The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

In Anti-Oedipus, Deleuze and Guattari claim that a general theory of society must be a generalised theory of flows. This is hardly a straightforward claim, and this paper attempts to examine the grounds for it. Why should socio-political theory be based on a theory of flows rather than, say, a theory of the social contract, or a theory of the State, or the questions of legitimation or revolution, or numerous other possible candidates? The concept of flow (and the related notions (...) of code and stock), I argue, is derived from contemporary economic theory, and most notably John Maynard Keynes. Deleuze and Guattari remained Marxists, not only because they held that contemporary political philosophy must inevitably be centred on the analysis of capitalism, but also because they held, following Marx himself, that the Marxist analysis of capital must constantly be transformed and adapted to new conditions. Thus, while certain aspects of Marx's analysis disappear from Capitalism and Schizophrenia, they are supplemented by the addition of new concepts adequate to the contemporary state of capitalism. The paper concludes, then, with an analysis of the role played by the concepts of flow, code and stock in Deleuze and Guattari's political philosophy. (shrink)

Nanotechnology, as with many technologies before it, places a strain on existing legislation and poses a challenge to all administrative agencies tasked with regulating technology-based products. It is easy to see how statutory schemes become outdated, as our ability to understand and affect the world progresses. In this article, we address the regulatory problems that nanotechnology posses for the Food and Drug Administration’s (FDA) classification structure for ‘‘drugs’’ and ‘‘devices.’’ The last major modification to these terms was in 1976, with (...) the enactment of the Medical Device Amendments. There are serious practical differences for a classification as a drug or device in terms of time to market and research. Drugs are classified, primarily, as acting by ‘‘chemical action.’’ We lay out some legal, philosophic, and scientific tools that serve to provide a useful, as well as legally and scientifically faithful, distinction between drugs and devices for the purpose of regulatory classification. These issues we raise are worth the consideration of anyone who is interested in the regulation of nano-products or other novel technologies. (shrink)

ArgumentIn the United States, scientific knowledge is brought before the courts by way of testimony – the testimony of scientific experts. We argue that this expertise is best understoodfirstas related to the quality of the underlying scienceand thenin terms of who delivers it. Bloodstain pattern analysis (BPA), a contemporary forensic science, serves as the vaulting point for our exploration of objectivity as a metric for the quality of a science in judicial contexts. We argue that BPA fails to meet the (...) minimal standard set by Helen Longino’s social-procedural account of objectivity (1990, 2002). In light of some pressing issues for social-procedural accounts, we offer an infrastructural account of objectivity. This account offers what amounts to a friendly amendment to Longino’s account and adds to the ways in which we might analyze social-procedural objectivity. Finally, we address an issue that is pressing in the legal context: given that scientific knowledge is delivered by individuals, not communities, at least in U.S. courts, we (may) need a way to evaluate individual scientific and epistemic agents. We suggest a means for making this evaluation that is derived from our infrastructural account of objectivity. (shrink)

This paper details how ghost hunting, as a set of learning activities, can be used to enhance critical thinking and philosophy of science classes. We describe in some detail our own work with ghost hunting, and reflect on both intended and unintended consequences of this pedagogical choice. This choice was partly motivated by students’ lack of familiarity with science and philosophic questions about it. We offer reflections on our three different implementations of the ghost hunting activities. In addition, we discuss (...) the practical nuances of implementing these activities, as well the relation of ghost hunting to our course content, including informal fallacies and some models for scientific inference. We conclude that employing ghost hunting along-side traditional activities and content of critical thinking and philosophy of science offers a number of benefits, including being fun, increasing student attendance, enhancing student learning, and providing a platform for campus wide dialogues about philosophy. (shrink)

There has been a recent explosion of undergraduate philosophy conferences across the United States. In this paper, we explore undergraduate conferences along three lines. First, we argue that, as a well-designed learning activity, undergraduate conferences can serve to increase gender parity in philosophical spaces—a widely accepted and important goal for our discipline. Second, we argue that this increase in parity is due, at least in part, to the proper design of undergraduate conferences as High-Impact Practices. Our empirical work on our (...) own undergraduate conference demonstrates that properly designing the conference as a High-Impact learning activity does, as expected, benefit underserved student populations, including women. Additionally, the study also revealed unexpected opportunities to intervene on student learning. Third, we argue, also in line with our data, that undergraduate conferences occupy a previously taxonomically unrecognized grouping among recognized High-Impact Practices. (shrink)

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

SNODENT is a dental diagnostic vocabulary incompletely integrated in SNOMED-CT. Nevertheless, SNODENT could become the de facto standard for dental diagnostic coding. SNODENT's manageable size, the fact that it is administratively self-contained, and relates to a well-understood domain provides valuable opportunities to formulate and test, in controlled experiments, a series of hypothesis concerning diagnostic systems. Of particular interest are questions related to establishing appropriate quality assurance methods for its optimal level of detail in content, its ontological structure, its construction and (...) maintenance. This paper builds on previous–software-based methodologies designed to assess the quality of SNOMED-CT. When applied to SNODENT several deficiencies were uncovered. 9.52% of SNODENT terms point to concepts in SNOMED-CT that have some problem. 18.53% of SNODENT terms point to SNOMED-CT concepts do not have, in SNOMED, the term used by SNODENT. Other findings include the absence of a clear specification of the exact relationship between a term and a termcode in SNODENT and the improper assignment of the same termcode to terms with significantly different meanings. An analysis of the way in which SNODENT is structurally integrated into SNOMED resulted in the generation of 1081 new termcodes reflecting entities not present in the SNOMED tables but required by SNOMED's own description logic based classification principles. Our results show that SNODENT requires considerable enhancements in content, quality of coding, quality of ontological structure and the manner in which it is integrated and aligned with SNOMED. We believe that methods for the analysis of the quality of diagnostic coding systems must be developed and employed if such systems are to be used effectively in both clinical practice and clinical research. (shrink)

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

Abstract The explosion of interest in large language models (LLMs) has been accompanied by concerns over the extent to which generated outputs can be trusted, owing to the prevalence of bias, hallucinations, and so forth. Accordingly, there is a growing interest in the use of ontologies and knowledge graphs to make LLMs more trustworthy. This rests on the long history of ontologies and knowledge graphs in constructing human-comprehensible justification for model outputs as well as traceability concerning the impact of evidence (...) on other evidence. Understanding the nature of arguments and argumentation is critical to each, especially when LLM output conflicts with what is expected by users. The central contribution of this article is to extend the Arguments Ontology (ARGO) - an ontology specific to the domain of argumentation and evidence broadly construed - into the space of LLM fact-checking in the interest of promoting justification and traceability research through the use of ARGO-based ‘blueprints’. (shrink)

In our daily lives, as in science and in all other domains, we encounter huge numbers of dispositions (tendencies, potentials, powers) which are realized in processes such as sneezing, sweating, shedding, melting. Among this plethora of what we can think of as ‘mere dispositions’ is a subset of dispositions in whose realizations we have an interest – a car responding well when driven on ice, a rabbit’s lungs responding well when it is chased by a wolf, and so on. We (...) call the latter ‘capabilities’ and we attempt to provide an ontological account of what capabilities are that is of sufficient generality to serve a variety of purposes, for example by providing a useful extension to ontology-based research in areas where capabilities data are being collected in siloed fashion. (shrink)

Mid-level ontologies are used to integrate data across disparate domains using vocabularies more specific than top-level ontologies and more general than domain-level ontologies. There are no clear, defensible criteria for determining whether a given ontology should count as mid-level, because we lack a rigorous characterization of what the middle level of generality is supposed to contain. Attempts to provide such a characterization have failed, we believe, because they have focused on the goal of specifying what is characteristic of those single (...) ontologies that have been advanced as mid-level ontologies. Unfortunately, single ontologies of this sort are generally a mixture of top- and mid-level, and sometimes even of domainlevel terms. To gain clarity, we aim to specify conditions for membership in what we call the middle architecture, which consists solely of mid-level ontologies. (shrink)

A collaborative article by the Editorial Collective of Social Imaginaries. Investigations into social imaginaries have burgeoned in recent years. From ‘the capitalist imaginary’ to the ‘democratic imaginary’, from the ‘ecological imaginary’ to ‘the global imaginary’ – and beyond – the social imaginaries field has expanded across disciplines and beyond the academy. The recent debates on social imaginaries and potential new imaginaries reveal a recognisable field and paradigm-in-the-making. We argue that Castoriadis, Ricoeur, and Taylor have articulated the most important theoretical frameworks (...) for understanding social imaginaries, although the field as a whole remains heterogeneous. We further argue that the notion of social imaginaries draws on the modern understanding of the imagination as authentically creative. We contend that an elaboration of social imaginaries involves a significant, qualitative shift in the understanding of societies as collectively and politically-instituted formations that are irreducible to inter-subjectivity or systemic logics. After marking out the contours of the field and recounting a philosophical history of the imagination, the essay turns to debates on social imaginaries in more concrete contexts, specifically political-economic imaginaries, the ecological imaginary, multiple modernities and their inter-civilisational encounters. The social imaginaries field imparts powerful messages for the human sciences and wider publics. In particular, social imaginaries hold significant implications for ontological, phenomenological and philosophical anthropological questions; for the cultural, social, and political horizons of contemporary worlds; and for ecological and economic phenomena. The essay concludes with the argument that social imaginaries as a paradigm-in-the-making offers valuable means by which movements towards social change can be elucidated as well providing an open horizon for the critiques of existing social practices. (shrink)

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

In a series of recent publications, orofacial researchers have debated the question of how ‘bruxism’ should be defined for the purposes of accurate diagnosis and reliable clinical research. Following the principles of realism-based ontology, we performed an analysis of the arguments involved. This revealed that the disagreements rested primarily on inconsistent use of terms, so that issues of ontology were thus obfuscated by shortfalls in terminology. In this paper, we demonstrate how bruxism terminology can be improved by paying attention to (...) the relationships between (1) particulars and types, and (2) continuants and occurrents. (shrink)

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

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open (...) Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers. (shrink)

Loneliness in medicine is a serious problem not just for patients, for whom illness is intrinsically isolating, but also for physicians in the contemporary condition of medicine. We explore this problem by investigating the ideal physician-patient relationship, whose analogy with friendship has held enduring normative appeal. Drawing from Talbot Brewer and Nir Ben-Moshe, we argue that this appeal lies in a dynamic form of companionship incompatible with static models of friendship-like physician-patient relationships: a mutual refinement of embodied virtue that draws (...) both persons together. The ideal physician-patient relationship has a dialectical character that fosters each member's improvement of phenomenologically recognizing and embodying moral virtues. A key component of this dynamic is a commitment to the common goal of the patient's health, realized through joint interactivities and conversations over time. The physician's presence to the patient's suffering—understood best as an alienating phenomenological condition for the patient—orients and discloses possibilities for virtuous caregiving by structuring the meanings of the goals, conversations, and joint narrative constitutive of their relationship. Presence to suffering, paradoxically, is perhaps an important prerequisite for this dynamic partnership. These activities dialectically build an interpretive horizon of understanding through which moral goods and character refinement—in and for the other—may become revealed for both persons in their shared being-in-the-world. This analysis of suffering, mood, and revealing of (possible) moral goods has implications for addressing the modern problem of loneliness for patients and physicians, who are increasingly inhibited from building flourishing relationships with each other. (shrink)

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...) diagnostics made possible by the Saliva Ontology and SDxMart. (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)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (shrink)

Perhaps the question “What is philosophy?” can only be posed late in life, when old age has come, and with it the time to speak in concrete terms. It is a question one poses when one no longer has anything to ask for, but its consequences can be considerable. One was asking the question before, one never ceased asking it, but it was too artificial, too abstract; one expounded and dominated the question, more than being grabbed by it. There are (...) cases in which old age bestows not an eternal youth, but on the contrary a sovereign freedom, a pure necessity where one enjoys a moment of grace between life and death, and where all the parts of the machine combine to dispatch into the future a trait that traverses the ages: Turner, Monet, Matisse. The elderly Turner acquired or conquered the right to lead painting down a deserted path from which there was no return, and that was no longer distinguishable from a final question. In the same way, in philosophy, Kant’s Critique of Judgment is a work of old age, a wild work from which descendants will never cease to flow.We cannot lay claim to such a status. The time has simply come for us to ask what philosophy is. And we have never ceased to do this in the past, and we already had the response, which has not varied: philosophy is the art of forming, inventing, and fabricating concepts. But it was not only necessary for the response to take note of the question; it also had to determine a time, an occasion, the circumstances, the landscapes and personae, the conditions and unknowns of the question. One had to be able to pose the question “between friends” as a confidence or a trust, or else, faced with an enemy, as a challenge, and at the same time one had to reach that moment, between dog and wolf, when one mistrusts even the friend. Gilles Deleuze was professor of philosophy at the University of Paris VIII, Vincennes-St.-Denis, until his retirement in 1987. Among his books translated into English are the two-volume Capitalism and Schizophrenia , the two-volume Cinema , The Logic of Sense , and Expressionism in Philosophy: Spinoza . Daniel W. Smith is a doctoral candidate in philosophy at the University of Chicago. He is at work on a study of the philosophy of Deleuze, and is translating Deleuze’s Francis Bacon: Logique de la sensation. Arnold I. Davidson, executive editor of Critical Inquiry, teaches philosophy at the University of Chicago and is currently Marta Sutton Weeks Fellow at the Stanford Humanities Center. (shrink)

This interview, conducted over the span of several months, tracks the respective journeys of Constantin V. Boundas and Daniel W. Smith with the philosophy of Gilles Deleuze. Rather than “becoming Deleuzian,” which is neither desirable nor possible, these exchanges reflect an array of encounters with Deleuze. These include the initial discoveries of Deleuze’s writings by Boundas and Smith, in-person meetings between Boundas and Deleuze, and the wide-ranging and influential philosophical work on Deleuze’s concepts produced by both Boundas and (...) Smith. At stake in this discussion are key contributions by Deleuze to continental philosophy, including the distinction between the virtual and the actual and the very nature of a “concept.” Also at stake is the formative or pedagogical impact of a philosopher, like Deleuze, on those who find and fully engage with his texts, concepts, and project. Cette interview, menée sur plusieurs mois, suit les parcours respectifs de Constantin V. Boundas et Daniel W. Smith avec la philosophie de Gilles Deleuze. Au lieu de « devenir Deleuzien, » ce qui n’est ni souhaitable ni possible, ces échanges reflètent un éventail de rencontres avec Deleuze. Il s’agit notamment des premières découvertes des écrits de Deleuze par Boundas et Smith, des rencontres en personne entre Boundas et Deleuze, et du travail philosophique vaste et in????luent sur les concepts de Deleuze produit par Boundas et Smith. L’enjeu ici étant les contributions clés de Deleuze à la philosophie continentale, y compris la distinction entre le virtuel et l’actuel, et la nature même d’un « concept. » Mais il y a aussi l’impact formateur ou pédagogique d’un philosophe, comme Deleuze, sur ceux qui trouvent et s’engagent pleinement dans ses textes, ses concepts et ses projets. (shrink)

Na długo przed rewolucją francuską oraz jej pierworodną Deklaracją Praw Człowieka i Obywatela w europejskiej myśli politycznej członek państwa przedzierzgnięty został z poddanego w obywatela. Ta fundamentalna zmiana w definiowaniu stanowiska jednostki w państwie korespondowała z humanistycznym postrzeganiem rozumu ludzkiego nie tylko jako instrumentu poznawania świata, ale też narzędzia głębokiej refleksji i krytycznej oceny mechanizmów światem rządzących. Siła rozumu kojarzona była przez oświeceniowych filozofów z porządkiem naturalnym, który jawił się przeciwwagą dla społecznych i politycznych realiów absolutnego władztwa monarszego. W XVIII (...) w. we francuskiej i niemieckiej filozofii państwa nastąpił istotny postęp w zakresie kształtowania się idei obywatela pojmowanego w sensie zbliżonym do Arystotelesowskiej istoty państwowej (politikon zoon). Stało się tak jednak w dużej mierze dzięki XVII-wiecznym angielskim reformom wolnościowym. Racjonalistyczne i materialistyczne podwaliny oświeceniowego światopoglądu konstytuowała też, powstała na bazie krytyki pism Thomasa Hobbesa, myśl Johna Locke’a, stymulująca do urządzania życia społecznego zgodnie z zaleceniami umysłu i potrzeb ludzkich, a wbrew bezwzględnym prawom samowładztwa, w tym jego monopolu na rację, który dusił inicjatywę jednostki. (shrink)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, (...) because these are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (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)

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

In this paper, I explore a possible convergence between two great twentieth century thinkers, Nishida Kitarō of Japan and Martin Heidegger of Germany. The focus is on the quasi-religious language they employ in discussing the grounding of human existence in terms of an encompassing Wherein for our being. Heidegger speaks of “the sacred” and “the passing of the last god” that mark an empty clearing wherein all metaphysical absolutes or gods have withdrawn but are simultaneously indicative of an opening wherein (...) beings are given. Nishida speaks of “the religious” dimension in the depths of one's being, that he calls “place,” and that somehow envelops the world through its kenotic self-negation. In both we find reference to a kind of originary space—the open or place—associated with quasireligious themes. I also point to their distinct approaches to metaphysical language in their attempts to give voice to that abysmal thought. (shrink)

This article examines Gilles Deleuze’s concept of the simulacrum, which Deleuze formulated in the context of his reading of Nietzsche’s project of “overturning Platonism.” The essential Platonic distinction, Deleuze argues, is more profound than the speculative distinction between model and copy, original and image. The deeper, practical distinction moves between two kinds of images or eidolon, for which the Platonic Idea is meant to provide a concrete criterion of selection “Copies” or icons (eikones) are well-grounded claimants to the transcendent Idea, (...) authenticated by their internal resemblance to the Idea, whereas “simulacra” (phantasmata) are like false claimants, built on a dissimilarity and implying an essential perversion or deviation from the Idea. If the goal of Platonism is the triumph of icons over simulacra, the inversion of Platonism would entail an affirmation of the simulacrum as such, which must thus be given its own concept. Deleuze consequently defines the simulacrum in terms of an internal dissimilitude or “disparateness,” which in turn implies a new conception of Ideas, no longer as self-identical qualities (the auto kath’hauto), but rather as constituting a pure concept of difference. An inverted Platonism would necessarily be based on a purely immanent and differential conception of Ideas. Starting from this new conception of the Idea, Deleuze proposes to take up the Platonic project anew, rethinking the fundamental figures of Platonism (selection, repetition, ungrounding, the question-problem complex) on a purely differential basis. In this sense, Deleuze’s inverted Platonism can at the same time be seen as a rejuvenated Platonism and even a completed Platonism. (shrink)

This paper discusses the idea of "pure experience" within the context of the Buddhist tradition and in connection with the notions of emptiness and dependent origination via a reading of Dale Wright's reading of 'Huangbo' in his 'Philosophical Meditations on Zen Buddhism'. The purpose is to appropriate Wright's text in order to engender a response to Steven Katz's contextualist-constructivist thesis that there are no "pure" (i.e., unmediated) experiences. In light of the Mahayana claim that everything is empty of substance, i.e., (...) originates dependently through conditions, contingencies, and contexts, what does the "purity" of the Enlightenment experience mean for Chan/Zen Buddhism? (shrink)

Deleuze argued that a fundamental mutation in the concept of time occurred in Kant. In antiquity, the concept of time was subordinated to the concept of movement: time was a ‘measure’ of movement. In Kant, this relation is inverted: time is no longer subordinated to movement but assumes an autonomy of its own: time becomes "the pure and empty form" of everything that moves and changes. What is essential in the theory of time is not the distinction between objective ‘clock (...) time’ (or physical time) and the subjective experience of ‘time consciousness,’ since both of them measure movements, whether the movement of extensive objects or intensive states. What is fundamental is rather the relation between time and movement, since time can only assume its own concept when it ceases to be subordinate to movement, whether that movement is objective or subjective. This article examines how Kant inverted the relation between time and movement, and how Deleuze’s own theory of time builds on Kant’s revolution and extends it further. (shrink)

Previous work has shown that the Complex Conceptual Spaces − Single Observation Mathematical framework is a useful tool for event characterization. This mathematical framework is developed on the basis of Conceptual Spaces and uses integer linear programming to find the needed similarity values. The work of this paper is focused primarily on space event characterization. In particular, the focus is on the ranking of threats for malicious space events such as a kinetic kill. To make the Conceptual Spaces framework work, (...) the similarity values between the contents of observations on the one hand and the properties of the entities observed on the other needs to be found. This paper shows how to exploit Dempster-Shafer theory to implement a statistical approach for finding these similarities values. This approach will allow a user to identify the uncertainty involved in similarity value data, which can later be propagated through the developed mathematical model in order for the user to know the overall uncertainty in the observation-to-concept mappings needed for space event characterization. (shrink)

This paper explores the question of whether the United Nations should engage in preventive military actions. Correlatively, it asks whether UN preventive military actions could satisfy just war principles. Rather than from the standpoint of the individual nation state, the ethics of preventive war is discussed from the standpoint of the UN. For the sake of brevity, only the legitimate authority, just cause, last resort, and proportionality principles are considered. Since there has been disagreement about the specific content of these (...) principles, a third question also is explored: How should they be formulated? Moreover, these questions are addressed in the context of a particular issue: the goals of the non-proliferation and the abolition of weapons of mass destruction. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:diacritics 35.1 (2005) 8-21MuseSearchJournalsThis JournalContents[Access article in PDF]Klossowski's Reading of Nietzsche Impulses, Phantasms, Simulacra, StereotypesDaniel W. SmithIn his writings on Nietzsche, Pierre Klossowski makes use of various concepts—such as intensities, phantasms, simulacra and stereotypes, resemblance and dissemblance, gregariousness and singularity—that have no place in Nietzsche's own oeuvre. These concepts are Klossowski's own creations, his own contributions to thought. Although Klossowski consistently refused to characterize himself as a philosopher ("Je (...) suis une 'maniaque,'" he once said, "Un point, c'est tout!"),1 his work in its entirety was marked by an extraordinary conceptual creation. From this point of view, his Nietzsche and the Vicious Circle can be read as a work in philosophy—at least in the idiosyncratic sense given to this term by Gilles Deleuze, who defined philosophy as the creation or invention of concepts [Deleuze and Guattari 2]. No doubt, Klossowski remains an almost unclassifiable figure—philosopher, novelist, essayist, translator, artist—and attempting to analyze his work through the prism of philosophy may seem to be a reductive approach that belies the complexity of his exceptional oeuvre. Reading Klossowski as a conceptual innovator, however, at least has the advantage of allowing us to chart a consistent trajectory through his difficult and often labyrinthine text, without denying its other dimensions (affective, perceptive, literary, and so on). In what follows, then, I would like to examine three of Klossowski's most characteristic and important concepts—impulses and their intensities, phantasms, and simulacra and their stereotypes—as well as the precise interrelations he establishes among them. Taken together, these three concepts describe what Klossowski terms the tripartite economy of soul, which constitutes the implicit model through which he interprets Nietzsche's thought.1Impulses as Fluctuating IntensitiesKlossowski describes his books on both Nietzsche and Sade as "essays devoted not to ideologies but to the physiognomies of problematic thinkers who differ greatly from each other" ["Postface" 137, emphasis added]. This emphasis on the "physiognomy" of thinkers reflects Nietzsche's insistence on taking the body rather than the mind as a guide for philosophy since the body is a more accessible phenomenon, less surrounded by myth and superstition. "The body and physiology as the starting point," Nietzsche wrote. "Why?... The phenomenon of the body is the richer, clearer, more tangible [End Page 8] phenomenon.... Belief in the body is more fundamental than belief in the soul" [WP §§492, 489, 491]. Klossowski himself, however, when writing of the intensive status of the impulses, frequently makes use of the term "soul" (âme), owing in part, no doubt, to his interest in the theological literature of the mystics, such as Meister Eckhardt and Teresa of Avila. For the mystics, the depth of the soul is something irreducible and uncreated: it eludes the exercise of the created intellect, and can only be grasped negatively.2 Nonetheless, if one can find a similar apophaticism (or "negative theology") in Klossowski, it is related exclusively to the immanent and chaotic movements of the soul's intensive affects, and not to the transcendence of God. What is incommunicable in the soul (or body) are its "impulses"—their fluctuations of intensity, their rises and falls, their manic elations and depressive descents, which are in constant variation.Nietzsche himself had recourse to a highly varied vocabulary to describe what Klossowski summarizes in the term "impulse": "drive" (Triebe), "desire" (Begierden), "instinct" (Instinke), "power" (Mächte), "force" (Kräfte), "impulse" (Reize, Impulse), "passion" (Leidenschaften), "feeling" (Gefülen), "affect" (Affekte), "pathos" (Pathos), and so on.3 Klossowski frequently employs the musical term tonalité to describe these states of the soul's fluctuating intensities—their diverse tones, timbres, and changing amplitudes—which can take on various forms ("aggressiveness, tolerance, intimidation, anguish, the need for solitude, the forgetting of oneself" [NVC 6]). At bottom, what these impulses express are what Klossowski calls the "obstinate singularity" of the human soul, which is by nature noncommunicable; they constitute "the unexchangeable depth" (le fond inéchangeable) or "the unintelligible depth" (le fond unintelligible) of the soul. What makes every individual... (shrink)

What is the concept of sense developed by Deleuze in his 1969 Logic of Sense? This paper attempts to answer this question analysing the three dimensions of language that Deleuze isolates: the primary order of noises and intensities ; the secondary order of sense ; and the tertiary organisation of propositions. What renders language possible is that which separates sounds from bodies and organises them into propositions, freeing them for the expressive function. Deleuze argues that it is the dimension of (...) sense that brings about this genesis of language, and he analyses in detail the three syntheses that bring about the production of this surface of sense. Yet Deleuze also distinguishes between two types of non-sense: the nonsense of Lewis Carroll's portmanteau words, which remain ensconced in the dimension of sense, and the more profound nonsense of Antonin Artaud's psychotic scream-breaths, which penetrate the almost unbearable world of the primary order of noise and intensities. In the end, the focus of Logic of Sense is less the surface domain of sense than the primary depth of corporeal intensities. What Deleuze calls a ‘minor’ use of language is nothing other than an intensive use of language that constitutes a principle of metamorphosis. (shrink)

This paper will attempt to assess the primary differences between what I take to be the two primary philosophical "traditions" in contemporary French philosophy, using Derrida (transcendence) and Deleuze (immanence) as exemplary representatives. The body of the paper will examine the use of these terms in three different areas of philosophy on which Derrida and Deleuze have both written: subjectivity, ontology, and epistemology. (1) In the field of subjectivity, the notion of the subject has been critiqued in two manners, either (...) by appealing either to the transcendence of the other (Levinas, Derrida) or to the immanent jlux of experience itself, in relation to which the Ego itself is trancendent (Deleuze, Foucault, Sartre, James). (2) In the field of ontology, a purely "immanent" ontology would be an ontology in which there is neither a "beyond" or an "otherwise" Being, nor "interruptions" in Being, both of which would require an appeal to a formal element of transcendence (Deleuze). Such a "transcendent" and aporetic structure, which can never appear or be present as such within Being, is what lies at the basis of the project of deconstruction, with its attendant aporias (Derrida). (3) This distinction, finally, finds parallels in Kant's epistemology, for whom the possible experience is conditioned by purely immanent criteria (Deleuze), whereas what goes beyond the limits of possible experience is transcendent (Derrida). Drawing on these three thread of analysis, the paper concludes with an assessment of what is at stake in the ethical differences between the two traditions. The question of "transcendence" is "What mast I do?", which is the question of morality (a duty or obligation that is beyond being, an "ought" beyond the "is"). The question of "immanence" is "What can I do?" (my power or capacity as an existing individual within being). For Levinas and Derrida, ethics precedes ontology because it is derived from an element of transcendence (the Other); for Deleuze, ethics is ontology because it is derived from the immanent relation of beings to Being at the level of their existence (Spinoza). (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)