange of ideas. Like conversation, O'Donnellʼs thesis is not terribly unified or orderly. He often makessidetracks from his focus on high technology and literacy into explaining such interestingthings as how we choose our cultural ancestry instead of merely evolving out of it, the errors (...) of current education, and perhaps more than you ever wanted to know aboutother avatars of the word such as St. Jerome, St. Augustine, and Cassiodorus. Greatcover too. (shrink)

In this paper I take up the question of the possible influence of J. G. Fichte on Wilhelm von Humboldt’s theory of language. I first argue that the historical record is unclear, but show that there is a deep philosophical difference between the two views and, as a result of this difference, we should conclude that the influence was small. Drawing on a distinction made by Michael Dummett, I show that Fichte understands language as encoding thought while Humboldt understands language (...) as a medium of thought. The consequences of this difference affect a wide range of issues from their views on the nature of personal pronouns, to their theories of communicative understanding, to their theories of the proper nature of inquiry into language. (shrink)

Eetu Pikkarainen describes the educational thinking of Johann AmosComenius (1592-1670) from a perspective of Bildung -theoretical problems. Comenius has had a remarkable influence on modern education, particularly through his language-learning and general didactical methods and principles. However, Comenius’ broader pansophic views have had somewhat more benign later effects. Comenius developed a reformation programme concerning the ‘main areas’ of reality, from theology and education to philosophy and language to social questions and world peace. This program has important connections to the modern (...) theories of Bildung. Comenius connects individual human growth with global issues such as the growth of scientific knowledge, the justice of political systems, and world peace. In his philosophy, Comenius strongly criticises the problems of the rising modern thinking such as trapping to dualisms. From that angle, Comenius appears an almost postmodern thinker with surprising similarity to the thoughts of C S Peirce. (shrink)

This study is about Brentano’s criticism of a version of phenomenalism that he calls “mental monism” and that he attributes to positivists philosophers such as Ernst Mach and John Stuart Mill. I am interested in Brentano’s criticism of Stuart Mill’s version of mental monism based on the idea of “permanent possibilities of sensation”. Brentano claims that this form of monism is characterized by the identification of the class of physical phenomena to that of mental phenomena and it commits itself to (...) a form of idealism. Brentano argues instead for a form of indirect or hypothetical realism based on intentional correlations. (shrink)

Some critics of Mill understand him to advocate the forced assimilation of people he regards as uncivilized, and to defend toleration and the principle of liberty only for civilized people of the West. Examination of Mill’s social and political writings and practice while serving the British East India Company shows, instead, that Mill is a ‘tolerant imperialist’: Mill defends interference in India to promote the protection of legal rights, respect and toleration for conflicting viewpoints, and a commercial society that can (...) cope with natural threats. He does not think the principle of liberty is waived for the uncivilized, or that the West should forcibly reshape them in its own monistic image. Mill’s tolerant imperialism reflects a tension between liberty and moral development that surfaces also when Mill thinks about the scope of government in civilized societies. (shrink)

Philosophy, that most misunderstood of intellectual pursuits, is often mocked; and no part of philosophy is as often mocked as metaphysics. The image of the ‘speculative metaphysician’ dreaming up abstract pictures of the world has been held up for ridicule by poets, playwrights, novelists, journalists as well as by other philosophers. The Logical Positivists in the first half of the 20th Century rejected all metaphysical speculations as ‘meaningless’ since they could not be verified by scientific experiment; in the later part (...) of the century, Wittgenstein criticised systematic metaphysics as being a kind of intellectual disease resulting from our reading false pictures of the world into the grammar of our language. The common suspicion underlying many of these attacks is that ultimately, all metaphysics is a kind of nonsense, and that metaphysicians don’t really know what they are talking about. This suspicion is not new. Nicolas-Sébastien Chamfort commented in 1796, ‘I am tempted to say of metaphysicians what Scaliger used to say of the Basques: they are said to understand one another, but I don’t believe a word of it.’ Some contemporary philosophers may agree. (shrink)

Computers may help us to better understand (not just verify) arguments. In this article we defend this claim by showcasing the application of a new, computer-assisted interpretive method to an exemplary natural-language ar- gument with strong ties to metaphysics and religion: E. J. Lowe’s modern variant of St. Anselm’s ontological argument for the existence of God. Our new method, which we call computational hermeneutics, has been particularly conceived for use in interactive-automated proof assistants. It aims at shedding light on the (...) meanings of words and sentences by framing their inferential role in a given argument. By employing automated theorem reasoning technology within interactive proof assistants, we are able to drastically reduce (by several orders of magnitude) the time needed to test the logical validity of an argu- ment’s formalization. As a result, a new approach to logical analysis, inspired by Donald Davidson’s account of radical interpretation, has been enabled. In computational hermeneutics, the utilization of automated reasoning tools ef- fectively boosts our capacity to expose the assumptions we indirectly commit ourselves to every time we engage in rational argumentation and it fosters the explicitation and revision of our concepts and commitments. (shrink)

The French theorist A. J. Greimas, inspired by such studies, is considered one of the founders of Narratology through the construction of models of analysis where these invariables would be centered in the subject of the narrative and based on the action and the transformation of them. The objective of the present essay is to analyze the ideas of Greimas, as well as to look for the logical mechanism that resides in each model.

In the last few decades, the historiographical categories rationalism and empiricism have been criticized for their limitations to explain the complex positions and the links held by the philosophers tradiotnally attached to them. This narrative was firstly conceived by Kantian German historians and began to become standard at the turn of the twentieh century. Nonetheless, nineteenth-century French historiography developed other narratives by which early modern philosophers were classified according to alternative criteria. In the first edition of Histoire comparée des systémes (...) de philosophie (1804), Joseph-Marie Degérando distinguishes three first-order early modern schools founded by Bacon, Descartes and Leibniz, respectively. Degérando introduces the empiricism and rationalism distinction as one among others, and not as the fundamental one. In addition, he separates empiricism from experimental philosophy. The last one, along with speculative philosophy, is said to conciliate senses and reason. As a result, this account offers philosophical groupings different from those constructed by the standard narrative. Furthermore, it draws on labels and classification criteria which were part of the early modern philosophical discourse. (shrink)

This volume collects a set of papers that were presented at a conference on “Big Questions in Free Will,” held at the University of Saint Thomas in October of 2014. It is dedicated to its editor, who passed away shortly after completing the manuscript. I will briefly summarize each of the 11 chapters and then offer a few critical comments.

This paper offers a new interpretation of John Austin’s views both on assertion and on adverbs, as result of which an expressivist thesis concerning the semantics for action sentences is advanced. First, Austin’s analysis of assertion based on various, specific assertive forces and his remarks on adverbs are systematically connected in order to obtain assertive schemata for action sentences. Finally, those schemata are put to work as the expression of inferential commitments implicit in argumentative practices of different sorts (exculpatory, justificatory (...) and illustrative) in the deployment of which, both logical contrariety and contradiction are exploited. (shrink)