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)

Achieving space situational awareness requires, at a minimum, the identification, characterization, and tracking of space objects. Leveraging the resultant space object data for purposes such as hostile threat assessment, object identification, and conjunction assessment presents major challenges. This is in part because in characterizing space objects we reference a variety of identifiers, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, operational processes, operational statuses, and so forth, which tend to be defined in highly heterogeneous and sometimes inconsistent (...) ways. The Space Domain Ontologies are designed to provide a consensus-based realist framework for formulating such characterizations in a way that is both consistent and computable. Space object data are aligned with classes and relations in a suite of ontologies built around the existing Space Object Ontology. They are stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space situational awareness and the needs of spacecraft operators and analysts. This paper provides an overview of the Space Domain Ontologies and their development and use. It presents the motivation for and advantages of the Space Domain Ontologies, including the benefits they provide for enhancing and maintaining long-term space situational awareness. (shrink)

The project of a 'naive physics' has been the subject of attention in recent years above all in the artificial intelligence field, in connection with work on common-sense reasoning, perceptual representation and robotics. The idea of a theory of the common-sense world is however much older than this, having its roots not least in the work of phenomenologists and Gestalt psychologists such as K hler, Husserl, Schapp and Gibson. This paper seeks to show how contemporary naive physicists can profit from (...) a knowledge of these historical roots of their discipline, which are shown to imply above alla critique of the set-theory-based models of reality typically presupposed by contemporary work in common-sense ontology [1]. (shrink)

Building on the writings of Wittgenstein on rule-following and deviance, Kristóf Nyíri advanced a theory of creativity as consisting in a fusion of conflicting rules or disciplines. Only such fusion can produce something that is both intrinsically new and yet capable of being apprehended by and passed on to a wider community. Creativity, on this view, involves not the breaking of rules, or the deliberate cultivation of deviant social habits, but rather the acceptance of enriched systems of rules, the adherence (...) to which presupposes simultaneous immersion in disciplines hitherto seen as being unrelated. The paper presents a demonstration of the fruitfulness of this theory by means of an account of some of the political, cultural and intellectual peculiarities of the Habsburg Monarchy. (shrink)

We can illustrate the phenomenon of model-induced escape by examining the phenomenon of spam filters. Spam filter A is, we can assume, very effective at blocking spam. Indeed it is so effective that it motivates the authors of spam to invent new types of spam that will beat the filters of spam filter A. -/- An example of this phenomenon in the realm of philosophy is illustrated in the work of Nyíri on Wittgenstein's political beliefs. Nyíri writes a paper demonstrating (...) convincingly that there are strong signals of a conservative strain of thought in the writings of Wittgenstein. This has initially a tiny effect; but then a more significant effect sets in as the authors of Wittgenstein secondary literature, consciously or unconsciously, draw attention to features of Wittgenstein which cast the conservatism thesis in a negative light. This is an example of what I call model-induced escape: the Nyíri model of Wittgenstein initiates a process which undermines the Nyíri model of Wittgenstein. -/- Wittgenstein, as obiectum philosophiae, is reduced to a constantly mutating set of interpretations of a certain body of work. -/- Perhaps this is what makes philosophy so problematic when viewed from the perspective of results, or in other words of signs of progress commonly accepted across the discipline. There are just too many ways of inducing escape from any given putative discovery; too many dimensions along which an interpretative or definitional arms race can be triggered. (shrink)

As engineering applications require management of ever larger volumes of data, ontologies offer the potential to capture, manage, and augment data with the capability for automated reasoning and semantic querying. Unfortunately, considerable barriers hinder wider deployment of ontologies in engineering. Key among these is lack of a shared top-level ontology to unify and organise disparate aspects of the field and coordinate co-development of orthogonal ontologies. As a result, many engineering ontologies are limited to their scope, and functionally difficult to extend (...) or interoperate with other engineering ontologies. This paper demonstrates how the use of a top-level ontology, specifically the Basic Formal Ontology (BFO), greatly facilitates interoperability of multiple engineering-related ontologies. We constructed a system of formal linked ontologies by re-engineering legacy ontologies to be conformant with BFO and developing new BFO-conformant ontologies to capture knowledge in the engineering design, enterprise, human factors, manufacturing, and application domain of additive manufacturing. The resulting Integrated Framework for Additively Manufactured Products (IFAMP), including the body knowledge instantiated on its basis, serve as the basis for a proposed Design with Additive Manufacturing Method (DWAM), which we believe can support the design of innovative products with semantically enhanced ideation tools and enhanced access to application domain knowledge. The method and its facilitation through the ontological framework are demonstrated using a case study in medicine. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology will greatly benefit software application ontologies. To this end LinKBase®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this, we aim to move beyond the level (...) of controlled vocabularies to yield an ontology with the ability to support reasoning applications. (shrink)

Eleven top Deleuze scholars reclaim Deleuzian philosophy as moral philosophy Ethics plays a crucial, if subtle, role in Gilles Deleuze's philosophical project. Michel Foucault claimed that Anti-Oedipus was `a book of ethics, the first book of ethics to be written in France in quite a long time'. But what is the nature of the immanent ethics that is developed in Deleuze's thought? How does it differ from previous conceptions of ethics? And what paths does it open for future thought, given (...) the ethical challenges facing humanity in so many domains? Each of the eleven essays in this collection explores the ethical dimension of Deleuze's thought along a new and singular trajectory, and in so doing, attempts to reclaim his philosophy as an ethical philosophy. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (shrink)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

In this article, we develop a new approach to integrating philosophical phenomenology with qualitative research. The approach uses phenomenology’s concepts, namely existentials, rather than methods such as the epoché or reductions. We here introduce the approach to both philosophers and qualitative researchers, as we believe that these studies are best conducted through interdisciplinary collaboration. In section 1, we review the debate over phenomenology’s role in qualitative research and argue that qualitative theorists have not taken full advantage of what philosophical phenomenology (...) has to offer, thus motivating the need for new approaches. In section 2, we introduce our alternative approach, which we call Phenomenologically Grounded Qualitative Research (PGQR). Drawing parallels with phenomenology’s applications in the cognitive sciences, we explain how phenomenological grounding can be used to conceptually front-load a qualitative study, establishing an explicit focus on one or more structures of human existence, or of our being in the world. In section 3, we illustrate this approach with an example of a qualitative study carried out by one of the authors: a study of the existential impact of early parental bereavement. In section 4, we clarify the kind of knowledge that phenomenologically grounded studies generate and how it may be integrated with existing approaches. (shrink)

“On the Subject Matter of Phenomenological Psychopathology” provides a framework for the phenomenological study of mental disorders. The framework relies on a distinction between (ontological) existentials and (ontic) modes. Existentials are the categorial structures of human existence, such as intentionality, temporality, selfhood, and affective situatedness. Modes are the particular, concrete phenomena that belong to these categorial structures, with each existential having its own set of modes. In the first section, we articulate this distinction by drawing primarily on the work of (...) Martin Heidegger—especially his study of the ontological structure of affective situatedness (Befindlichkeit) and its particular, ontic modes, which he calls moods (Stimmungen). In the second section, we draw on a study of grief to demonstrate how this framework can be used when conducting phenomenological interviews and analyses. In the concluding section, we explain how this framework can be guide phenomenological studies across a broad range of existential structures. (shrink)

Several philosophers have suggested that certain aspects of people’s experience of agency partly explains why people tend to report that it seems to them, in perceptual experience, as though time robustly passes. In turn, it has been suggested that people come to believe that time robustly passes on the basis of its seeming to them in experience that it does. We argue that what require explaining is not just that people report that it seems to them as though time robustly (...) passes, and that they believe that it does, but rather, the substantial variation (a) in people’s reports regarding whether it seems as though time robustly passes, and (b) their beliefs about whether time robustly passes. We empirically investigate the agentive explanation of (a), according to which variation in people’s agentive experiences explains variation in people’s reports regarding whether it seems to them as though time robustly passes. We also empirically investigate the experiential seeming explanation of belief, according to which variation in people’s beliefs about whether time robustly passes is explained by variation in their reports regarding whether it seems in experience as though time robustly passes. We found empirical support for the agentive explanation, but not for the experiential seeming explanation of passage beliefs. We consider the implications of our results for three views about temporal experience and temporal beliefs: dynamism, passage illusionism and deflationism. (shrink)

We explore the role of episodic imagining in explaining why people both differentially report that it seems to them in experience as though time robustly passes, and why they differentially report that they believe that time does in fact robustly pass. We empirically investigate two hypotheses, the differential vividness hypothesis, and the mental time travel hypothesis. According to each of these, the degree to which people vividly episodically imagine past/future states of affairs influences their tendency to report that it seems (...) to them as though time robustly passes and to judge that time does robustly pass. According to the former, a greater degree of vividness will tend to increase the extent to which people make such reports, while according to the latter, it will tend to decrease the extent to which people make such reports. We found weak evidence in favour of the former hypothesis. We reflect on the implications of this finding for theorising about such reports. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

The ability to access and share data is key to optimizing and streamlining any industrial production process. Unfortunately, the manufacturing industry is stymied by a lack of interoperability among the systems by which data are produced and managed, and this is true both within and across organizations. In this paper, we describe our work to address this problem through the creation of a suite of modular ontologies representing the product life cycle and its successive phases, from design to end of (...) life. We call this suite the Product Life Cycle (PLC) Ontologies. The suite extends proximately from The Common Core Ontologies (CCO) used widely in defense and intelligence circles, and ultimately from the Basic Formal Ontology (BFO), which serves as top level ontology for the CCO and for some 300 further ontologies. The PLC Ontologies were developed together, but they have been factored to cover particular domains such as design, manufacturing processes, and tools. We argue that these ontologies, when used together with standard public domain alignment and browsing tools created within the context of the Semantic Web, may offer a low-cost approach to solving increasingly costly problems of data management in the manufacturing industry. (shrink)

Since ancient times, legal systems have held owners responsible for harm caused by their property. Across 4 experiments, we show that children aged 3–7 also hold owners responsible for such harm. Older children judge that owners should repair harm caused by property, and younger children may do this as well. Younger and older children judge that owners should apologize for harm, even when children do not believe the owners allowed the harm to occur. Children are also as likely to hold (...) owners responsible for harm caused by property as for harm caused by the owners themselves. The present findings contribute to psychological accounts of ownership by showing that ownership not only confers rights to control property, but also responsibility for harm caused by property. The findings also contribute to our understanding of the attribution of responsibility, and challenge accounts claiming that directly causing harm, or allowing it to happen, is a prerequisite for responsibility. The findings provide support for an account claiming that property is an extension of its owner, and likewise reveal that responsibility for harm caused by property is an early developing aspect of the psychology of ownership. 2018 APA, all rights reserved). (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...) reality and re-entering the matrix. Not only does reason compel us to admit the existence of the external world, it also requires us to face this world, to build for ourselves meaningful lives within it, and to engage, as adults, in the serious business of living. (shrink)

Recently, mainstream philosophy journals have tended to implement more and more stringent forms of peer review, probably in an attempt to prevent editorial decisions that are based on factors other than quality. Against this trend, we propose that journals should relax their standards of acceptance, as well as be less restrictive about whom is to decide what is admitted into the debate. We start by arguing, partly on the basis of the history of peer review in the journal Mind, that (...) past and current peer review practices attest to partisanship with respect to philosophical approach. Then, we explain that such partisanship conflicts with the standard aims of peer review, and that it is both epistemically and morally problematic. This assessment suggests that, if feasible, journals should treat all available and proposed standards of acceptance in philosophy as epistemically equal, and that philosophical work should be evaluated in terms of the novelty and significance of its contribution to developing thought in ways that are of value. Finally, we show, in a programmatic way, that improving the current situation is feasible, and can be done fairly easily. (shrink)

We describe on-going work on IAO-Intel, an information artifact ontology developed as part of a suite of ontologies designed to support the needs of the US Army intelligence community within the framework of the Distributed Common Ground System (DCGS-A). IAO-Intel provides a controlled, structured vocabulary for the consistent formulation of metadata about documents, images, emails and other carriers of information. It will provide a resource for uniform explication of the terms used in multiple existing military dictionaries, thesauri and metadata registries, (...) thereby enhancing the degree to which the content formulated with their aid will be available to computational reasoning. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

We present an ontology of pain and of other pain-related phenomena, building on the definition of pain provided by the International Association for the Study of Pain (IASP). Our strategy is to identify an evolutionarily basic canonical pain phenomenon, involving unpleasant sensory and emotional experience based causally in localized tissue damage that is concordant with that experience. We then show how different variant cases of this canonical pain phenomenon can be distinguished, including pain that is elevated relative to peripheral trauma, (...) pain that is caused neuropathically (thus with no necessary peripheral stimulus), and pain reports arising through deception either of self or of others. We describe how our approach can answer some of the objections raised against the IASP definition, and sketch how it can be used to support more sophisticated discrimination of different types of pain resulting in improved data analysis that can help in advancing pain research. (shrink)

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)

Basic Formal Ontology (BFO) is a top-level ontology used in hundreds of active projects in scientific and other domains. BFO has been selected to serve as top-level ontology in the Industrial Ontologies Foundry (IOF), an initiative to create a suite of ontologies to support digital manufacturing on the part of representatives from a number of branches of the advanced manufacturing industries. We here present a first draft set of axioms and definitions of an IOF upper ontology descending from BFO. The (...) axiomatization is designed to capture the meanings of terms commonly used in manufacturing and is designed to serve as starting point for the construction of the IOF ontology suite. (shrink)

This chapter offers a new criticism of the Mind argument that is both decisive and instructive. It introduces a plausible principle (γ) that places a requirement on one’s having a choice about an event whose causal history includes only other events. Depending on γ’s truth-value, the Mind argument fails in such a way that one or the other of the two main species of libertarianism is the best approach to the metaphysics of freedom. Libertarians argue the compatibility of freedom and (...) indeterminism, and their biggest obstacle is the Mind argument that argues an incompatibility between the two. The chapter aims to build a case for the truth of γ, and so for nonreductive libertarianism. This is achieved by defending it from the best objections that have been brought to light, thereby emphasizing γ’s prima facie plausibility. (shrink)

Commentary on: Olaf Blanke, Thomas Metzinger, Full-body illusions and minimal phenomenal selfhood, Trends in Cognitive Sciences, Volume 13, Issue 1, January 2009, Pages 7-13, ISSN 1364-6613, DOI: 10.1016/j.tics.2008.10.003.

Aggregating individuals’ consistent attitudes might produce inconsistent collective attitudes. Some groups therefore need the capacity to form attitudes that are irreducible to those of their members. Such groups, group-agent realists argue, are agents in control of their own attitude formation. In this paper, however, I show how group-agent realism overlooks the important fact that groups consist of strategically interacting agents. Only by eliminating group agency from our social explanations can we see how individuals vote strategically to gain control of their (...) groups and produce collective attitudes we cannot make sense of if we treat groups as agents. (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)

Public reason liberals expect individuals to have justificatory reasons for their views of certain political issues. This paper considers how groups can, and whether they should, give collective public reasons for their political decisions. A problem is that aggregating individuals’ consistent judgments on reasons and a decision can produce inconsistent collective judgments. The group will then fail to give a reason for its decision. The paper considers various solutions to this problem and defends a deliberative procedure by showing how it (...) incentivizes information sharing and leads to outcomes most acceptable to the group members. (shrink)

Kit Fine has proposed a new solution to what he calls ‘a familiar puzzle’ concerning modality and existence. The puzzle concerns the argument from the alleged truths ‘It is necessary that Socrates is a man’ and ‘It is possible that Socrates does not exist’ to the apparent falsehood ‘It is possible that Socrates is a man and does not exist’. We discuss in detail Fine’s setting up of the ‘puzzle’ and his rejection, with which we concur, of two mooted solutions (...) to it. (One of these uses standard, Kripkean, notions, and the other rests on work done by Arthur Prior.) We set out, and reject, the philosophy of modality underlying Fine’s new solution, and we defend an alternative response to the alleged puzzle. Our solution follows the work of David Wiggins in distinguishing between the sentential operator ‘It is necessary that’ and the predicate modifier ‘necessarily’. We briefly provide this distinction with a possible- world semantics on which it is neither a necessary truth, in some sense, that Socrates exists nor true, in some sense, that Socrates necessarily exists. (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)

The revival of republicanism was meant to challenge the hegemony of liberalism in contemporary political theory on the grounds that liberals show insufficient concern with institutional protection against political misrule. This article challenges this view by showing how neorepublicanism, particularly on Philip Pettit’s formulation, demands no greater institutional protection than does political liberalism. By identifying neutrality between conceptions of the good as the constraint on institutional requirements that forces neorepublicanism into the liberal framework, the article shows that neutrality is what (...) neorepublicans must jettison to offer a tenable critique of liberalism. Only then can neorepublicans ensure greater protection against misrule by demanding that citizens participate more actively in politics. They can then also criticize liberalism for failing to appreciate the importance of such protection. (shrink)

Can groups really be agents or is group agency just a fiction? Christian List and Philip Pettit argue influentially for group-agent realism by showing how certain groups form and act on attitudes in ways they take to be unexplainable at the level of the individual agents constituting them. Group agency is therefore considered not a fiction or a metaphor but a reality we must account for in explanations of certain social phenomena. In this paper, I challenge this defence of group-agent (...) realism by showing how it is undermined by individual-level analysis of how individuals interact within groups. While group agency can be a useful fiction, real agents are at the individual level, not the collective level. (shrink)

In the debate on how we ought to define political freedom, some definitions are criticized for implying that no one can ever be free to perform any action. In this paper, I show how the possibility of freedom depends on a definition that finds an appropriate balance between absence of interference and protection against interference. To assess the possibility of different conceptions of freedom, I consider the trade-offs they make between these two dimensions. I find that pure negative freedom is (...) clearly possible. Republican freedom might also be possible, though its protection requirement is too vague for a definitive verdict. Finally, the recently proposed ‘freedom as independence’ is impossible since it is an attempt to avoid the unavoidable trade-off. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Este ensayo considera la estructura del sujeto ético que se encuentra en los últimos trabajos de Foucault sobre ética, y da cuenta de sus dos conceptos éticos fundamentales: “cuidado de sí” y “estética de la existencia”. El “cuidado de sí”, se argumenta, da a Foucault una manera de conceptualizar la ética que no depende de categorías jurídicas, y que no concibe al sujeto ético en el modelo de la sustancia. “El cuidado de sí” conlleva una comprensión del sujeto ético como (...) un proceso que siempre es relacional, especialmente en relación consigo mismo. Valiéndonos de su ensayo “Qué es un Autor”, se argumenta que al sujeto de la “estética de la existencia”, igual que al autor de un texto, se les entiende como totalmente inmanentes al “objeto”, que usualmente es considerado como opuesto y separado. En lugar de proponer una expresión verdadera de una sustancia interior “auténtica”, la “estética de la existencia” de Foucault se orienta más bien a las prácticas de “creatividad”, cuya forma no puede anticiparse. (shrink)

The Kurdish movement has revitalised the idea of democracy. Under the most difficult of circumstances – squeezed between ISIS on one side and the Turkish armed forces on the other – a radical form of democracy has been implemented that has inspired many both inside and outside the region. Introducing the special issue “Rethinking Democracy in Kurdistan”, this article explores the ingenious challenge to the nation-state system posed by this new democratic theory and practice, focusing on the prison writings of (...) Abdullah Öcalan. These remarkable texts are read as proposing a new philosophy of world-history which decisively breaks with Marxism, displaces the central place of Europe, and drastically extends the point in time at which philosophies of history typically begin. (shrink)

We address the ethics of scenarios in which one party entraps, intentionally tempts or intentionally tests the virtue of another. We classify, in a new manner, three distinct types of acts that are of concern, namely acts of entrapment, of intentional temptation and of virtue testing. Our classification is, for each kind of scenario, of itself neutral concerning the question whether the agent acts permissibly. We explain why acts of entrapment are more ethically objectionable than like acts of intentional temptation (...) and why these, in turn, are more ethically objectionable than like acts of virtue testing. Along the way, we scrutinize, and eventually reject, the view that acts of entrapment are ethically unacceptable because intentional temptation is involved in entrapment. (shrink)

Principles of justice, David Estlund argues, cannot be falsified by people’s unwillingness to satisfy them. In his Utopophobia, Estlund rejects the view that justice must bend to human motivation to deliver practical implications for how institutions ought to function. In this paper, I argue that a substantive argument against such bending of justice principles must challenge the reasons for making these principles sensitive to motivational limitations. Estlund, however, provides no such challenge. His dispute with benders of justice is therefore a (...) verbal one over the true meaning of justice, which need not worry those with the intuition that justice should perform a function that requires bending. By focusing on John Rawls’s reasons for bending his justice principles, I point towards a substantive critique of bent justice. (shrink)

John Rawls thinks republicanism is compatible with his political liberalism. Philip Pettit insists that the two conflict in important ways. In this paper, I make sense of this dispute by employing David Chalmers’s method of elimination to reveal the meaning underlying key terms in Rawls’s political liberalism and Pettit’s republicanism. This procedure of disambiguating terms will show how the two theories defend the same institutional arrangement on the same grounds. The procedure thus vindicates Rawls’s view of the two theories being (...) compatible. The reason for this compatibility is that both theories are politicized—that is, they are constructed to attract the compliance of all reasonable members of a modern, pluralistic society. (shrink)

Our question is this: What makes an act one of entrapment? We make a standard distinction between legal entrapment, which is carried out by parties acting in their capacities as (or as deputies of) law- enforcement agents, and civil entrapment, which is not. We aim to provide a definition of entrapment that covers both and which, for reasons we explain, does not settle questions of permissibility and culpability. We explain, compare, and contrast two existing definitions of legal entrapment to commit (...) a crime that possess this neutrality. We point out some problems with the extensional correctness of these definitions and propose a new definition that resolves these problems. We then extend our definition to provide a more general definition of entrapment, encompassing both civil and legal cases. Our definition is, we believe, closer to being extensionally correct and will, we hope, provide a clearer basis for future discussions about the ethics of entrapment than do the definitions upon which it improves. (shrink)

Some legal theorists say that legal entrapment to commit a crime is incoherent. So far, there is no satisfactorily precise statement of this objection in the literature: it is obscure even as to the type of incoherence that is purportedly involved. (Perhaps consequently, substantial assessment of the objection is also absent.) We aim to provide a new statement of the objection that is more precise and more rigorous than its predecessors. We argue that the best form of the objection asserts (...) that, in attempting to entrap, law-enforcement agents lapse into a form of practical incoherence that involves the attempt simultaneously to pursue contrary ends. We then argue that the objection, in this form, encompasses all cases of legal entrapment only if it is supplemented by appeal to the premise that law-enforcement agents have an absolute duty never to create crimes. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)