The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

What is mind? This book attempts to give a philosophical answer to that question in language accessible to the layperson, but with a rigor acceptable to the specialist. Published on the centenary of the birth of Wittgenstein and the 40th anniversary of the publication of Gilbert Ryle 's classic The Concept of Mind, this work testifies to the influence of those thinkers on Kenny's own work in the philosophy of mind, and assembles Kenny's ideas on philosophical psychology into a (...) systematic whole. (shrink)

The articles on ‘thinking’ by Gilbert Ryle brought together by Konstantin Kolenda were not very well received, even by those who acknowledge, as awhole generation of philosophers must, a considerable intellectual debt to him. Bernard Williams in his review ‘Ryle Remembered’ ) seemed to capture the general impression created by the book. My suspicion is that this was so because readers approached it with a resistance built up over years of hearingRyle flounder on the topic. They read the book (...) expecting to find nothing init that they had not already assimilated or rejected. To pick up the metaphor G. E. L. Owen employed in the obituary he wrote for the Aristotelian Society, they had come to regard Ryle's work as a philosophical seam which during his own lifetime had already been so extensively and profitably minedthat by the time of his death it was already producing diminishing returns. Although Williams in his review did provide a rationale for Ryle's floundering I suspect that his rationale, like most readers’ expectations, preventedhim from reading the articles in the volume at all closely. Williams's viewwas that towards the end of his life, with whatever he had had in the way of theory collapsing around him, Ryle was left with nothing but his massive common sense together with the resources of a style of writing which had bythen become a caricature of itself. As against this I shall argue that Ryle, puzzled by the notion of thinking, took the problem back to his own philosophical roots where he finally came to think that the solution lay. (shrink)

A magisterial exploration of poetry’s place in the fine arts by one of the twentieth century's leading poets In this book, eminent poet Anthony Hecht explores the art of poetry and its relationship to the other fine arts. While the problems he treats entail both philosophic and theoretical discussion, he never allows abstract speculation to overshadow his delight in the written texts that he introduces, or in the specific examples of painting and music to which he refers. After discussing (...) literature’s links with painting and music, Hecht investigates the theme of paradise and wilderness, especially in Shakespeare’s The Tempest. He then turns to the question of public and private art, exploring the ways in which all the arts participate in balances between private and public modes of discourse, and between an exclusive or elitist role and the openly political. Beginning with a discussion of architecture as an illustration of a more general theme of discord and balance, the penultimate lecture probes the inner contradictions of works of art and our reactions to them, while the final piece concerns art and morality. (shrink)

Margaret Gilbert has recently argued in ProtoSociology against what she called my rejectionist’s view according to which (i) we have to make a distinction between the intentional states of believing and accepting and (ii) genuine group beliefs, i.e. group beliefs that cannot be reduced to the beliefs of the individual members of a group, should be understood in terms of the acceptance of a view rather than of beliefs proper. In this reply I discuss Gilbert’s objections.

The ways in which mental concepts can seem problematic are various, and consequently the idea of a coherent body of issues forming one part of philosophy, namely the philosophy of mind, is highly misleading. When Ludwig Wittgenstein and Gilbert Ryle inaugurated the flood of recent writings about the concept of mind there was some similarity, although not identity, in the problems which led them to concentrate their attention on mental concepts. Wittgenstein saw that lack of clarity about such notions (...) as willing, thinking, feeling and imagining generated powerful but misleading pictures about logic—about the difference between sense and nonsense —so that if we were to become clear about one we should have to become clear about the other. Worries about logic generated his interest in what it is to have a mind. In the case of Ryle, if we are to accept his own autobiographical remarks, an exposition of the logic of mental concepts was undertaken to illustrate whatever clarity had already been achieved by him and others with regard to logic and logical investigations. ‘The Concept of Mind was a philosophical book written with a meta-philosophical purpose’. Although I think it should be open for speculation just why specifically mental notions were singled out by him for such an illustrative purpose. In each case questions about logic prompted writing about the mind. There remains an echo of this in some of the books under review, but, as often with deepseated changes, the original impetus can soon be lost, and debates about distinctions in which it was first embodied can take on a life of their own. (shrink)

This article is an attempt to develop a practical politico-jurisprudential account of the corporate person, which it does by building on contemporary ideas about collective and shared intentions. It argues for a model of shared intentions, which posits a set of interlocking preferences, and other supporting attitudes. It examines the work of Bratman, Gilbert, Hurley, and Sugden and addresses issues of choice, coercion and will.

The essay deals with the issue of how a non-summativist account of collective epistemic traits can be properly justified. We trace the roots of this issue in virtue epistemology and collective epistemology and then critically examine certain views advanced to justify non-summativism. We focus on those considered by Fricker, including Gilbert’s concept of plural subjects, which she endorses. We find her analysis of these views problematic for either going beyond the parameters of the summativism-nonsummativism debate or contradicting common intuitions (...) about epistemic trait ascriptions. As an alternative, we advance the idea that collective epistemic traits are system properties; or that epistemic traits act as system properties when attributed to collectives taken in their own right. Working as a system, the individual members of a collective perform their designated roles or tasks in coordination and cooperation with each other to achieve theirjoint intentions. Being attributes exclusive to systems, collective epistemic traits cannot, therefore, be attributed in the same respect to the individuals comprising these systems, thereby blocking any summative account of these traits. This model also easily sidesteps the problems besetting Fricker’s preferred one. (shrink)

Jakob von Uexküll’s (1864-1944) account of Umwelt has been proposed as a mediating concept to bridge the gap between ecological psychology’s realism about environmental information and enactivism’s emphasis on the organism’s active role in constructing the meaningful world it inhabits. If successful, this move would constitute a significant step towards establishing a single ecological-enactive framework for cognitive science. However, Uexküll’s thought itself contains different perspectives that are in tension with each other, and the concept of Umwelt is developed in representationalist (...) terms that conflict with the commitments of both enactivism and ecological psychology. One central issue shared by all these approaches is the problem of how a living being experiences its environment. In this paper, we will look at Uexküll’s reception in French philosophy and highlight the different ways in which the concept of Umwelt functions in the work of Georges Canguilhem, Maurice Merleau-Ponty, and Gilles Deleuze. This analysis helps clarify different aspects of Uexküll’s thought and the deeper philosophical implications of importing his concepts into embodied cognitive science. This paper is part of a recent trend in which enactivism engages with continental philosophy in a way that both deepens and transcends the traditional links to phenomenology, including most recently the thought of Georg W. F. Hegel and Gilbert Simondon. However, no more than a brief outline and introduction to the potentials and challenges of this complex conceptual intersection can be given here. Our hope is that it serves to make more explicit the philosophical issues that are at stake for cognitive science in the question of experienced environments, while charting a useful course for future research. (shrink)

There is no question, of course, that music is a temporal art. Stravinsky, noting that it is inconceivable apart from the elements of sound and time, classifies it quite simply as "a certain organization in time, a chrononomy."1 His definition stands as part of a long and honored tradition that encompasses such diverse figures as Racine, Lessing, and Schopenhauer. Schopenhauer, putting the case in its strongest terms, remarks that music is "perceived solely in and through time, to the complete exclusion (...) of space," thus making explicit the opposition between time and space and ruling out the latter as a possible area for legitimate musical experience. Yet anyone familiar with the philosophical and theoretical literature dealing with music must be struck by the persistence with which spatial terminology and categories appear. Indeed, it would seem to be impossible to talk about music at all without invoking spatial notions of one kind or another. Thus in discussing even the most elementary aspects of pitch organization—and among the musical elements, only pitch, we should remember, is uniquely musical—one finds it necessary to rely upon such spatially oriented oppositions as "up and down," "high and low," "small and large" , and so on. Space, then, pace Schopenhauer, apparently forms an inseparable part of the musical experience. · 1. Igor Stravinsky, Poetics of Music in the Form of Six Lessons, trans, Arthur Knodel and Ingolf Dahl , p. 28. Robert P. Morgan is active as both a music composer and theorist. A professor of music at the University of Chicago, he is currently composing a concerto for flute, oboe, and string orchestra to be performed at Swarthmore College. His previous contribution to Critical Inquiry, "On the Analysis of Recent Music," appeared in the Autumn 1977 issue. Anthony Gilbert responds to the current essay in "Musical Space: A Composer's View". (shrink)

:In response to Roemer's reformulation of the Marxian concept of exploitation in terms of comparative wealth distributions, Vrousalis treats economic exploitation as an explicitly relational phenomenon in which one party takes advantage of the other's economic vulnerability in order to extract a net benefit. This paper offers a critical assessment of Vrousalis's account, prompting a revised formulation that is analysed in the context of a matching and bargaining model. This analysis yields precise representations of Vrousalis's conditions of economic vulnerability and (...) economic exploitation and facilitates comparison to the alternative conceptions of Marx and Roemer. (shrink)

From the late-fifteenth century onwards, scholars across Europe began to write books about how to read and evaluate histories. These pioneering works - which often take surprisingly modern-sounding positions - grew from complex early modern debates about law, religion, and classical scholarship. In this book, based on the Trevelyan Lectures of 2005, Anthony Grafton explains why so many of these works were written, why they attained so much insight - and why, in the centuries that followed, most scholars gradually (...) forgot that they had existed. Elegant and accessible, What Was History? is a deliberate evocation of E. H. Carr’s celebrated and icononclastic Trevelyan Lectures on What Is History?, and will appeal to a broad readership of students, scholars and historical enthusiasts. Anthony Grafton is one of the most celebrated historians writing in English today, and What Was History? is a powerful and imaginative exploration of some central themes in the history of European ideas. (shrink)

Sidgwick famously claimed that an argument in favour of utilitarianism might be provided by demonstrating that a set of defensible philosophical intuitions undergird it. This paper focuses on those philosophical intuitions. It aims to show which specific intuitions Sidgwick endorsed, and to shed light on their mutual connections. It argues against many rival interpretations that Sidgwick maintained that six philosophical intuitions constitute the self-evident grounds for utilitarianism, and that those intuitions appear to be specifications of a negative principle of universalization (...) (according to which differential treatments must be based on reasonable grounds alone). In addition, this paper attempts to show how the intuitions function in the overall argument for utilitarianism. The suggestion is that the intuitions are the main positive part of the argument for the view, which includes Sidgwick's rejection of common-sense morality and its philosophical counterpart, dogmatic intuitionism. The paper concludes by arguing that some of Sidgwick's intuitions fail to meet the conditions for self-evidence which Sidgwick himself established and applied to the rules of common-sense morality. (shrink)

Volume 28, Issue 2, March 2020, Page 417-420.

This article analyzes Zygmunt Bauman’s notion of moral blindness against the backdrop of his designation of modern culture as a dynamic process of liquefaction constantly dissolving every paradigm and subject to the flexible and indeterminate power of individual choice. Bauman argued that the social conditions of this radically individualistic liquid modernity result in a kind of moral insensitivity that he calls adiaphorization. Adiaphorization for him places certain human acts outside the “universe of moral obligations.” It defies the entire orthodox theory (...) of the social origins of morality as it reveals that some dehumanizing monstrous atrocities like the holocaust and genocides are not exclusively reserved for monsters, but can be attributable to “frighteningly normal” moral agents. The present text therefore attempts to discuss the various moral implications of Bauman’s analysis of moral blindness, with a view to highlighting its weaknesses. It moves on to explore Bauman’s recourse to Emmanuel Levinas’ ethics of the “face of the Other” as a viable ethical remedy that trumps the uncanny effects of this whole adiaphorization effect. Finally, the paper further advances his call for a rediscovery of the sense of belonging, by appealing to some major insights originating from African traditions of ethical communalism in order to propose a possible route towards the avoidance and amelioration of this moral challenge. (shrink)

The first in a new series with Australian Catholic University, this collection of essays deals with two important themes. 'Faith' and 'reason' are heavily weighted words. They point to elemental aspects of human existence. The papers and discussions presented strive to clarify and corelate these basic activities or dimensions of human beings. In all the complexities of the possible relationships and interweaving of faith and reason, two kinds of questions keep recurring. One the one hand, what is the value of (...) human intelligence, and how is it endorsed and supported by faith' On the other hand, what is the distinctive intelligence or rationality of faith, and how does it relate to the perennial search for wisdom represented in it various philosophical forms' Contributors include: Marilyn McCord Adams, Raimond Gaita, John Haldane, John McDermott SJ, Kevin Hart, and Anthony Kelly CSsR. (shrink)

St. Thomas Aquinas treats penance as both a sacrament and a virtue. In either form, penance’s principal human act is contrition—a willed sorrow for one’s sins and an intention to avoid future sins. A look at Aquinas’s understanding of penitential contrition reveals a complex interplay of the different objects of love, the gift of fear, and finally friendship with God. This article offers an analysis of Aquinas’s accounts of penance and contrition with respect to these key elements. I argue that (...) contrition performs a fundamental role in countering, restoring, and safeguarding a proper ordering of love and attainment of the ultimate good of union with God. In short, contrition is the act that directly counters the interior disorder wrought by sin and provides an ongoing counter to the threat of additional disorder. Sin’s disorder is the aversion to God and conversion to self, while contrition involves the aversion to self and a conversion to God. (shrink)

It is almost commonplace to suggest that what is morally right for one person to do must also be right for anyone else similarly situated. The author suggests that this "universalization requirement" applies to only a limited sphere of the moral life, chiefly to duties of perfect obligation. Extending the requirement beyond this sphere fails to leave room for human freedom in vocation or for a clear recognition of human finitude.