The purpose of this paper is to examine the central role of praxis in Arendt’s conception of the human world and the structure of political life as a site of subjective interaction and narrative discourse. First, Arendt’s use of Aristotle will be presented in terms of the meaning of action as a unique philosophical category. Second, Arendt’s encounter with the work of Martin Heidegger will be shown to involve a critical response to his reading of Aristotle. Finally, the revised conception (...) of praxis that derives from her philosophical reflections will be related to the experience of narrative as a necessary complement to human plurality. (shrink)

This paper argues that Paul Ricoeur’s hermeneutical philosophy attempts to reopen the question of human transcendence in contemporary terms. While his conception of language as self-transcending is deeply Husserlian, Ricoeur also responds to the analytical challenge when he deploys a basic distinction in Fregean logic in order to clarify Heidegger’s phenomenology of world. Ricoeur’s commitment to a transcendental view is evident in his conception of narrative, which enables him to emphasize the role of the performative in literary reading. The meaning (...) of the self in time provides Ricoeur with a discursive basis for distinguishing his own position from that of Kant and other philosophers in the transcendental tradition. (shrink)

This paper argues that Hegel attempts to appropriate the irreversible aspects of Romantic aesthetics in four ways: (i) Hegel radicalizes Kantian aesthetics on the basis of a basically textual approach to sublime experience that opens up the question of community as a philosophical one; (ii) without demoting classical conceptions of art, Hegel privileges Romantic conceptions that demonstrate the ascendancy of sign over symbol in a spiraling chain; (iii) Hegel laments the fate of art in the triumph of Romantic subjectivism but (...) also suggests how communities can reconstitute themselves on the horizon of aesthetic dissolution; so that, finally, (iv) art can be reconceived as a emancipatory adventure that redefines metaphysics through its historical unfolding as an unending series of semiotic transformations. (shrink)

Heidegger's interpretation of Nietzsche has been canonized in the philosophical tradition as an almost perfect demonstration of how the forgetfulness of Being continues the dominant positions of modern metaphysics. However, the role of reading in the interpretative process casts a different light on Heidegger's approach to Nietzsche and his relationship to the philosophical tradition. This paper is concerned with three aspects of Heidegger's work, namely, (i) the role of Kant and Schopenhauer in Nietzsche's critique of metaphysics; (ii) Nietzsche's 'inversion' of (...) Platonism; and (iii) Heidegger's contribution to a hermeneutical reappraisal of Nietzsche's thought. (shrink)

This article demonstrates how a new reading of Rilke’s poetry can provide a basis for comparing and contrasting the aesthetic approach to art and the language-based approach that foregrounds the role of metaphor and materiality in literary production. Lessing’s Laocoön is discussed in terms of an implied dialogue between painting and poetry, which, however, acquires a different valence when the Fifth of Rilke’s 'Duino Elegies' suggests that poetry itself functions as a ‘metaphorical hypoicon’ allowing for shared meanings. My concluding remarks (...) emphasize the importance of the performing self to a complete understanding of Rilke’s semiotic potential. (shrink)

The main purpose of this paper is to demonstrate how Gianni Vattimo offers a new interpretation of history that challenges standard accounts of the modern period and promotes a new approach to literature. The paper begins with a discussion of how the Cartesian cogito provides an inadequate basis for historical research, and then proposes that modern history can be 'read' when it is reassessed through recent hermeneutics. In 'The End of Modernity' (1985), Vattimo indicates that Heidegger's understanding of the "overcoming (...) of metaphysics" shifted in time, thus suggesting new insights into modernity. The conclusion to the paper applies these insights to show how the notion of a unified literary period is difficult to sustain in a postmodern framework. -/- . (shrink)

As presented in the early work, 'Revolution in Poetic Language,' Julia Kristeva’s 'subject-in-process' can be interpreted as a semiotic alternative to older conceptions of the philosophical subject.This discussion of Kristeva’s early work will attempt to demonstrate that new interpretations of Fregean logic and Freudian psychoanalysis radically displace the traditional subject. This act of displacement allows Kristeva to employ Hegelian dialectics to introduce a “textual” conception of meaning of experience. As a consequence, the Kristevan semiotexte offers a basis for both understanding (...) and misunderstanding in which language mediates between semiotic meaning and cultural practices. The conclusion of the paper maintains that Kristeva's unique formulation of the semiotexte re-defines human subjectivity in relation to the existing world. (shrink)

This paper is concerned with Maurice Merleau-Ponty’s contribution to the hermeneutical theory of expressive meaning that has been developed on the basis of an ongoing dialogue with traditional phenomenology. The early portion of the paper examines the unstable boundaries between expression and indication as a key to a new approach to expressive meaning. The paper then takes up Merleau-Ponty’s understanding of expressive life as it emerges in ‘Phenomenology of Perception,’ his first attempt to discuss perception, aesthetics, and temporality in comprehensive (...) terms. The third part of the paper examines Merleau-Ponty’s return to the paintings of Paul Cezanne, which not only clarifies his earlier position but also deepens the philosophical meaning of his reflections on language. My final comments are concerned with how phenomenology can be broadened in a way that can become responsive to the hermeneutical theory of expressive meaning. (shrink)

A critical discussion of DAVID WILSON and WILLIAM DIXON, A History of Homo Economicus. The nature of the moral in economic theory, London and New York, Routledge, pp. xviii+123 ISBN 978-0-415-59568-1. I declare agreement with one basic idea in this book, that economic discourse is performative, or economic theory is not pure theorìa. I add several objections to the historical reconstruction carried out os such authors as Malthus and Ricardo and I object to the definition adopted of homo (...) economicus. (shrink)

Adorno’s dialectical approach to aesthetics is perhaps understood better in terms of his monumental work, 'Aesthetic Theory,' which attempts to relate the speculative tradition in philosophical aesthetics to the situation of art in twentieth-century society, than in terms of purely theoretical claims. This paper demonstrates that Adorno embraces the Kantian thesis concerning art’s autonomy and that he criticizes transcendental philosophy. It also discusses how Adorno provides the outlines for a dialectical conception of artistic truth in relation to his argument with (...) Hegel. Adorno’s assessment of the Enlightenment is linked to his interpretation of twentieth-century literature. The conclusion of this paper emphasizes the political implications of Adorno’s position when the philosopher approaches art as a sign of historical truth. (shrink)

This paper examines how semiotics, in conjunction with hermeneutics, can illuminate the structure of James Joyce's 'Ulysses' as a literary text. The paper begins with an account of two poet-critics who examined Joyce's novel in terms of classical myths and literary precedents. A crucial turning-point in the essay occurs when Jean Michel Rabate's Lacanian reading of the novel is introduced to clarify Joyce's use of the "signifier of absence" to clarify the meaning of paternity in the novel. The function of (...) the intertext is then examined, particularly in view of the relationship between Stephen Dedalus and Leopold Bloom. The conclusion of the paper shows how a dialogical reading supports the belief in a 'hermeneutical self' as part of the text's underlying meaning. (shrink)

The paper argues that Sartre’s work as both a literary critic and social philosopher is deeply indebted to his early commitment to phenomenology. The first part of the paper examines the nature of reading and writing in the account of literary meaning that is presented in the transitional text, 'Qu’est-ce que la littérature?' While acknowledging the political turn that occurs in Sartre’s work, we then discuss how the theme of history emerges in the later essay, 'Questions de méthode,' as one (...) that opens up a “double reading” of human motivation. Our conclusion maintains that the Marxist phase of Sartre’s work is based on the hermeneutical notion of comprehension, which provides an anthropological grounding for his existential philosophy. (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)

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 translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Philosophers have rightly condemned lookism—that is, discrimination in favor of attractive people or against unattractive people—in education, the justice system, the workplace and elsewhere. Surprisingly, however, the almost universal preference for attractive romantic and sexual partners has rarely received serious ethical scrutiny. On its face, it’s unclear whether this is a form of discrimination we should reject or tolerate. I consider arguments for both views. On the one hand, a strong case can be made that preferring attractive partners is bad. (...) The idea is that choosing partners based on looks seems essentially similar to other objectionable forms of discrimination. (In particular, the preference for attractive partners is arguably both unfair and harmful to a significant degree.) One can try to resist this conclusion in several ways. I consider three possible replies. The first has to do with the possibility of controlling our partner preferences. The second pertains to attractiveness and “good genes”. The last attempts to link certain aspects of attractiveness to a prospective partner’s personality and values. I argue that the first two replies fail conclusively, while the third only amounts to a limited defense of a particular kind of attractiveness preference. So the idea that we should often avoid preferring attractive partners is compelling. (shrink)

The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)

We discuss potential biorisks from large language models (LLMs). AI assistants based on LLMs such as ChatGPT have been shown to significantly reduce barriers to entry for actors wishing to synthesize dangerous, potentially novel pathogens and chemical weapons. The harms from deploying such bioagents could be further magnified by AI-assisted misinformation. We endorse several policy responses to these dangers, including prerelease evaluations of biomedical AIs by subject-matter experts, enhanced surveillance and lab screening procedures, restrictions on AI training data, and access (...) controls on biomedical AI. We conclude with a suggestion about future research directions in bioethics. (shrink)

The field of AI safety aims to prevent increasingly capable artificially intelligent systems from causing humans harm. Research on moral alignment is widely thought to offer a promising safety strategy: if we can equip AI systems with appropriate ethical rules, according to this line of thought, they'll be unlikely to disempower, destroy or otherwise seriously harm us. Deontological morality looks like a particularly attractive candidate for an alignment target, given its popularity, relative technical tractability and commitment to harm-avoidance principles. I (...) argue that the connection between moral alignment and safe behavior is more tenuous than many have hoped. In general, AI systems can possess either of these properties in the absence of the other, and we should favor safety when the two conflict. In particular, advanced AI systems governed by standard versions of deontology need not be especially safe. (shrink)

Mathematicians distinguish between proofs that explain their results and those that merely prove. This paper explores the nature of explanatory proofs, their role in mathematical practice, and some of the reasons why philosophers should care about them. Among the questions addressed are the following: what kinds of proofs are generally explanatory (or not)? What makes a proof explanatory? Do all mathematical explanations involve proof in an essential way? Are there really such things as explanatory proofs, and if so, how do (...) they relate to the sorts of explanation encountered in philosophy of science and metaphysics? (shrink)

Defense of an account of intrinsic properties in terms of (what is now called) grounding rather than naturalness.

Gauss’s quadratic reciprocity theorem is among the most important results in the history of number theory. It’s also among the most mysterious: since its discovery in the late 18th century, mathematicians have regarded reciprocity as a deeply surprising fact in need of explanation. Intriguingly, though, there’s little agreement on how the theorem is best explained. Two quite different kinds of proof are most often praised as explanatory: an elementary argument that gives the theorem an intuitive geometric interpretation, due to Gauss (...) and Eisenstein, and a sophisticated proof using algebraic number theory, due to Hilbert. Philosophers have yet to look carefully at such explanatory disagreements in mathematics. I do so here. According to the view I defend, there are two important explanatory virtues—depth and transparency—which different proofs (and other potential explanations) possess to different degrees. Although not mutually exclusive in principle, the packages of features associated with the two stand in some tension with one another, so that very deep explanations are rarely transparent, and vice versa. After developing the theory of depth and transparency and applying it to the case of quadratic reciprocity, I draw some morals about the nature of mathematical explanation. (shrink)

This chapter examines the ways in which French philosopher Gilles Deleuze offers conceptual resources for an enactive account of language, in particular his extensive consideration of language in The Logic of Sense. Specifically, Deleuze’s distinction between the nonsense of Lewis Carroll’s portmanteau creations and that of Antonin Artaud’s “transla- tion” of Carroll’s Jabberwocky highlights the need for an enactive, rather than merely embodied, approach to sense-making, particularly with regard to the general category of what Jakobson and Halle (1956) call “sound (...) symbolism”. (shrink)

According to a widespread view in metaphysics and philosophy of science, all explanations involve relations of ontic dependence between the items appearing in the explanandum and the items appearing in the explanans. I argue that a family of mathematical cases, which I call “viewing-as explanations”, are incompatible with the Dependence Thesis. These cases, I claim, feature genuine explanations that aren’t supported by ontic dependence relations. Hence the thesis isn’t true in general. The first part of the paper defends this claim (...) and discusses its significance. The second part of the paper considers whether viewing-as explanations occur in the empirical sciences, focusing on the case of so-called fictional models. It’s sometimes suggested that fictional models can be explanatory even though they fail to represent actual worldly dependence relations. Whether or not such models explain, I suggest, depends on whether we think scientific explanations necessarily give information relevant to intervention and control. Finally, I argue that counterfactual approaches to explanation also have trouble accommodating viewing-as cases. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

Philosophers of science since Nagel have been interested in the links between intertheoretic reduction and explanation, understanding and other forms of epistemic progress. Although intertheoretic reduction is widely agreed to occur in pure mathematics as well as empirical science, the relationship between reduction and explanation in the mathematical setting has rarely been investigated in a similarly serious way. This paper examines an important particular case: the reduction of arithmetic to set theory. I claim that the reduction is unexplanatory. In defense (...) of this claim, I offer evidence from mathematical practice, and I respond to contrary suggestions due to Steinhart, Maddy, Kitcher and Quine. I then show how, even if set-theoretic reductions are generally not explanatory, set theory can nevertheless serve as a legitimate foundation for mathematics. Finally, some implications of my thesis for philosophy of mathematics and philosophy of science are discussed. In particular, I suggest that some reductions in mathematics are probably explanatory, and I propose that differing standards of theory acceptance might account for the apparent lack of unexplanatory reductions in the empirical sciences. (shrink)

Mathematicians often describe the importance of well-developed intuition to productive research and successful learning. But neither education researchers nor philosophers interested in epistemic dimensions of mathematical practice have yet given the topic the sustained attention it deserves. The trouble is partly that intuition in the relevant sense lacks a usefully clear characterization, so we begin by offering one: mature intuition, we say, is the capacity for fast, fluent, reliable and insightful inference with respect to some subject matter. We illustrate the (...) role of mature intuition in mathematical practice with an assortment of examples, including data from a sequence of clinical interviews in which a student improves upon initially misleading covariational intuitions. Finally, we show how the study of intuition can yield insights for philosophers and education theorists. First, it contributes to a longstanding debate in epistemology by undermining epistemicism, the view that an agent’s degree of objectual understanding is determined exclusively by their knowledge, beliefs and credences. We argue on the contrary that intuition can contribute directly and independently to understanding. Second, we identify potential pedagogical avenues towards the development of mature intuition, highlighting strategies including adding imagery, developing associations, establishing confidence and generalizing concepts. (shrink)

We defend a noetic account of intramathematical explanation. On this view, a piece of mathematics is explanatory just in case it produces understanding of an appropriate type. We motivate the view by presenting some appealing features of noeticism. We then discuss and criticize the most prominent extant version of noeticism, due to Inglis and Mejía Ramos, which identifies explanatory understanding with the possession of well-organized cognitive schemas. Finally, we present a novel noetic account. On our view, explanatory understanding arises from (...) meeting specific explanatory objectives. We defend a cluster-concept account of explanatory objectives and identify four important subfamilies within the relevant network of resemblance relations. The resulting view is objectivist (in the sense that it takes explanatory success to be a matter of observer-independent fact), broader in scope than why-question-based accounts, compatible with empirical findings on experts’ explanatory judgments, and capable of generalizing (with appropriate provisos) to scientific explanation as a whole. It thus fulfills Friedman’s half-century-old demand for a general and objectivist theory which accounts for the link between explanation and understanding. (shrink)

Models are indispensable tools of scientific inquiry, and one of their main uses is to improve our understanding of the phenomena they represent. How do models accomplish this? And what does this tell us about the nature of understanding? While much recent work has aimed at answering these questions, philosophers' focus has been squarely on models in empirical science. I aim to show that pure mathematics also deserves a seat at the table. I begin by presenting two cases: Cramér’s random (...) model of the prime numbers and the function field model of the integers. These cases show that mathematicians, like empirical scientists, rely on unrealistic models to gain understanding of complex phenomena. They also have important implications for some much-discussed theses about scientific understanding. First, modeling practices in mathematics confirm that one can gain understanding without obtaining an explanation. Second, these cases undermine the popular thesis that unrealistic models confer understanding by imparting counterfactual knowledge. (shrink)

A proof P of a theorem T is transferable when a typical expert can become convinced of T solely on the basis of their prior knowledge and the information contained in P. Easwaran has argued that transferability is a constraint on acceptable proof. Meanwhile, a proof P is fixable when it’s possible for other experts to correct any mistakes P contains without having to develop significant new mathematics. Habgood-Coote and Tanswell have observed that some acceptable proofs are both fixable and (...) in need of fixing, in the sense that they contain nontrivial mistakes. The claim that acceptable proofs must be transferable seems quite plausible. The claim that some acceptable proofs need fixing seems plausible too. Unfortunately, these attractive suggestions stand in tension with one another. I argue that the transferability requirement is the problem. Acceptable proofs need only satisfy a weaker requirement I call “corrigibility”. I explain why, despite appearances, the corrigibility standard is preferable to stricter alternatives. (shrink)

The problem of truth in fiction concerns how to tell whether a given proposition is true in a given fiction. Thus far, the nearly universal consensus has been that some propositions are ‘implicitly true’ in some fictions: such propositions are not expressed by any explicit statements in the relevant work, but are nevertheless held to be true in those works on the basis of some other set of criteria. I call this family of views ‘implicitism’. I argue that implicitism faces (...) serious problems, whereas the opposite view is much more plausible than has previously been thought. After mounting a limited defence of explicitism, I explore a difficult problem for the view and discuss some possible responses. (shrink)

Bill D'Alessandro talks to Kenny Easwaran about fractal music, Zoom conferences, being a good referee, teaching in math and philosophy, the rationalist community and its relationship to academia, decision-theoretic pluralism, and the city of Manhattan, Kansas.

Recent progress in artificial intelligence (AI) has drawn attention to the technology’s transformative potential, including what some see as its prospects for causing large-scale harm. We review two influential arguments purporting to show how AI could pose catastrophic risks. The first argument — the Problem of Power-Seeking — claims that, under certain assumptions, advanced AI systems are likely to engage in dangerous power-seeking behavior in pursuit of their goals. We review reasons for thinking that AI systems might seek power, that (...) they might obtain it, that this could lead to catastrophe, and that we might build and deploy such systems anyway. The second argument claims that the development of human-level AI will unlock rapid further progress, culminating in AI systems far more capable than any human — this is the Singularity Hypothesis. Power-seeking behavior on the part of such systems might be particularly dangerous. We discuss a variety of objections to both arguments and conclude by assessing the state of the debate. (shrink)

In a recent letter, Dillion et. al (2023) make various suggestions regarding the idea of artificially intelligent systems, such as large language models, replacing human subjects in empirical moral psychology. We argue that human subjects are in various ways indispensable.

A review of Matt Cook's book Sleight of Mind: 75 Ingenious Paradoxes in Mathematics, Physics, and Philosophy.

David Sloan Wilson has recently revived the idea of a group mind as an application of group selectionist thinking to cognition. Central to my discussion of this idea is the distinction between the claim that groups have a psychology and what I call the social manifestation thesis-a thesis about the psychology of individuals. Contemporary work on this topic has confused these two theses. My discussion also points to research questions and issues that Wilson's work raises, as well as (...) their connection to externalist conceptions of the mind familiar since the work of Putnam and Burge. (shrink)

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Mindfulness-based interventions are reported as being efficacious treatments for a variety of psychological and somatic conditions. However, concerns have arisen relating to how mindfulness is operationalized in mindfulness-based interventions and whether its ‘spiritual essence’ and full potential treatment efficacy have remained intact. This qualitative study used interpretative phenomenological analysis to examine participant experiences regarding the acceptability and effectiveness of a newly designed secularized intervention called meditation awareness training (MAT) that follows a more traditional Buddhist approach to meditation. Participants (with issues (...) of stress and low mood) reported experiencing improvements in psychological well-being due to receiving MAT. The wider implications are discussed. (shrink)

The prevalence of workaholism in Western populations is approximately 10%,although estimates vary considerably according to how “workaholism” is defined.There is growing consensus that workaholism is a bona fide behavioral addiction that exists at the extreme end of the work-engagement continuum and causes similar negative consequences to other behavioral addictions such as salience, conflict, tolerance, withdrawal symptoms,and mood modification. Other more specific consequences include burnout, work compulsion,work–family conflict, impaired productivity, asociality,and psychological/somatic illness.

This paper points to some problems for the position that D.M. Walsh calls "alternative individualism," and argues that in defending this view Walsh has omitted an important part of what separates individualists and externalists in psychology. Walsh's example of Hox gene complexes is discussed in detail to show why some sort of externalism about scientific taxonomy more generally is a more plausible view than any extant version of individualism.

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

William James’ argument against William Clifford in The Will to Believe is often understood in terms of doxastic efficacy, the power of belief to influence an outcome. Although that is one strand of James’ argument, there is another which is driven by ampliative risk. The second strand of James’ argument, when applied to scientific cases, is tantamount to what is now called the Argument from Inductive Risk. Either strand of James’ argument is sufficient to rebut Clifford's strong evidentialism (...) and show that it is sometimes permissible to believe in the absence of compelling evidence. However, the two considerations have different scope and force. Doxastic efficacy applies in only some cases but allows any values to play a role in determining belief; risk applies in all cases but only allows particular conditional values to play a role. (shrink)

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

L’érosion actuelle de la confiance du public envers les campagnes de vaccination et les décisions de politiques publiques qui y sont associées, aggravée par des scandales comme ceux relatifs à la pandémie H1N1 et l’utilisation du Tamiflu™, risque de diminuer de façon significative l’efficacité de ces interventions importantes pour la santé publique. Un manque de confiance de la population envers les acteurs de santé publique peut conduire à une méfiance accrue face aux interventions, pouvant ainsi compromettre l’atteinte des objectifs recherchés (...) par une intervention spécifique et, conséquemment, avoir un impact important sur les bénéfices attendus pour la population visée par cette intervention. Dans la production des avis d’experts, les membres des comités consultatifs d’experts en immunisation (CCEI) peuvent avoir une influence importante sur la prise de décision publique, notamment, sur la sélection par les décideurs de santé publique de vaccins en particulier et la façon dont les campagnes de vaccination seront déployées. En contrepartie de cette influence sur les décisions publiques, une indépendance et une transparence sont attendues de leur part puisque des mécanismes de divulgation et de gestion de conflits d’intérêts (CI) imparfaits peuvent affecter négativement la confiance du public à l’égard de telles décisions. Il apparaît donc important de s’assurer que des mécanismes de gestion des CI, transparents et robustes, existent pour ces comités. Dans cette étude, les avis ou rapports d’évaluation de la pertinence de la vaccination préparés par un CCEI au Québec ont été examinés pour quatre types de maladies évitables par la vaccination (infections invasives à méningocoques et à pneumocoques, coqueluche et virus du papillome humain). Le but était de : 1) identifier les CI divulgués par les membres du CCEI dans leurs rapports comparativement à ceux déclarés dans leurs publications scientifiques pour ces mêmes infections ; 2) analyser la nature des CI (réel, potentiel, apparent, personnel, financier, institutionnel, etc.) et l’impact potentiel (risque) sur la prise de décision impartiale et sur la confiance du public ; et 3) évaluer les mécanismes de gestion de CI actuellement utilisés par ce CCEI. Les résultats de cette étude montrent que très peu de rapports du CCEI contiennent une section sur les CI par rapport à la pléthore divulguée dans les publications scientifiques publiées par les membres du CCEI. De plus, les CI divulgués dans les rapports fréquemment ne correspondent pas à ceux décrits dans les publications scientifiques. Il serait donc important d’introduire des mesures visant à accroître la transparence des experts en immunisation et d’améliorer les mécanismes de divulgation et de gestion des CI afin de veiller à ce que la confiance du public envers les décideurs en santé publique soit maintenue et améliorée. (shrink)

Cette note devait introduire à un public anglophone la traduction de la « Lettre de Louis Althusser datée du 18 mars 1966 et adressée au Comité central du PCF », elle est ici enrichie dans une version livrée au public français. Elle apporte le contexte historique et théorique nécessaire à la compréhension des interventions « anti-humanistes » de Louis Althusser qui questionne les choix politiques opérés par le PCF au cours des années 1960. Nulle part ailleurs, dans les écrits publiés (...) d’Althusser, nous ne voyons aussi clairement les enjeux politiques imbriqués dans son projet philosophique, ni comment ce projet évolua progressivement d’une entreprise « théoriciste » à la recherche d’une philosophie en lien plus étroit avec la pratique. Cette lettre nous paraît de la plus haute importance pour les spécialistes de l’œuvre d’Althusser, les historiens de la pensée marxiste, mais aussi plus largement à tous ceux qui s’intéressent à l’importance que peut revêtir le travail d’Althusser dans les débats actuels dans le champ de la philosophie marxiste. (shrink)

Almost everyone who has a limb amputated will experience a phantom limb--the vivid impression that the limb is not only still present, but in some cases, painful. There is now a wealth of empirical evidence demonstrating changes in cortical topography in primates following deafferentation or amputation, and this review will attempt to relate these in a systematic way to the clinical phenomenology of phantom limbs. With the advent of non-invasive imaging techniques such as MEG (magnetoencephalogram) and functional MRI, topographical reorganization (...) can also be demonstrated in humans, so that it is now possible to track perceptual changes and changes in cortical topography in individual patients. We suggest, therefore, that these patients provide a valuable opportunity not only for exploring neural plasticity in the adult human brain but also for understanding the relationship between the activity of sensory neurons and conscious experience. We conclude with a theory of phantom limbs, some striking demonstrations of phantoms induced in normal subjects, and some remarks about the relevance of these phenomena to the question of how the brain constructs a 'body image.'. (shrink)

One might suppose that Everettian quantum mechanics (EQM) is inhospitable to metaphysial indeterminacy (MI), given that, as A. Wilson (2020) puts it, "the central idea of EQM is to replace indeterminacy with multiplicity" (77). But as Wilson goes on to suggest, the popular decoherence-based understanding of EQM (henceforth: DEQM) appears to admit of indeterminacy in both world number and world nature, where the latter indeterminacy---our focus here---is plausibly metaphysical. After a brief presentation of DEQM (S1), we bolster the (...) case for there being MI in world nature in DEQM (S2). The remainder of the paper is devoted to a comparative assessment of the two main approaches to MI for purposes of accommodating this MI---namely, a metaphysical supervaluationist approach (as per Barnes and Williams 2011) and a determinable-based approach (as per Wilson 2013 and Calosi and Wilson 2018 and 2021). We briefly describe each approach (S3), then offer arguments in favour of a determinable-based approach to world nature MI in DEQM (S4). (shrink)

Daniel Dennett has offered a set of necessary and sufficient conditions for something's being the proper object of our moral commitment, that is, for something's being a person. Strict application of these largely pragmatic conditions, however, would result in a moral community with quite a surprising membership roster, because of both who is on it and who isn't. The problem is that "your" being a person should amount to more than a function of "my" goals and cleverness.

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Over decades of teaching systematic theology at Union Theological Seminary (New York), Christopher Morse has set out to salvage “dogmatics” as a postmodern theological discipline that nevertheless retains a (more or less literal) construal of the apocalyptic gospel message. This article attempts to clarify this project in conversation with William James’ best-known work on religious belief.