Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (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)

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

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)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

For much of the first fifty years of its existence, analytic philosophy shunned discussions of normativity and ethics. Ethical statements were considered as pseudo-propositions, or as expressions of pro- or con-attitudes of minor theoretical significance. Nowadays, in contrast, prominent analytic philosophers pay close attention to normative problems. Here we focus our attention on the work of Searle, at the same time drawing out an important connection between Searle’s work and that of two other seminal figures in this development: H.L.A. Hart (...) and John Rawls. We show that all three thinkers tend to assume that there is but one type of normativity within the realm of social institutions – roughly, the sort of normativity that is involved in following the results of chess – and that they thereby neglect features that are of crucial significance for an adequate understanding of social reality. (shrink)

The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...) comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each component (...) being designed to solve some one part of the total problem and at the same time reflect well-defined needs on the prat of our customers. We compare our strategy with the research roadmap proposed by the Question Answering Committee of the National Institute of Standards and Technology (NIST), paying special attention to the role of ontology. (shrink)

Radical democratic thinking is becoming intrigued by the material situatedness of its political agents and by the role of nonhuman participants in political interaction. At stake here is the displacement of narrow anthropocentrism that currently guides democratic theory and practice, and its repositioning into what we call ‘the nonhuman condition’. This Critical Exchange explores the nonhuman condition. It asks: What are the implications of decentering the human subject via a new materialist reading of radical democracy? Does this reading dilute political (...) agency? Or should this be seen, on the contrary, as an invitation for new voices and demands to enter into democratic assemblages? How might engagement with the more-than-human disrupt or extend theories of radical democracy? Hans Asenbaum and Amanda Machin discuss the human democratic subject both through radical democratic and new materialist lenses. They suggest that a new materialist decentred subject does not lose agency but further gains political responsibility in radical democracy. Jean-Paul Gagnon highlights the possibility of becoming through loss. In losing our anthropocentric arrogance—our understanding of being other and better than animal—we become more connected and discover our place in human-nonhuman assemblages. Melissa Orlie agrees that something can be gained through renouncing dominant human fantasies and presents a ‘radical democratic naturalism’. By renouncing land violence and acknowledging nature’s subjectivity, we can further nonexploitative radical democratic politics. This is where the notion of ‘tidalectic’ processes introduced by James L. Smith is helpful. Focusing on water and the Indigenous knowledges around rivers, he considers how democracy and community can be reimagined as plural, cyclical and attentive to the nonhuman with which the human is inevitably entangled. Diana Leong offers a different approach. Considering the nonhuman from the perspective of Black Studies demands an awareness to how blackness has long been constituted as non- or partially human. (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 banks 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)

It is now generally recognized that figures such as Reid, Peirce, and Reinach formulated theories of speech acts avant la lettre of Austin and Searle, in Reid and Reinach’s cases under the heading ‘theory of social acts’. Here we address the question as to what conditions would have to be satisfied for such theories to count as ‘theories of speech acts’ in the now familiar sense.

The most obvious varieties of mental phenomena directed to non- existent objects occur in our experiences of works of art. The task of applying the Meinongian ontology of the non-existent to the working out of a theory of aesthetic phenomena was however carried out not by Meinong by his disciple Stephan Witasek in his Grundzüge der allgemeinen Ästhetik of 1904. Witasek shows in detail how our feelings undergo certain sorts of structural modifications when they are directed towards what does not (...) exist. He draws a distinction between genuine mental phenomena and what he calls `phantasy-material', asserting that `the job of the aesthetic object, whether it is a work of art or a product of nature, is to excite and support the actualisation of phantasy-material in the experiencing subject'. We might think of such phantasy-material as a matter of Ersatz-emotions or emotional `slop'. We could then see Witasek's aesthetics as an elaborate taxonomy of the various different sorts of Ersatz-emotions which the subject allows to be stimulated within himself in his intercourse with works of art, and see works of art themselves as machines for the production of ever more subtle varieties of such phantasy-material in the perceiving subject. (shrink)

Le présent article est une tentative nouvelle d’articuler le rôle d’une théorie des vérifacteurs. Nous soutenons que la théorie de la vérifaction constitue une pierre angulaire dans une bonne méthodologie en métaphysique, mais que l’amalgame entre la théorie de la vérifaction et la théorie de la vérité a été responsable de certains excès associés aux approches vérifactionnistes dans la littérature récente. Nous montrons que la théorie de la vérifaction conserve son attrait comme instrument d’investigation métaphysique, et ce, malgré notre accord (...) avec les doctrines déflationnistes telles que celles défendues par Ayer, Quine, Field et Horwich (ou, du moins, malgré notre neutralité à leur égard). Nous soutenons en outre que les intuitions sous-jacentes à la théorie de la vérifaction s’éclairent quand nous les dissocions d’une théorie de la vérité et, par-dessus tout, de la tentative de fournir une définition de la vérité. (shrink)

The current economic/political system, neoliberalism, has touched every aspect of life globally. The doctrine of neoliberalism consists of three central propositions, that the market is real and part of the natural universal law; that unlimited economic growth is both possible and even desirable; and that human nature is coincident with market values and based solely on self-interest. All three of these propositions are seriously flawed and have caused immense human suffering and staggering environmental destruction. This paper is a reminder of (...) the failures of neoliberal policy and an appeal for change to a new institutional arrangement in which development trumps economic growth. This position is in contrast to Francis Fukuyama’s end-of-history thesis. He alleges there are no economic/political ideologies to compete with neoliberalism, the “TINA principle: There Is No Alternative”: the West has won. It is time to reintroduce Henry David Thoreau’s, and to a lesser extent, Adam Smith’s moral economies. Both have encourgaging insights, often overlooked by current academic economists, which could figure prominently in the conception of a new economy. (shrink)

La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui (...) existent indépendamment de nos actes cognitifs (par exemple: la planète Terre, sa surface extérieure); et des objets qui existent seulement grâce à ces actes (par exemple: l'équateur, la Mer du Nord). Le champ visuel, lui aussi, peut être conçu comme un exemple d'une entité à extension spatiale qui est dépendante dans le sens proposé ci-dessus. L'étude présente suggère une extension de cette analogie en postulant les entités qui, pour les vrais jugements, seraient ce que le champ visuel est pour les actes de perception visuelle. Le champ de jugement est défini plus précisément comme une entité étendue complexe, contenant toutes les entités essentielles pour la vérité d'un (vrai) jugement donné. Il est possible de démontrer que le travail des linguistes cognitifs tel Talmy ou Langacker, si l'on l'interprète convenablement, produit une explication détaillée des structures des champs de jugement correspondant aux phrases de sortes différentes. Un genre nouveau de définition de la vérité en tant que correspondance pour les expressions de la langue naturelle peut donc être formulé sur cette base. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

This chapter explores the place of remorse in Sophie de Grouchy’s moral theory, as presented in her 1798 work, Letters on Sympathy, which was originally published with her translation of Adam Smith’s Theory of Moral Sentiments. I argue that, for Grouchy, a cultivated sense of remorse weakens our self-conceit by drawing our attention to the ways in which we harm others, even for seemingly justifiable reasons. In so doing, we are led to recognize the equal standing of others, which (...) gives rise to the “sentiment of natural equality.” This “sentiment of natural equality” places a check on our norms and institutions and allows for the potential of moral progress. While Grouchy frames the Letters as a commentary on Smith’s writings, her discussion of remorse, equality, and moral progress shows her to be a bold and original thinker, and one worth taking seriously. (shrink)

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

Michael Slote’s Moral Sentimentalism is a wonderful model of a particular, under-appreciated philosophical method. It demonstrates that exciting, original work can be created by putting old ideas to new uses, proving once again that the classics of moral and political philosophy offer too rich an array of intellectual resources to leave to historians alone. Whenever one is reclaiming old ideas, however, the most important decision is which ideas to reclaim, and which to leave in the dustbin of history. Slote makes (...) use of many ideas drawn from history’s greatest moral sentimentalist, David Hume, but he rejects many others. The work of Hume’s closest friend and greatest sentimentalist ally, Adam Smith, is rejected without adequate explanation. Smith is mentioned, but quickly dismissed. Yet even though Smith makes little contribution to Slote’s own version of sentimentalism, I think he deserved greater discussion in this book. Smith and Slote address many of the same subjects, using the same basic sentimentalist approach, but they come to very different conclusions. It is thus possible to construct a fruitful debate between them—a debate in which, since he can no longer speak on his own behalf, I will be taking Smith’s side. (shrink)

The ancient theory of substance and accident is supposed to make sense of complex unities in a way that respects both their unity and their complexity. On Hume’s view such complex unities are only fictitiously unities. This result follows from his thoroughgoing critique of the theory of substance. I will characterize the theory Hume is critiquing as it is presented in Locke, presupposing what Bennett calls the “Leibnizian interpretation.” Locke uses the word ‘substance’ in two senses. Call substance in the (...) first sense “individual substance” and in the second sense “pure substance.” I will discuss the seven main parts of Hume’s view: (I) that we have no idea of pure substance, (II) that there is no complex individual substance, except in a loose sense, (III) that the fiction of complex individual substance arises in a way parallel to that of the fiction of identity through time, and (IV) results in the fiction of pure substance, (V) that simple qualities and perceptions satisfy the definition of individual substance, (VI) that there is no such thing as inherence, and (VII) that there is no such thing as pure substance. Hume’s views on substance are often mentioned without being discussed in detail. Kemp Smith, Stroud, and Garrett, for example, mostly summarize various claims of Hume in the course of expounding on his theory of the idea of personal identity. In contrast, I will attempt to present a systematic treatment of Hume on substance as a refutation of Locke. (shrink)

John Rawls shares the Enlightenment's commitment to finding moral and political principles which can be reflectively endorsed by all individuals autonomously. He usually presents reflective autonomy in Kantian, rationalist terms: autonomy is identified with the exercise of reason, and principles of justice must be constructed which are acceptable to all on the basis of reason alone. Yet David Hume, Adam Smith and many other Enlightenment thinkers rejected such rationalism, searching instead for principles which can be endorsed by all on (...) the basis of all the faculties of the human psyche, emotion and imagination included. The influence of these sentimentalists on Rawls is clearest in his descriptive moral psychology, but I argue that it is also present in Rawls's understanding of the sources of normativity. Although this debt is obscured by Rawls's explicit "Kantianism," his theory would be strengthened by a greater understanding of its debts to the sentimentalist Enlightenment. (shrink)

With Being Me Being You, Samuel Fleischacker provides a reconstruction and defense of Adam Smith’s account of empathy, and the role it plays in building moral consensus, motivating moral behavior, and correcting our biases, prejudices, and tendency to demonize one another. He sees this book as an intervention in recent debates about the role that empathy plays in our morality. For some, such as Paul Bloom, Joshua Greene, Jesse Prinz, and others, empathy, or our capacity for fellow-feeling, tends to (...) misguide us in the best of cases, and more often reinforces faction and tribalism in morals and politics. These utilitarians, as Fleischacker refers to them, propose that empathy take a back seat to cost-benefit analysis in moral decision-making. As an intervention, the book is largely successful. Fleischacker’s defense of empathy is nuanced and escapes the myopic enthusiasm to which many partisans of empathy are prone. Anyone looking to understand the relationship between empathy and morality would do well to grapple with Being Me Being You. Still, Fleischacker overlooks that Smith would most likely be less convinced of the idea that greater empathy can help us overcome the great challenges of our time. (shrink)

First published in 1995. Routledge is an imprint of Taylor & Francis, an informa company.

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

The central hypothesis of the collaboration between Language and Computing (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is that the methodology and conceptual rigor of a philosophically inspired formal ontology greatly benefits application ontologies. To this end r®, L&C’s ontology, which is designed to integrate and reason across various external databases simultaneously, has been submitted to the conceptual demands of IFOMIS’s Basic Formal Ontology (BFO). With this project we aim to move beyond the level of (...) controlled vocabularies to yield an ontology with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase® are standardized in a framework of first-order logic. In this paper we describe how this standardization has already led to an improvement in the LinKBase® structure that allows for a greater degree of internal coherence than ever before possible. We then show the use of this philosophical standardization for the purpose of mapping external databases to one another, using LinKBase® as translation hub, with a greater degree of success than possible hitherto. We demonstrate how this offers a genuine advance over other application ontologies that have not submitted themselves to the demands of philosophical scrutiny. LinKBase® is one of the world’s largest applications-oriented medical domain ontologies, and BFO is one of the world’s first philosophically driven reference ontologies. The collaboration of the two thus initiates a new phase in the quest to solve the so-called “Tower of Babel”. (shrink)

Whether it was John Searle’s Chinese Room argument (Searle, 1980) or Roger Penrose’s argument of the non-computable nature of a mathematician’s insight – an argument that was based on Gödel’s Incompleteness theorem (Penrose, 1989), we have always had skeptics that questioned the possibility of realizing strong Artificial Intelligence (AI), or what has become known by Artificial General Intelligence (AGI). But this new book by Landgrebe and Smith (henceforth, L&S) is perhaps the strongest argument ever made against strong AI. It (...) is a very extensive review of what building a mind essentially amounts to drawing on insights and results from biology, physics, linguistics, computability, philosophy, and mathematics. (shrink)

This review article offers a discussion of some aspects of the historical and conceptual context when the term “ontology” (Lat. ontologia) was first introduced in the scholarly circles of the early 17th century. In particular, Barry Smith's (2022) analysis of the birth of ontology provides a springboard for some further remarks on the author of the work with the first known occurrence of the word “ontologia”, Jacob Lorhard, including an analysis of his relationship with earlier philosophers Petrus Ramus and (...) Clemens Timpler. (shrink)

Robert Kraut has proposed an analogy between valuing a loved one as irreplaceable and the sort of “rigid” attachment that (according to Saul Kripke’s account) occurs with the reference of proper names. We wanted to see if individuals with Kripkean intuitions were indeed more likely to value loved ones (and other persons and things) as irreplaceable. In this empirical study, 162 participants completed an online questionnaire asking them to consider how appropriate it would be to feel the same way about (...) a perfect replica of a loved one, as well as other questions about replaceability. Participants who previously had endorsed Kripkean reference (n = 96) rated loved ones as less replaceable on two different measures than participants who had previously endorsed Descriptivist reference (n = 66, t(160)> 2.27, p <.02, eta2> .03). Additional results suggest that this difference extends to other targets as well and is at least partially dependent on sentimental attachment. (shrink)

This paper argues that it is prudentially wise to defer to groups about how they are essentially constituted and defined. After a few words situating the paper in my greater research project (§1), I articulate the kind of deference I have in mind (§2). Then I offer two conditional arguments on why it is epistemically desirable to let other people tell you how they ought to be identified (§3). The first argument is that people are owed lexical sovereignty because denying (...) it is absurd; the second is that modest skeptics ought to agree with it on the basis of some relatively anodyne and plausible epistemic considerations. (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 paper explores the possibility that Hobbesian jurisprudence is best understood as a ‘third way’ in legal theory, irreducible to classical natural law or legal positivism. I sketch two potential ‘third theories’ of law -- legal pragmatism and legal dualism -- and argue that, when considered in its broadest sense, Leviathan is best viewed as an example of legal pragmatism. I consider whether this legal pragmatist interpretation can be sustained in the examination of Leviathan’s treatment of civil law, and argue (...) that the pragmatic interpretation can only be successful if we can resolve two textual issues in that chapter. First, while Hobbes argues that law entails the existence of public (sharable) reasons, he does not adequately defend the view that the sovereign is the unique authority over such reasons in all cases, especially as far as they concern known collective emergencies. Second, Hobbes both affirms and denies that a sovereign can fail to do justice, which is paradoxical. Both problems are best resolved by legal pragmatism, though the second problem resists a fully satisfying resolution. The upshot is that, although Leviathan ought to be regarded as an episode of legal pragmatism, there are trade-offs on every reading. (shrink)

What follows is an attempt to do some conceptual housekeeping around the notion of secret law as provided by Christopher Kutz (2013). First I consider low-salience (or merely obscure) law, suggesting that it fails to capture the legal and moral facts that are at stake in the case which Kutz used to motivate it. Then I outline a theoretical contrast between mere obscurity and secrecy, in contrast to the 'neutral' account of secrecy provided by Sissela Bok (1989). The upshot of (...) the two sections is that low-salience law is neither secret law nor necessarily problematic, though it closely resembles a kind of law that is both secret and problematic: namely, those legal obscurities that subvert manifest interests related to the informational needs of citizens. The ensuing argument undermines the fiction of constructive presence found in Austin and Blackstone. (shrink)

There at least three ways of thinking about rationality: instrumental, substantive, and intentional. By far, the instrumental account is most influential. This essay proposes that intentional rationality can provide substantive accounts with room to breathe, and in a way that is facially distinct from instrumental accounts. I suggest that the intentionality of a judgment is made up of what it is about and the orientation through which it is judged, while irrationality is the subversion of a strict supporting connection between (...) the judgment and its corresponding set of coordinated attitudes (reasons). It follows that irrational intentionality is made up of episodic states where a judgment is subverted because of a misalignment between what it is about and the way the judge is oriented towards its contents. Four examples of irrational intentionality are considered: passivity towards ends, constitutive ignorance towards facts, delirious paranoia towards objects, and a disjunctive orientation towards categorizations. (shrink)

In this paper, I outline a theory of social kinds. A general theory of social kinds has to set out at least three conditions: existence conditions, persistence conditions, and identity conditions. For the sake of expediency, I focus on the existence and persistence conditions. The paper is organized just as life: first with existence, then persistence. I argue that anti-realism is more attractive than realism as an account of the existence conditions, despite the fact that realism has been under-appreciated. Then (...) I argue for a particular theory of the persistence conditions, which I call the basic overlapping traits theory (BOTT), based on an analogy to an approach to personal identity. The upshot of the argument is that from an anti-realist metaphysics we have the capacity to discuss a wider diversity of social phenomena. (shrink)

In this paper I argue that textualism is far less attractive as a theory of written law than some of its modern proponents think. For it is not usually sensible to expect the grammatical meaning of a provision to determine its appropriate legal meaning. Factors that are unrelated to grammar in the identification of law (e.g., legal theory, context) do too much of the work. **Draft -- acknowledgments welcome, but please do not cite.**.

The very idea of promulgation has been given little to no treatment in the philosophy of law. In this exploratory essay, I introduce three possible theories of promulgation: the ‘no-theory theory’ (which treats promulgation as a matter of particular contexts), the ‘conveyance theory’ (which treats promulgation as a function of intellectual good faith interpreters), and ‘agonistic theory’ (which treats promulgation as indistinguishable from propaganda). I suggest that (at least) three kinds of models are consistent with the theories, and can potentially (...) help us understand when law is successfully promulgated in particular legal contexts: the spread model, the chain model, and the memetic model. I end the paper by comparing the two theories with respect to a case study. Throughout I will show that the conveyance and agonistic theories have a serious advantage over the no-theory theory, in that they allow us to comparatively examine the epistemic weaknesses of diverse theories about the grounding of law on the basis of their contents. (shrink)

As a contribution to a wider discussion on moral discernment in theological anthropology, this paper seeks to answer the question “What is the impact of mental illness on an individual’s ability to make moral decisions?” Written from a clinical psychiatric perspective, it considers recent contributions from psychology, neuropsychology and imaging technology. It notes that the popular conception that mental illness necessarily robs an individual of moral responsibility is largely unfounded. Most people who suffer from mental health problems do not lose (...) the capacity to make moral decisions, and mental illness on its own rarely explains anti-social or criminal behaviour. Moreover, the assumptions of some scientists, that recent developments in neuropsychology and brain imaging suggest biological determinism, must be treated with caution. (shrink)

Nicole Hassoun’s sufficientarian theory is based on a particular conception of caring, which she calls ‘care, simpliciter’. However, ‘care, simpliciter’ is not described in any detail. This essay tries to offer a critical revision of Hassoun’s concept of care in a way that would put the MGL theory on its strongest footing. To that end, I will contrast her view with a taxonomy of care that supplements the accounts of care provided by Stephen Darwall and Lori Gruen. I then put (...) forward a form of empathy that is best suited to the MGL theory, which fits the description of ‘care, simpliciter’. **Unpublished manuscript: feel free to cite.**. (shrink)

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

The concept of sustainable development considers environmental, social and economic issues in general. And the goals of resource conservation and socio-economic development do not contradict each other, but contribute to mutual reinforcement. The purpose of this study is to build and test an economic and mathematical model for the formation of strategies for the behavior of an economic entity with an increase in the impact of negative environmental factors. The proposed strategies and their models are based on the income-expenditure balance (...) equation, which takes into account both quantitative and qualitative characteristics. The constructed models are considered in the state space. The research methodology is based on building models in the form of linear combinations of functions of a homogeneous external impact and various spatial combinations of economic sources (sinks). The study makes it possible to assess the dependence of the amount of resources used for life support on the chosen adaptive strategy. Within the framework of the proposed model, it was found that the criterion for the effectiveness of the applied strategy can be an indicator of satisfaction with the state, the preservation of which, simultaneously with the preservation of the size of resources used, corresponds to the direction of optimization. This approach is consistent with the concept of sustainable development. (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)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data (...) from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

In this paper, we propose a new concept named the uniform single valued neutrosophic graph. An illustrative example and some properties are examined. Next, we develop an algorithmic approach for computing the complement of the single valued neutrosophic graph. A numerical example is demonstrated for computing the complement of single valued neutrosophic graphs and uniform single valued neutrosophic graph.

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (shrink)

Inducing the rubber hand illusion (RHI) requires that participants look at an imitation hand while it is stroked in synchrony with their occluded biological hand. Previous explanations of the RHI have emphasized multisensory integration, and excluded higher cognitive functions. We investigated the relationship between the RHI and higher cognitive functions by experimentally testing task switch (as measured by switch cost) and mind wandering (as measured by SART score); we also included a questionnaire for attentional control that comprises two subscales, attention-shift (...) and attention-focus. To assess experience of RHI, the Botvinick and Cohen (1998) questionnaire was used and illusion onset time was recorded. Our results indicate that rapidity of onset reliably indicates illusion strength. Regression analysis revealed that participants evincing less switch cost and higher attention-shift scores had faster RHI onset times, and that those with higher attention-shift scores experienced the RHI more vividly. These results suggest that the multi-sensory hypothesis is not sufficient to explain the illusion: higher cognitive functions should be taken into account when explaining variation in the experience of ownership for the rubber hand. (shrink)

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

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)