Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

An algebraic semantics, based on factor algebras, for one-way and two-way implicative verbs is proposed. Implicative verbs denote elements of filters or of ideals generated by identity functions in factor algebras. This semantics explains in particular the problem of implicational equivalence raised by two-way implicative verbs, and shows that the negation necessary to establish the implicativity of these verbs is the negation which preserves the presuppositions of sentences with implicative verbs. In addition, it follows from the proposed semantics that any (...) two implicative verbs denoting in the same algebra but belonging to different categories, are semantically related. (shrink)

R T Allen; Rational Autonomy: the destruction of freedom, Journal of Philosophy of Education, Volume 16, Issue 2, 30 May 2006, Pages 199–207, https://doi.org/10.

The ethics of belief involves an inquiry into what beliefs are legitimate to hold, including religious beliefs. Whatever the criteria determined in such an investigation, adopting a belief that does not meet this criterion is seen as illegitimate and it is considered an ethical violation. English mathematician W. K. Clifford (d. 1879) defines “sufficient evidence” as a criterion in his famous essay, “The Ethics of Belief”. Clifford’s evidence-centered argument becomes one of the most frequent references in the evidentialist objection against (...) theism. It turns out that this argument is not functional in the face of the diversity of beliefs. In this context, different suggestions are presented about what the ethics of belief could be. American philosopher William James (d. 1810), one of the founding names of pragmatism, offers a new proposal. In his classic work, “The Will to Believe”, James claims that Clifford is wrong in seeking the requirement of evidence for all beliefs. Because it is not possible to prove beliefs from the passionate nature of human beings, especially religious beliefs. Following this distinction, James proposes a new criterion for religious beliefs: a religious belief can be vivid or dead, forced or avoidable; and momentous or trivial. If a religious belief is vivid, forced, and momentous, it is necessary to have the courage to believe in it instead of suspending it. James' proposal is often valued as a strong counter-challenge or defense of religious beliefs. However, this argument also has aspects that are open to criticism. One of them is that the will to believe argument concurrently accepts conflicting religious beliefs or, in other words, confronts the issue of religious diversity. According to J. Hick, for example, this argument inevitably results in religious pluralism, even though James does not want to. Contrary to Hick, S. F. Aikin claims that the will to believe does not result in religious pluralism. According to Aikin, who draws attention to the relationship of argument with pragmatism, James obscures religious beliefs and removes them from being claims about truth. Therefore, there is no contradiction in the classical sense. So, which of the objections is valid? Does the will-to-believe argument result in religious pluralism by legitimizing more than one religious belief at the same time, or does it make a purely pragmatic proposition by devaluing religious beliefs? Which religion do I have the right to believe in according to the will to believe? The aim of this article is to provide an answer to the mentioned question. In the article, unlike the current evaluations, it is argued that the argument is closely related to James's theory of knowledge, radical empiricism, not pragmatism as it is usually made. For this purpose, after showing the relationship between the arguments of Clifford and James, the argument will be re-examined in this context and it will be revealed that James has two steps regarding religious beliefs: to make religious beliefs independent from factual beliefs; leaving theism to accept a monistic vision of God and basing religion on mystical experience, which is an emotional experience. As details emerge, it will become clear that James defends a natural religion that excludes traditional religions in his philosophical system and that he defends the beliefs of a humanized religion. With an individual definition of religion based on emotion, James on the one hand ensures the commonality of religious feeling, on the other hand, he makes religion independent from the field of facts. Therefore, with this study, it will be seen that the argument of the will to believe does not aim to legitimize believing in traditional religions, and diversity is not a fundamental problem. (shrink)

This essay explores some of the dogmatic challenges involved in developing a distinctively evangelical account of the doctrine of theosis, that is, humanity’s participation in the life of God. After offering some preliminary clarifications regarding the terminology of theosis, the paper sketches in broad strokes how an account of theosis might take shape within the structures of evangelical theology. David Bebbington’s famous evangelical quadrilateral— biblicism, crucicentrism, conversionism, and activism—serves as the basic framework (Bebbington 1989: 1-19). It will be argued that (...) evangelical theology can accommodate a version of theosis within this structure, but that evangelicals’ understanding of these categories may require some ‘flexing’ in order to make room for a more Christocentric and participatory conceptualization of redemption, one that culminates in the beatific vision of the redeemed when ‘God will be all in all’ (1 Cor 15:28). The final section of the paper points to a pair of important figures who may serve as resources for an evangelical retrieval of theosis. (shrink)

R T Allen; I'll Say it Again: a rejoinder to Jim Mackenzie, Journal of Philosophy of Education, Volume 22, Issue 1, 30 May 2006, Pages 113–114, https://doi.org/.

R T Allen; Metaphysics in Education, Journal of Philosophy of Education, Volume 23, Issue 2, 30 May 2006, Pages 159–169, https://doi.org/10.1111/j.1467-9752.198.

R. E. Allen's superb new translation of Plato's Symposium brings this classic text to life for modern readers. Allen supplements his translation with a commentary that not only enriches our understanding of Plato's philosophy and the world of Greek antiquity but also provides insights into present-day philosophical concerns. Allen reveals the unity of Plato's intentions in the Symposium, explores the dialogue's major themes, and links them with Plato's other dialogues. His wide-ranging commentary includes discussions of Greek religious, social, and sexual (...) practices, the conceptual connections between the Symposium and Freud, the influence of the Symposium on later writers, and recent scholarship on the dialogue. Allen's primary focus is philosophical, however, and he succeeds in explicating the doctrine of Eros in Plato's Symposium so that the reader can see how wish and desire relate to Plato's moral philosophy, epistemology, and metaphysics. (shrink)

ACCORDING TO POPPER, SCIENTIFIC THEORIES ARE TO BE ACCEPTED IN SO FAR AS THEY ARE FALSIFIABLE AND IN SO FAR AS THEY HAVE BEEN CORROBORATED. THE CONCEPTS OF FALSIFIABILITY AND CORROBORATION ARE SUBMITTED TO DETAILED ANALYSIS. THE POINT OF ACCEPTING THEORIES, ACCORDING TO POPPER, IS TO OBTAIN THEORIES OF HIGH VERISIMILITUDE. HOWEVER THE BEST WE CAN DO IS TO OBTAIN THEORIES OF HIGH PROBABLE VERISIMILITUDE. POPPER’S CRITERIA FOR ACCEPTING THEORIES WILL ONLY LEAD TO THEORIES OF HIGH PROBABLE VERISIMILITUDE ON NON-POPPERIAN (...) ASSUMPTIONS ABOUT INDUCTION. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:R. D. Ackerman BELIEVING IN A FICTION: WALLACE STEVENS AT THE LIMITS OF PHENOMENOLOGY The "ring of men" of "Sunday Morning" will chant their "devotion to the sun, / Not as a god, but as a god might be, / Naked among them, like a savage source" (CP, pp. 69-70).' Solar nakedness is deferred even as it is named. The problem for belief is the question of appearance and (...) representation. Things appear as and like.... The phenomenological return to things is also a turn to fiction, as Husserl understood: "If anyone loves a paradox, he can really say... that the element which makes up the life of phenomenology... is fiction. ' " The sun is divine, and it is not; it is both naked and clothed, savage and civilized, source (or end) and means. But such paradox is ultimately unsatisfying, and as we will see with Stevens, the need for belief—for an image or idea of totality—forces the issue of fiction and reality. The Stevens we will have in view is not the Stevens—as if there were such a creature. Our Stevens is the one most persuaded by promises such as those of phenomenology, the one most concerned with decreation (reduction) and fresh beginnings, with discovery and recognition, with imagination, the body, and the earth. This is the Stevens for whom the barrier of language presages at last not absence and difference but fictive recovery of presence and identity, the one for whom poetry represents a way of belief beyond mysticism even as it bodes mythic proximity. Finally, this is the Stevens who predominates throughout the prose (as well as in much of the poetry), who tries mightily to secure a belief while disencumbering himself of metaphysics—but alas, I think, with small success. Although Stevens's association of the problem of belief with the idea of fiction occurs in early poems such as "A High-Toned Old Christian 79 80Philosophy and Literature Woman" and "To the One of Fictive Music," his most intensive involvement with fiction as belief dates from the early 1940s and spans the period of his major essays and his last four volumes of poems. He recounts, for instance, a 1942 conversation with a student: "I said that I thought that we had reached a point at which we could no longer really believe in anything unless we recognized that it was a fiction. The student said that that was an impossibility, that there was no such thing as believing in something that one knew was not true. It is obvious, however, that we are doing that all the time" (L, p. 430). What does it mean to believe in a fiction? That is my main subject here, as we seek out the limits of the phenomenological Stevens. His letters of this period are preoccupied with the problem of fictive belief: "If one no longer believes in God (as truth), it is not possible merely to disbelieve; it becomes necessary to believe in something else.... A good deal of my poetry recently has concerned an identity for that thing.... In one of the short poems that I have just sent to the harvard advocate, I say that one's final belief must be in a fiction. I think that the history of belief will show that it has always been in a fiction" (L, p. 370). The poem referred to, "Asides on the Oboe," begins: The prologues are over. It is a question now, Of final belief. So, say that final belief Must be in a fiction. It is time to choose. (CP, p. 250) Acknowledging that "in the long run, poetry would be the supreme fiction" (L, pp. 430-31), Stevens nonetheless singles out the nominative function of poetry as the essence of its claim to supremacy: "Poetry means not the language of poetry but the thing itself.... The subject matter is what comes to mind when one says of the month of August... 'Thou art not August, unless I make thee so'" (L, p. 377). The quoted line (also from "Asides") underscores the paradox that for Stevens the essence of fiction (the nontrue) is its capacity to nominate the true or the real. This... (shrink)

İslâm coğrafyasının genişlemesi neticesinde Arap olmayan toplulukların İslâm dini ile tanışmaları beraberinde bir takım problemleri de getirmiştir. Bu problemler arasında, Kur’ân’ın yanlış anlaşılma endişesi en başı çekmektedir. Arapçaya hâkim olmamaktan kaynaklanan dil hatalarının âyetlere kadar sirayet ettiğini gösteren birçok rivayetin varlığı da bunu teyit etmektedir. Bundan dolayı hicrî birinci yüzyılın ikinci yarısından itibaren dil ile ilgili faaliyetler aralıksız bir şekilde devam etmiştir. Bu faaliyetler arasında, Kur’ân’ın üslûbunu, âyetlerde yer alan kelimelerin delâleti ve sesletimini, cümlelerin iç bütünlüğü ile filolojik tahlillerini ele (...) alan çalışmalar bulunmaktadır. Bu çalışmalar, Arap gramerinin oluşturulması ve bazı gramer ekollerinin ortaya çıkmasıyla birlikte genellikle “Ma‘âni’l-Ḳur’ân” ve “İ‘râbü’l-Ḳur’ân” başlıkları kullanılarak daha sistemli bir şekilde hicri dördüncü yüzyılın sonlarına kadar devam etmiştir. “Ma‘âni’l-Ḳur’ân” başlığını kullanarak eser yazan âlimler arasında gramer ilmiyle birlikte tefsir alanında da önemli bir konuma sahip olan Yahyâ b. Ziyâd el-Ferrâ da bulunmaktadır. Sözü edilen eserde Ferrâ’nın, lügavî tahlilleri esnasında özellikle sözcüklerin siygası ve çok anlamlılığı doğrultusunda dil-kültür ilişkisine örnek olabilecek birçok bireysel değerlendirmesine rastlanılmaktadır. Onun bazı ayetler etrafında sergilenen çeşitli görüşlere yer verdikten sonra Arap toplumu nezdinde bir yönüyle de bile olsa kabul gören semantik tahlillere ayrıca yer vermesi, müfessirlerin, çoğu zaman anlaşılması güç ayetlerle birlikte murad edilenin dışında bir yorumun önlenmesi için dönemin kültüründen yararlanmaları gerektiği şeklinde de değerlendirilebilir. Bu bakımdan Kur’ân-ı Kerîm’in insanlığa sunduğu mesajların en doğru şekilde anlaşılabilmesi adına bazı âyetlerin tefsiri ve değerlendirmesi yapılırken başvurulacak ilmî merci ve disiplinlerin geniş tutulması önem arz etmektedir. Binâenaleyh makalede Ferrâ’nın kendisine özgü tahlilleriyle beraber, görüşlerine yer verdiği başka âlimlerin analizlerinden sadece dil-kültür ilişkisine örnek olabilecek tespitler üzerinde durularak kültür ve dil etkileşiminin âyet yorumundaki rolüne işaret edilecektir. (shrink)

Every person acquires a worldview, a picture of reality. Within that picture, the existence of some things will be taken wholly for granted as the background to, and support of, everything else. Their existence will rarely be questioned. The cosmos or universe, the gods, God, Brahman, Heaven, the Absolute--R. T. Allen claims that all these and other world- views have been held to be that which necessarily exists and upon which all other beings depend in one way or another. European (...) philosophers, since antiquity, have offered arguments to show that their chosen candidates for the role of the necessary being or beings that support the rest of reality do actually exist. The Necessity of God sets the valid core of previous ontological arguments. It does not and cannot prove that God exists, but only that something necessarily exists. In an a priori manner and without inferring anything from what in fact exists, Allen proceeds to show that which necessarily exists is one, transfinite, eternal, and the archetype of personal existence: in short, that it is God as classically conceived. As for everything else that may exist, it must be finite and dependent for its existence upon God as its creator and sustainer. Few things are more erroneous in philosophy and disastrous in practice than artificial constructions produced without constant reference to concrete reality. That which necessarily exists may be the one exception. Before this constructive argument, Allen examines previous examples of ontological arguments in order to show exactly where they go wrong and to extract the valid core obscured within them. This will make clear the difference between them and his new version. The reader who is eager to engage the philosophical sources of belief will find a distinct treasure in The Necessity of God. (shrink)

I can get away with it because no one is in a position to call me on it. Professor Robinson cannot consistently complain that (A) begs the question against his thesis that there is no such fallacy. He would discourage anyone from "helping" him by accusing me of committing the fallacy against him. With advocates like that, who needs adversaries? I. EMBEDDING PERSPECTIVES After all, Robinson has a viable reply to my argument. He should simply deny my premise. Later I (...) will show how (A) might rationally persuade Robinson. But my immediate goal is not to convert the skeptic about the existence of the fallacy but rather to use his extreme position to make a point about the nature of question-begging. Those who object that argument (A) begs the question against Robinson must do so on behalf of Robinson. This assistance requires that one launch the accusation from Robinson's perspective and with his dialectical interests at heart. (shrink)

Annihilationism provides a fruitful point of contact between philosophers and theologians for further reflection on nonexistence. In this paper I articulate a key commitment of annihilationism; namely, that some persons cease to exist. Such a commitment, I argue, amounts to the claim that some persons exist at time t and then do not exist at t+1, become ‘annihilated objects.’ Claims about annihilated objects induct the annihilationist into a wider realism/anti-realism debate about nonexistent objects. I survey some major viewpoints in this (...) debate. I then draw out some implications for each view for the annihilationist’s commitment to annihilated objects. I show that annihilationism is consistent with some forms of realism and anti-realism and inconsistent with others. (shrink)