The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Ontologies – structured, controlled, vocabularies – are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the virus research domain, following the principles of the Open Biological and Biomedical Ontology (OBO) Foundry and drawing on the resources of the Infectious Disease Ontology (IDO) Core. We report the development of the Virus Infectious (...) Disease Ontology (VIDO), a reference ontology extending IDO Core covering viral infectious diseases. We examine newly minted terms, showcase ontology term reuse, and illustrate the use of VIDO by annotating selections from recent life science research on SAR-CoV-2, in the interest of supporting machine learning projects. (shrink)

Peter Abelard (1079–1142 ce) was the most wide‐ranging philosopher of the twelfth century. He quickly established himself as a leading teacher of logic in and near Paris shortly after 1100. After his affair with Heloise, and his subsequent castration, Abelard became a monk, but he returned to teaching in the Paris schools until 1140, when his work was condemned by a Church Council at Sens. His logical writings were based around discussion of the “Old Logic”: Porphyry's Isagoge, aristotle'S Categories and (...) On Interpretation and boethius'S textbook on topical inference. They comprise a freestanding Dialectica (“Logic”; probably c.1116), a set of commentaries (known as the Logica [Ingredientibus], c. 1119) and a later (c. 1125) commentary on the Isagoge (Logica Nostrorum Petititoni Sociorum or Glossulae). In a work Abelard called his Theologia, issued in three main versions (between 1120 and c.1134), he attempted a logical analysis of trinitarian relations and explored the philosophical problems surrounding God's claims to omnipotence and omniscience. The Collationes (“Debates,” also known as “Dialogue between a Christian, a Philosopher and a Jew”; probably c.1130) present a rational investigation into the nature of the highest good, in which the Christian and the Philosopher (who seems to be modeled on a philosopher of pagan antiquity) are remarkably in agreement. The unfinished Scito teipsum (“Know thyself,” also known as the “Ethics”; c.1138) analyses moral action. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

With this issue we initiate the policy of expanding the scope of Tulane Studies in Philosophy to include, in addition to the work of members of the department, contributions from philosophers who have earned advanced degrees from Tulane and who are now teaching in other colleges and universities. The Editor THE LOGIC OF OUR LANGUAGE ROBERT L. ARRINGTON Wittgenstein wrote in the Tractatus that "logic is not a body of doctrine, but a mirror-image of the world. " 1 In line (...) with his suggestion that a proposition is a 'picture', Wittgenstein argued that propositions 'show' the logical structure of the real. He was insistent, however, that "the apparent logical form of a proposition need not be its real one. " 2 As a result of this we can misunderstand the structure of fact. Philosophical problems arise just when "the logic of our language is mis understood. " 3 It is common knowledge that much of this view of logic was rejected by Wittgenstein himself in the Philosophical Investi gations. There we are told that language has no ideal or sublime 4 logic which mirrors the structure of the extra-linguistic world. Consequently, inferences from the structure of language to the structure of that extra-linguistic world are invalid. Reality can be 'cut up' in any of a number of ways by language. Wittgenstein adopted a view of philosophy which would render that discipline a non-explanatory, non-critical study of the multiple ways in which language can be used. (shrink)

Lindsay Judson and Vassilis Karasmanis present a selection of philosophical papers by an outstanding international team of scholars, assessing the legacy and continuing relevance of Socrates's thought 2,400 years after his death. The topics of the papers include Socratic method; the notion of definition; Socrates's intellectualist conception of ethics; famous arguments in the Euthyphro and Crito; and aspects of the later portrayal and reception of Socrates as a philosophical and ethical exemplar, by Plato, the Sceptics, and in the early (...) Christian era. Contributors include Lesley Brown, David Charles, John Cooper, Michael Frede, Terence Irwin, Charles Kahn, Vassilis Karasmanis, Carlo Natali, Vasilis Politis, Dory Scaltsas, Gerhard Seel, and C. C. W. Taylor. (shrink)

The essays in this collection treat historical, literary, and philosophical topics related to Ayn Rand's Anthem, an anti-utopia fantasy set in the future. The first book-length study on Anthem, this collection covers subjects such as free will, political freedom, and the connection between freedom and individual thought and privacy.

This book examines influential conceptions of sport and then analyses the interplay of challenging borderline cases with the standard definitions of sport. It is meant to inspire more thought and debate on just what sport is, how it relates to other activities and human endeavors, and what we can learn about ourselves by studying sport.

BackgroundThe COVID-19 pandemic has had a significant impact on the health system worldwide. The organ and tissue donation and transplantation (OTDT) system is no exception and has had to face ethical challenges related to the pandemic, such as risks of infection and resource allocation. In this setting, many Canadian transplant programs halted their activities during the first wave of the pandemic.MethodTo inform future ethical guidelines related to the COVID-19 pandemic or other public health emergencies of international concern, we conducted a (...) literature review to summarize the ethical issues.ResultsThis literature review identified three categories of ethical challenges. The first one describes the general ethical issues and challenges reported by OTDT organizations and transplantation programs, such as risks of COVID-19 transmission and infection to transplant recipients and healthcare professionals during the transplant process, risk of patient waitlist mortality or further resource strain where transplant procedures have been delayed or halted, and resource allocation. The second category describes ethical challenges related to informed consent in the context of uncertainty and virtual consent. Finally, the third category describes ethical issues related to organ allocation, such as social considerations in selecting transplant candidates.ConclusionThis literature review highlights the salient ethical issues related to OTDT during the current COVID-19 pandemic. As medical and scientific knowledge about COVID-19 increases, the uncertainties related to this disease will decrease and the associated ethical issues will continue to evolve. (shrink)

It is often argued that a shared culture, or at least shared cultural references or practices, can help to foster peace and prevent war. This essay examines in detail and criticizes one such argument, made by Patrick Leigh Fermor, in the context of his discussing an incident during World War II, when he and a captured German general found a form of agreement, a ground for peace between them, in their both knowing Horace's ode I.9 by heart in Latin. By (...) way of introducing the sixth and final installment of the Common Knowledge symposium “Peace by Other Means,” this essay proposes that Leigh Fermor's narrative be understood in terms of commerce, rather than consensus. It concludes by examining Ezra Pound's use of the word commerce in his poem “A Pact” to define his relationship with his “detested” and “pig-headed” poetic “father,” Walt Whitman. (shrink)

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 and X-linked CLDN2 through a two-stage genome-wide study. The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is (...) associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men. © 2012 Nature America, Inc. All rights reserved. (shrink)

Unpopular in its day, David Hume's sprawling, three-volume 'A Treatise of Human Nature' (1739-40) has withstood the test of time and had enormous impact on subsequent philosophical thought. Hume's comprehensive effort to form an observationally grounded study of human nature employs John Locke's empiric principles to construct a theory of knowledge from which to evaluate metaphysical ideas. A key to modern studies of eighteenth-century Western philosophy, the Treatise considers numerous classic philosophical issues, including causation, existence, freedom and necessity, and (...) morality. Unabridged republication of the edition originally published by Oxford at the Clarendon Press, London, 1888. (shrink)

The coming of bioethics to Singapore / W. Calvin Ho and Sylvia S.N. Lim -- The impact of the bioethics advisory committee on the research community in Singapore / Charmaine K.M. Chan and Edison T. Liu -- Engaging the public : the role of the media / Chang Ai-Lien and Judith Tan -- Confucian trust and the biomedical regulatory framework in Singapore / Anh Tuan Nuyen -- The clinician-researcher : a servant of two masters? / Alastair V. Campbell, Jacqueline Chin, (...) and Teck Chuan Voo -- The US model for oversight of human stem cell research / Lindsay Parham and Bernard Lo -- Genetics and stem cell research : models of international policy-making / Bartha Maria Knoppers, Emily Kirby and Rosario Isasi -- Public engagement and bioethics commissions / Thomas H. Murray and Ross S. White -- Norm-making on human-animal chimeras and hybrids in Singapore, the United Kingdom and the international domain / W. Calvin Ho and Martin Bobrow -- How will future bioethical issues engage Singapore? / John Elliott. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:The Lost Sutras of Jesus: Unlocking the Ancient Wisdom of the Xian Monks, and: The Buddha's Gospel: A Buddhist Interpretation of Jesus' WordsJohn D'Arcy MayThe Lost Sutras of Jesus: Unlocking the Ancient Wisdom of the Xian Monks. Edited by Ray Riegert and Thomas Moore. London: Souvenir Press, 2004. 140 + xi pp.The Buddha's Gospel: A Buddhist Interpretation of Jesus' Words. By Lindsay Falvey. Adelaide: Institute for International (...) Development, 2002. 108 pp.Since Roy C. Amore's Two Masters, One Message (1987) revived the hypothesis of Buddhist influence on Christian origins and Hans-Joachim Klimkeit's research established links between Nestorian Christianity, Gnostic Manichaeism, and Mahayana Buddhism in Central Asia, there is scope for further reflection on commonalities between the two traditions over and above the purely doctrinal and philosophical. The two books under review, though intended for a general readership, are indications that interest in these matters is very much alive.Riegert and Moore preface their selection of texts with the story of Bishop Aleben (A-lo-pen), who travelled the Silk Road from Persia and was received with honour at the imperial capital of Xian (Chang-an) at the beginning of the Tang dynasty (635 CE). The emperor Taizong was sympathetic to what he called the "Luminous Religion," a Nestorian version of Christianity, possibly in Syriac, as presented by Aleben. It seems that these teachings were translated into Chinese in the form of sutras. One of them, preserved in stone as the Monument Sutra, features the cross rising from the lotus, the symbol chosen by Karl Reichelt for Tao-fung Shan, his Christian center in Buddhist style at Sha-tin outside Hong Kong, many centuries later. Thousands of Buddhist texts were preserved in the library cave at Dunhuang monastery, about one thousand miles west of Xian, where they were rediscovered by the Taoist priest Wang Yuanlu, who arrived there in the 1890s and became the self-appointed guardian of the scrolls.Included in this treasure trove were the Jesus Sutras, which are now scattered in museums and private collections, largely inaccessible to the public. But if the selection published here in a very elegant translation is anything to go by, they are [End Page 190] extremely significant religious documents with a spiritual value all their own. For the uninitiated, there is no way of checking the authenticity of these translations. The commentaries that accompany them could be slightly tendentious in that they nudge us in the direction of the editors' particular holistic worldview. But the texts themselves have a beauty and integrity that speaks for itself. They represent a Higher Dharma of perfect purity (p. 86), which, like a mirror, reflects the world with no trace of self: no desire, no action, no virtue, no truth (pp. 80–83, 126–129). The Jesus story is retold, and Jesus is portrayed as the teacher of this Higher Path. The sutras speak of One Spirit who is self-created, One God who is creator of the world, and One Lord, the Messiah who will return. There are prayers, too: "O Loving Father, Enlightened Son, Holy Spirit King"; "Lamb of Love and Bliss"; "O Holy Sage, Universal Lord, Messiah" (pp. 110–113). The texts obviously bear witness to a Buddhist-Christian dialogue much earlier and at a far deeper level than many would have thought possible. Whether they represent the religion of the future, as the editors suggest, remains to be seen.Lindsay Falvey's project of interpreting the canonical texts of Buddhism and Christianity in reference to one another has a similar orientation. In the course of agricultural development work in Thailand he came to realize "that the striking similarity between the two teachers may well be a seamless cloak of congruence beneath the mantle of culture and lore" (p. 13); the texts, in other words, may be quite literally translatable into one another's terms. Though aware that Q, the collection of Jesus' sayings that is supposed to have been available to the synoptic evangelists, is a hypothetical reconstruction, he still feels able to use a version of it as a basis for his experiment. He prefaces this with what he calls "A... (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:The Lost Sutras of Jesus: Unlocking the Ancient Wisdom of the Xian Monks, and: The Buddha's Gospel: A Buddhist Interpretation of Jesus' WordsJohn D'Arcy MayThe Lost Sutras of Jesus: Unlocking the Ancient Wisdom of the Xian Monks. Edited by Ray Riegert and Thomas Moore. London: Souvenir Press, 2004. 140 + xi pp.The Buddha's Gospel: A Buddhist Interpretation of Jesus' Words. By Lindsay Falvey. Adelaide: Institute for International (...) Development, 2002. 108 pp.Since Roy C. Amore's Two Masters, One Message (1987) revived the hypothesis of Buddhist influence on Christian origins and Hans-Joachim Klimkeit's research established links between Nestorian Christianity, Gnostic Manichaeism, and Mahayana Buddhism in Central Asia, there is scope for further reflection on commonalities between the two traditions over and above the purely doctrinal and philosophical. The two books under review, though intended for a general readership, are indications that interest in these matters is very much alive.Riegert and Moore preface their selection of texts with the story of Bishop Aleben (A-lo-pen), who travelled the Silk Road from Persia and was received with honour at the imperial capital of Xian (Chang-an) at the beginning of the Tang dynasty (635 CE). The emperor Taizong was sympathetic to what he called the "Luminous Religion," a Nestorian version of Christianity, possibly in Syriac, as presented by Aleben. It seems that these teachings were translated into Chinese in the form of sutras. One of them, preserved in stone as the Monument Sutra, features the cross rising from the lotus, the symbol chosen by Karl Reichelt for Tao-fung Shan, his Christian center in Buddhist style at Sha-tin outside Hong Kong, many centuries later. Thousands of Buddhist texts were preserved in the library cave at Dunhuang monastery, about one thousand miles west of Xian, where they were rediscovered by the Taoist priest Wang Yuanlu, who arrived there in the 1890s and became the self-appointed guardian of the scrolls.Included in this treasure trove were the Jesus Sutras, which are now scattered in museums and private collections, largely inaccessible to the public. But if the selection published here in a very elegant translation is anything to go by, they are [End Page 190] extremely significant religious documents with a spiritual value all their own. For the uninitiated, there is no way of checking the authenticity of these translations. The commentaries that accompany them could be slightly tendentious in that they nudge us in the direction of the editors' particular holistic worldview. But the texts themselves have a beauty and integrity that speaks for itself. They represent a Higher Dharma of perfect purity (p. 86), which, like a mirror, reflects the world with no trace of self: no desire, no action, no virtue, no truth (pp. 80–83, 126–129). The Jesus story is retold, and Jesus is portrayed as the teacher of this Higher Path. The sutras speak of One Spirit who is self-created, One God who is creator of the world, and One Lord, the Messiah who will return. There are prayers, too: "O Loving Father, Enlightened Son, Holy Spirit King"; "Lamb of Love and Bliss"; "O Holy Sage, Universal Lord, Messiah" (pp. 110–113). The texts obviously bear witness to a Buddhist-Christian dialogue much earlier and at a far deeper level than many would have thought possible. Whether they represent the religion of the future, as the editors suggest, remains to be seen.Lindsay Falvey's project of interpreting the canonical texts of Buddhism and Christianity in reference to one another has a similar orientation. In the course of agricultural development work in Thailand he came to realize "that the striking similarity between the two teachers may well be a seamless cloak of congruence beneath the mantle of culture and lore" (p. 13); the texts, in other words, may be quite literally translatable into one another's terms. Though aware that Q, the collection of Jesus' sayings that is supposed to have been available to the synoptic evangelists, is a hypothetical reconstruction, he still feels able to use a version of it as a basis for his experiment. He prefaces this with what he calls "A... (shrink)

The history of the dyestuffs industry during the period 1775–1860 is interesting for three reasons. In the first place it was in connection with the manufacture of synthetic dyestuffs, begun in 1856, that the industrial research laboratory and the organization scientist first unmistakably appeared in the last decades of the nineteenth century. Secondly, there are the enigmas of W. H. Perkin, the man who discovered and manufactured the first coal-tar colours, but who retired somewhat abruptly from the industry in 1874: (...) just after the synthesis of alizarine. Thirdly, the dyestuffs industry was in intimate association with the textile industries which had for a long time been subject to frequent radical scientific and technological innovation. Among the most important of these we may mention John Smeaton's classic paper of 1759 on the maximum work obtainable from a given fall of water: a problem important not only for the abstract science of mechanics, but also for the design of waterwheels—the main source of power for the early textile mills. (The waterwheel was not, during the eighteenth century, the epitome of the quaint and picturesque: it was in the van of scientific and technical progress.) Again, the textile industries were quick to employ the Watt rotative engine; previously a two cylinder Newcomen engine had been tried out. Bleaching powders, based on Scheele's discovery of chlorine and its properties, were rapidly adopted: in this context one cannot help contrasting the indifference of medical science to Davy's early suggestion of using nitrous oxide as an anaesthetic; or Faraday's comment in 1818 on the anaesthetic power of sulphuric ether. The textile industries saw, over this period, a rapid succession of new machines, the pace of invention being so hot that in 1832 Charles Babbage reported that machines became obsolete long before they wore out. A Salford cotton mill was the first industrial establishment to use gas lighting: James Thomson, calico printer, introduced gas lighting to the town of Clitheroe when he installed it in his works. And there were many other important technical and scientific innovations. It was to supply these industries, so well accustomed to change, that the synthetic coal-tar dyestuffs were introduced from 1856 onwards. It is interesting that, so far as we can see, the appearance of these synthetic dyestuffs was the last in the series of major innovations in the textiles and related industries: at least until recent times. (shrink)

The esteemed psychologist and thinker John Dewey headed for previously unexplored philosophical territory with this influential work. Written shortly after World War I, it embodies Dewey's system of pragmatic humanism and maintains that individuals can attain "a more ordered and intelligent happiness" by reconsidering the ultimate effects of their deepest beliefs and feelings. With its promise of achieving an understanding of the past and attaining a brighter future, Reconstruction in Philosophy remains ever relevant. "A modern classic." — Philosophy and (...) Phenomenological Research. (shrink)