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)

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)

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)

(Shoshana Smith now goes by her married name, Shoshana Brassfield: http://philpapers.org/profile/37640) Descartes famously claims that everything we perceive clearly and distinctly is true. Although this rule is fundamental to Descartes’s theory of knowledge, readers from Gassendi and Leibniz onward have complained that unless Descartes can say explicitly what clear and distinct perception is, how we know when we have it, and why it cannot be wrong, then the rule is empty. I offer a detailed analysis of clear and distinct (...) perception, showing how Descartes answers these questions. Many doubts about the usefulness of the clarity and distinctness rule arise from the mistaken assumption that in clear and distinct perception, like sense perception, we must be able to establish a correspondence between perception and reality before we can have knowledge. I show that Descartes has a different metaphysical picture of clear and distinct perception. Clear and distinct perception is direct perception, typically of essences. On this view, by relying on the intellect instead of the senses, we can have direct perception not only of our own ideas, but also of a mind-independent reality. Because clear and distinct perception is direct perception, problems of correspondence do not arise. My account of clear and distinct perception also yields unique insight into other issues in Descartes, such as the Cartesian Circle and the doctrine of the free creation of the eternal truths. Completed at the University of California, 2005. Dissertation advisers: Janet Broughton, Hannah Ginsborg, Anthony A. Long. ProQuest UMI: 3187156. (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)

This paper follows Francois Laruelle’s non-philosophy and his non-religion and non-theology to suggest anon-philosophical approach to the sociology of religious pluralism. The entanglements of experiences of the religious end-user are analysed vis-a-vis Laruelle’s thought and a dogma free inclusive approach to religion is envisaged.

Whether intentional suppression of an unpleasant or unwanted memory reduces the ability to recall that memory subsequently is a contested issue in contemporary memory research. Building on findings that similar processes are recruited when individuals remember the past and imagine the future, we measured the effects of thought suppression on memory for imagined future scenarios. Thought suppression reduced the ability to recall emotionally negative scenarios, but not those that were emotionally positive. This finding suggests that intentionally avoiding thoughts about emotionally (...) negative episodes may inhibit representations of those memories, progressively reducing their availability to recall. (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.

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Skepticism is one of the most enduring and profound of philosophical problems. With its roots in Plato and the Sceptics to Descartes, Hume, Kant and Wittgenstein, skepticism presents a challenge that every philosopher must reckon with. In this outstanding collection philosophers engage with skepticism in five clear sections: the philosophical history of skepticism in Greek, Cartesian and Kantian thought; the nature and limits of certainty; the possibility of knowledge and related problems such as perception and the debates between objective knowledge (...) and constructivism; the transcendental method as a response to skepticism and the challenge of naturalism; overcoming the skeptical challenge. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Proponents of public reason views hold that the exercise of political power ought to be acceptable to all reasonable citizens. This article elucidates the common structure shared by all public reason views, first by identifying a set of questions that all such views must answer and, second, by showing that the answers to these questions stand in a particular relationship to each other. In particular, we show that what we call the ‘rationale question’ is fundamental. This fact, and the common (...) structure more generally, are often overlooked or distorted within the literature. As a result, we argue, several prominent argumentative moves made by both critics and defenders of public reason are unsuccessful. Our overall conclusion is that discussions of public reason views would be more fruitful if they made consistent use of the common structure we identify. (shrink)

This paper applies the ontological framework developed by Roman Ingarden in his Controversy over the Existence of the World to the domain of mathematics, concluding with some remarks on parallels between the mode of existence of mathematical entities on the one hand and of values on the other.

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

I provide two arguments against value-free naturalism. Both are based on considerations concerning biological teleology. Value-free naturalism is the thesis that both (1) everything is, at least in principle, under the purview of the sciences and (2) all scientific facts are purely non-evaluative. First, I advance a counterexample to any analysis on which natural selection is necessary to biological teleology. This should concern the value-free naturalist, since most value-free analyses of biological teleology appeal to natural selection. My counterexample is unique (...) in that it is likely to actually occur. It concerns the creation of synthetic life. Recent developments in synthetic biology suggest scientists will eventually be able to develop synthetic life. Such life, however, would not have any of its traits naturally selected for. Second, I develop a simple argument that biological teleology is a scientific but value-laden notion. Consequently, value-free naturalism is false. I end with some concluding remarks on the implications for naturalism, the thesis that (1). Naturalism may be salvaged only if we reject (2). (2) is a dogma that unnecessarily constrains our conception of the sciences. Only a naturalism that recognizes value-laden notions as scientifically respectable can be true. Such a naturalism is a functional naturalism. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

In their article ’Is Pregnancy a Disease? A Normative Approach’, Anna Smajdor and Joona Räsänen contend that, on several of the most prominent accounts of disease, pregnancy should be considered a disease. More specifically, of the five accounts they discuss, each renders pregnancy a disease or suffers serious conceptual problems otherwise. They take issue specifically with the dysfunction account of disease and argue that it suffers several theoretical difficulties. In this response, we focus on defending the dysfunction account against their (...) main objections and show why a version of the dysfunction account is viable on account of the indispensability of normativity in biology and medicine. After disarming their main objections to the dysfunction account, we briefly respond to their treatment of the normality of pregnancy and then draw a distinction between adverse symptoms and underlying causes to show why even though pregnancy may have ’disease-like’ features, it is not a disease. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Digital technology has prompted philosophers to rethink some of the fundamental categories we use to make sense of the world and ourselves. Particularly, the concept of ‘identity’ and its reconfiguration in the digital age has sparked much debate in this regard. While many studies have addressed the impact of the digital on personal and social identities, the concept of ‘collective identity’ has been remarkably absent in such inquiries. In this article, I take the context of social movements as an entry (...) point to discuss the reconfiguration of collective identity in social media environments. I do so by introducing a narrative approach to collective identity. I argue that Twitter’s affordances invite new ways of constructing collective identities and imply a shifting relationship between the individual and the collective. (shrink)

This is the first book-length philosophical study of Husserl’s transcendental phenomenology and Freud’s theory of the unconscious. The book investigates the possibility for Husserl’s transcendental phenomenology to clarify Freud’s concept of the unconscious with a focus on the theory of repression as its centre. Repression is the unconscious activity of pushing something away from consciousness, while making sure that it remains active as something foreign within us. How this is possible is the main problem addressed in the work. Unlike previous (...) literature (including Ricœur, Merleau-Ponty and Derrida) this book makes full use of the resources of genetic phenomenology and passivity in the attempt to clarify the Freudian unconscious. The central argument developed is that the structure of the lebendige Gegenwart as the core of Husserl’s theory of passivity consists of preliminary forms of bodily kinaesthesia, feelings and drives in a constantly ongoing process where repression occurs as a necessary part of all constitution. The clarification of Freudian repression thus takes place by showing how it presupposes a broad conception of consciousness such as that presented by Husserl’s genetic phenomenology. By arguing that “repression” is central to any philosophical account of subjectivity, this book takes on the most distinct challenge to philosophy posed by Freud. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

The proper relationship between phenomenology and naturalism has reemerged as a pressing issue following interdisciplinary developments in the cognitive sciences. Most solutions opt for a naturalized phenomenology, rather than a phenomenological naturalism. This article takes up the latter approach, confronting the implications of Merleau-Ponty's reformulation of Husserl's paradox of subjectivity. I argue that Merleau-Ponty's formulation—which I term “the paradox of madness”—reveals a deep, ontological contingency in what Husserl took to be necessary transcendental structures of consciousness and world, revealing that these (...) transcendental structures are in fact embedded in and contaminated by the very world they constitute and disclose. (shrink)

History has left a territory composed of two municipalitics, whose shape is unique, belonging partly to the Netherlands and partly to Belgium. Earlier both parts belonged to the former Duchy of Brabant, a tenitory that is now split up into the Dutch province of Noord-Brabant (including Baarle-Nassau) and thc Belgian provinces of Antwerp (which includes Baarle-Hertog), Vlaams Brabant, Brussels, and Brabant-Wallon. People are quite comfortable with this situation, even though it raises many complicated and difficult problems that even the most (...) brilliant jurists are puzzled. Baarle-Hertog is called on older Belgian maps Barle-Duc (Hertog = Duke, fr: duc) and must not be confused with the prefectoral town of Bar-le-Duc, Meuse, France. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

Recently, there have been calls to develop a more contextual approach to phenomenological psychopathology—an approach that attends to the socio-cultural as well as personal and biographical factors that shape experiences of mental illness. In this Perspective article, we argue that to develop this contextual approach, phenomenological psychopathology should adopt a new paradigm case. For decades, schizophrenia has served as the paradigmatic example of a condition that can be better understood through phenomenological investigation. And recent calls for a contextual approach continue (...) to use schizophrenia as their primary example. We argue, in contrast, that substance misuse provides a better paradigm case around which to develop a contextually sensitive phenomenological psychopathology. After providing a brief vignette and analysis of a case of substance misuse, we explain why this kind of condition requires considerable sensitivity and attention to context, better motivating the incorporation and development of new contextually sensitive approaches. (shrink)

Certain states in the Global North have responded to refugees seeking safety on their territories through harmful practices of border violence, detention, encampment and containment that serve to prevent and deter refugee arrivals. These practices are ostensibly justified through an appeal to a right to control borders. This paper therefore assesses whether these harmful practices can indeed be morally justified by a state’s right to control borders. It analyses whether Christopher Heath Wellman’s account of a state’s right to freedom of (...) association, which represents the most restrictive account of a state’s right to control borders available in the literature, can extend to justify current harmful practices against refugees. If not, then no available justification will be able to do so, and thus contemporary harmful practices used against refugees cannot be justified by a state’s right to control borders. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. Terms in OBCS, including ‘data collection’, ‘data transformation in statistics’, ‘data visualization’, ‘statistical data (...) analysis’, and ‘drawing a conclusion based on data’, cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. By representing statistics-related terms and their relations in a rigorous fashion, OBCS facilitates standard data analysis and integration, and supports reproducible biological and clinical research. (shrink)

Empathy is a topic of continuous debate in the nursing literature. Many argue that empathy is indispensable to effective nursing practice. Yet others argue that nurses should rather rely on sympathy, compassion, or consolation. However, a more troubling disagreement underlies these debates: There’s no consensus on how to define empathy. This lack of consensus is the primary obstacle to a constructive debate over the role and import of empathy in nursing practice. The solution to this problem seems obvious: Nurses need (...) to reach a consensus on the meaning and definition of empathy. But this is easier said than done. Concept analyses, for instance, reveal a profound ambiguity and heterogeneity of the concept of empathy across the nursing literature. Since the term “empathy” is used to refer to a range of perceptual, cognitive, emotional, and behavioral phenomena, the presence of a conceptual ambiguity and heterogeneity is hardly surprising. Our proposal is simple. To move forward, we need to return to the basics. We should develop the concept from the ground up. That is, we should begin by identifying and describing the most fundamental form of empathic experience. Once we identify the most fundamental form of empathy, we will be able to distinguish among the more derivative experiences and behaviors that are addressed by the same name and, ideally, determine the place of these phenomena in the field of nursing. The aim of this article is, consequently, to lay the groundwork for a more coherent concept of empathy and thereby for a more fruitful debate over the role of empathy in nursing. In Part 1, we outline the history of the concept of empathy within nursing, explain why nurses are sometimes warry of adapting concepts from other disciplines, and argue that nurses should distinguish between adapting concepts from applied disciplines and from more theoretical disciplines. In Part 2, we show that the distinction between emotional and cognitive empathy—borrowed from theoretical psychology—has been a major factor in nurses’ negative attitudes toward emotional empathy. We argue, however, that both concepts fail to capture the most fundamental form of empathy. In Part 3, we draw on and present some of the seminal studies of empathy that can be found in the work of phenomenological philosophers including Max Scheler, Edmund Husserl, and Edith Stein. In Part 4, we outline how their understanding of empathy may facilitate current debates about empathy’s role in nursing. (shrink)

The article recalls Dr. B. R. Ambedkar's critique of sacred narratives and liberatory practices to let the reader to get a taste of how philosophy can play out on the political level in the society.

One of the most intriguing claims in Sven Rosenkranz’s Justification as Ignorance is that Timothy Williamson’s celebrated anti-luminosity argument can be resisted when it comes to the condition ~K~KP—the condition that one is in no position to know that one is in no position to know P. In this paper, I critically assess this claim.

Bare plural generic sentences pervade ordinary talk. And yet it is extremely controversial what semantics to assign to such sentences. In this paper, I achieve two tasks. First, I develop a novel classification of the various standard uses to which bare plurals may be put. This “variety data” is important—it gives rise to much of the difficulty in systematically theorizing about bare plurals. Second, I develop a novel account of bare plurals, the radical account. On this account, all bare plurals (...) fail to express propositions. The content of a bare plural has to be pragmatically “completed” by a speaker in order for her to make an assertion. At least the content of a quantifier expression has to be supplied. But sometimes, the content of a sentential operator or modal verb is also supplied. The radical account straightforwardly explains the variety data: Speakers’ communicative intentions vary wildly across different contexts. (shrink)

A review of Anthony Appiah's Experiments in Ethics.

Sartre draws a sharp distinction between consciousness, on the one hand, and inner sense or knowledge of (it)self, on the other: ‘La conscience n’est pas un mode de connaisance particullier, appelé sens intime ou connaisance de soi’ (B& N: 7). I explore in detail the meaning of the terms involved in that distinction with a view to highlight its significance.

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)

Today, many philosophers write on topics of contemporary interest, such as emerging technologies, scientific advancements, or major political events. However, many of these reflections, while philosophically valuable, fail to contribute to those who may benefit the most from them. In this article, we discuss our own experience of engaging with nursing researchers and practicing nurses. By drawing on the field of philosophical phenomenology, we intervene in a longstanding debate over the meaning of “empathy” in nursing, which has important implications for (...) nursing research, training, and practice. However, our intention is not only to introduce and discuss this philosophical intervention. Rather, we present this intervention as a model for how philosophers might successfully engage with the field of nursing, and perhaps with other fields as well, with the aim of effecting positive change in research or practice. The article proceeds in five parts. First, we introduce the problem of conceptual clarity in nursing and explain why many nursing concepts are still in need of refinement. Second, we discuss the origins of the concept of empathy in nursing and outline the challenges associated with borrowing theory from other fields. Third, we explain how nurses tend to conceptualize empathy today, drawing upon the psychological distinction between cognitive and emotional empathy. Fourth, we discuss our intervention in this debate and explain how we attempt to resolve existing conceptual confusions by developing the concept of empathy from the ground up. Fifth, we conclude by briefly reflecting upon some of the challenges of interdisciplinary engagement and providing some recommendations based upon our own experience. (shrink)

There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summarizes what (...) is known about Kafka’s relations to the Brentanist movement. It draws on Brentanian ideas on the evidence of inner perception, on oblique consciousness, on active introspection, on correct and incorrect judgment, and on consciousness as a species of inner tribunal, in order to throw light on central features of Kafka’s writings, including stylistic features. Special attention is directed towards Die Verwandlung and Der Prozess, and a reading of the latter is offered according to which the trial of Joseph K. occurs entirely within the mind of K. himself. The revisions in the 1997 version of the paper relate especially to the treatment of Kafka and Brentano in Arnold Heidsieck’s book The Intellectual Contexts of Kafka’s Fiction: Philosophy, Law, Religion, of 1994. (shrink)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

Functionalists hold that the territorial rights of states are grounded solely in their successful performance of their morally mandated functions. In this paper, I defend a distinctive functionalist view of the right of territorial jurisdiction. I develop this view over the course of considering a variety of objections to functionalism that arise from reflection on cases of non- violent and otherwise rights-respecting annexation. Functionalism’s critics argue that it is committed to counterintuitive implications in these cases, as it is unable to (...) explain why the usurper states do not gain rights over the territory they take over. Against these critics, I argue that functionalism can in fact deliver intuitively plausible verdicts regarding: (a) the territorial rights of unsuccessful states; (b) the morality of military occupation; and (c) the appropriate response to past territorial injustices. (shrink)

A philosophical discussion of children's well-being in which various existing views of well-being are discussed to determine their implications for children's well-being and a variety of views of children's well-being are considered and evaluated.