Historical research has recently made it clear that, prior to Austin and Searle, the phenomenologist Adolf Reinach (1884-1917) developed a full-fledged theory of speech acts under the heading of what he called "social acts". He we consider a second instance of a speech act theory avant la lettre, which is to be found in the common sense philosophy of Thomas Reid (1710-1796). Reid’s s work, in contrast to that of Reinach, lacks both a unified approach and the detailed (...) analyses of pertinent examples. But his writings leave no doubt that he is acutely aware of the very problems concerning language structure and use out of which contemporary speech act theory has evolved and that he goes a good way towards solving these problems in the spirit of the modern theory. (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.

Provides a survey of the development of speech act theory from Aristotle through Reid and Peirce to Edmund Husserl, Anton Marty, Johannes Daubert, Adolf Reinach, and finally to Austin and Searle. A special role is played by Husserl's theory of objectifying acts (meaning, roughly, acts of naming or stating) and of the efforts by his followers to extend this theory to cover phenomena such as questioning and commanding. These efforts culminated in the work of Adolf Reinach, who developed the (...) first systematic theory of speech acts in connection with his monograph of 1913 on “The A Priori Foundations of the Civil Law”. (shrink)

W dziełach Arystotelesa, lub z medievals, jak również w pismach późniejszych zdroworozsądkowe filozofów, takich jak Thomas Reid czy GE Moore’a, możemy znaleźć rodzinę różnych prób uporania się ze strukturami rozsądku i wspólnego -sense świat, który jest nam dany w normalnym, doświadczenie pre-teoretycznym. Będziemy argumentować, co wynika, że ​​teoria takich struktur stanowi ważny i dotychczas niedoceniany związek między wczesnym psychologii Gestalt z jednej strony, oraz współczesnych osiągnięć w filozofii i sztucznej inteligencji badań na innych.

Provides a survey of the development of speech act theory from Aristotle through Reid and Peirce to Edmund Husserl, Anton Marty, Johannes Daubert, Adolf Reinach, and finally to Austin and Searle. A special role is played by Husserl's theory of objectifying acts (meaning, roughly, acts of naming or stating) and of the efforts by his followers to extend this theory to cover phenomena such as questioning and commanding. These efforts culminated in the work of Adolf Reinach, who developed the (...) first systematic theory of speech acts in connection with his monograph of 1913 on “The A Priori Foundations of the Civil Law”. (shrink)

The theory of proper names proposed by J.S. Mill in A system of logic (1843), and discussed in S. Kripke’s Naming and necessity (1980), is shown to be predated by A. Rosmini’s Nuovo saggio sull’origine delle idee (1830) and T. Reid’s Essays on the intellectual powers of man (1785). For philological reasons, Rosmini probably did not obtain his view of proper names from Reid. For philosophical reasons, it is unlikely that he got it from Hobbes, Locke, Smith, (...) or Stewart. Although not explicitly indicated by Rosmini himself, he may have been influenced by St. Thomas, who in Summa theologica discusses suppositum and natura in relation to the equivocal functions of the terms ”God” and ”sun” as common and proper names. As previously observed, forerunners of the idea can be found in Antiquity, in Plato’s Theaetetus and Aristotle’s Metaphysics. From a historical point of view, the fully developed ”Millian” opinion that connotation is not a fundamental aspect of proper names, and that their referents are not fixed by description, could more accurately be termed the Reid-Rosmini-Mill theory. (shrink)

Introduction to our edited volume on Wittgensteinian ethics with papers by Oskari Kuusela, Edward Harcourt, Anne-Marie Christensen, Sabina Lovibond, Alexander Miller, Benjamin De Mesel, Cora Diamond, Lars Hertzberg, Jeremy Johnson, Craig Taylor, Alice Crary, Lynette Reid.

Taking my cue from Michael Smith, I try to extract a decent argument for non-cognitivism from the text of the Treatise. I argue that the premises are false and that the whole thing rests on a petitio principi. I then re-jig the argument so as to support that conclusion that Hume actually believed (namely that an action is virtuous if it would excite the approbation of a suitably qualified spectator). This argument too rests on false premises and a begged (...) question. Thus the Motivation Argument fails BOTH as an argument for noncognitivism AND as an argument for what Hume actually believed, that moral distinctions are not derived from reason and that moral properties are akin to secondary qualities. So far as the Motivation Argument is concerned, both cognitivists and rationalists can rest easy. Themes: 1) Hume’s Slavery of Reason thesis is only defensible if passions are not only desires but sometimes dispositions to acquire desires (DTADs). 2) A desire for our good on the whole, which Humeans need to posit to fend off apparent counterexamples to the Slavery of Reason Thesis, does not sit well with the Humean theory of how novel desires arise (an objection due originally to Reid). 3) Hume is wrong to suppose that ‘abstract or demonstrative reasoning never influences any of our actions, but only as it directs our judgment concerning causes and effects’ as the examples of Russell and Hobbes convincingly demonstrate. This ironic as both Russell and Hobbes subscribed to the Slavery of Reason Thesis. 4) I critique Michael Smith’s critique of motivational externalism. (shrink)

This book tells the story of modern ethics, namely the story of a discourse that, after the Renaissance, went through a methodological revolution giving birth to Grotius’s and Pufendorf’s new science of natural law, leaving room for two centuries of explorations of the possible developments and implications of this new paradigm, up to the crisis of the Eighties of the eighteenth century, a crisis that carried a kind of mitosis, the act of birth of both basic paradigms of the two (...) following centuries: Kantian ethics and utilitarianism. The new science of natural law carried a fresh start for ethics, resulting from a mixture of the Old and the New. It was, as suggested by Schneewind, an attempt at rescuing the content of Scholastic and Stoic doctrines on a new methodological basis. The former was the claim of existence of objective and universal moral laws; the latter was the self-aware attempt at justifying a minimal kernel of such laws facing skeptical doubt. What Bentham and Kant did was precisely carrying this strategy further on, even if restructuring it each of them around one out of two alternative basic claims. The nineteenth- and twentieth-century critics of the Enlightenment attacked both not on their alleged failure in carrying out their own projects, but precisely on having adopted Grotius’s and Pufendorf’s project. What counter-enlightenment has been unable to spell out is which alternative project could be carried out facing the modern condition of pluralism, while on the contrary, if we takes a closer look at developments in twentieth-century ethics or at on-going discussions on practical issues, we might feel inclined to believe that Grotius’s and Pufendorf’s project is as up-to-date as ever. -/- Table of Contents -/- Preface I. Fathers of the Reformation and Schoolmen 1.1. Luther: passive justice and the good deeds; 1.2. Calvin: voluntarism and predestination; 1.3. Baroque Scholasticism; 1.4. Casuistry and Institutiones morales -/- II Neo-Platonists, neo-Stoics, neo-Sceptics 2.1. Aristotelian, neo-Platonic, neo-Epicurean and neo-Cynic Humanists; 2.2. Oeconomica and the art of living; 2.3. Neo-Stoics; 2.4. Neo-Sceptics; 2.5. Moralistic literature -/- III Neo-Augustinians 3.l. The Jansenists on natura lapsa, sufficient grace, pure love; 3.2. Nicole on the impossibility of self-knowledge; 3.3. Nicole on self-love and charity; 3.4. Nicole against civic virtue, for Christian civility; 3.5. Malebranche on general laws and necessary evil; 3.6. Malebranche on Neo-Augustinianism and Platonism. -/- IV Grotius, Pufendorf and the new moral science 4.1. Grotius against Aristotle and the sceptics; 4.2. Mersenne and Gassendi; 4.3. Descartes on ethics as the last branch of philosophy’s tree; 4.4. Hobbes on scepticism and the new moral science; 4.5. Spinoza on the new moral science as a descriptive science;4.6. Locke on voluntarism and probabilism; 4.7. Pufendorf on natural law as an exact science; 4.8. Pufendorf on physical and moral entities; 10. Pufendorf on self-preservation -/- V The empiricist version of the new moral science: from Cumberland to Paley 5.1. Cumberland against Hobbesian voluntarism; 5.2. Cumberland and theological consequentialism; 5.3. Cumberland on universal benevolence and self-love; 5.4. Shaftesbury on the moral sense; 5.5. Hutcheson on natural law and moral faculties; 5.6. Gay, Brown, Paley and theological consequentialism. -/- VI The rationalist version of the new moral science: from Cudworth to Price 6.1. The Cambridge Platonists; 6.2. Shaftesbury on the moral sense; 6.3. Butler and a third way between voluntarism and scepticism; 6.4. Price and the rational character of moral truths; -/- VII Leibniz’s compromise between the new moral science and Aristotelianism 1.Leibniz against voluntarism; 2.Leibniz against the division between the physical and the moral good; 3.Leibniz on la place d’autrui and theological consequentialism; 4.Thomasius, Wolff, Crusius -/- VIII French eighteenth-century philosophers without the new moral science 8.1. The genealogy of our ideas of virtue and vice; 8.2. Maupertuis and moral arithmetic 8.3. The philosophes and the harmony of interests; 8.4. Rousseau on corruption, self-love, and virtue; 8.5. Sade on the merits of vice -/- IX Experimental moral science: Hume and Adam Smith 9.1. Mandeville’s paradox; 9.2. Hutcheson on the law of nature and moral faculties; 9.3. Hume on experimental moral philosophy and the intermediate principles; 9.4. Hume’s Law; 9.5. Hume on the fellow-feeling; 9.6. Hume on natural and artificial virtues and disinterested pleasure for utility; 9.7. Adam Smith’s anti-realist metaethics; 9.8. Adam Smith on self-deception and the paradox of happiness; 9.9. Adam Smith on sympathy and the impartial spectator; 9.10. Adam Smith on the twofold criterion for moral judgement and its paradox; 9.11. Reid on the refutation of scepticism and the self-evidence of duty -/- X Kantian ethics 10.1. Kantian metaethics: moral epistemology; 10.2. Kantian metaethics: moral ontology; 10.3. Kantian metaethics: moral psychology; 10.4. Kantian normative ethics; 10.5. Kant on the impracticability of applied ethics; 10.6. Kantian moral anthropology; 10.7. Civilisation and moralisation; 10.8. Theology on a moral basis and the origins of evil; 10.9. Fichte and the transformation of theoretical philosophy into practical philosophy XI Bentham and utilitarianism 11.1. Bentham’s linguistic theory; 11.2. Bentham’s moral ontology, psychology, and theory of action; 11.3. The principle of greatest happiness; 11.4. The critique of religious ethics; 11.5. The new morality; 11.6. Interest and duty; 11.7. Virtues; 11.8. Private ethics and legislation -/- XII Followers of the Enlightenment: liberal Judaism and Liberal Theology 12.1. Mendelssohn; 12.2. Salomon Maimon; 12.3. Haskalā and liberal Judaism; 12.4. Liberal Theology. -/- XIII Counter-Enlighteners 13.1.Romanticism and the fulfilment of individuality as the Summum Bonum; 13.2. Hegel on history as the making of liberty; 13.3. Hegel on the unhappy consciousness and the beautiful soul; 13.4. Hegel on Morality and Sittlichkeit; 13.5. Marx on ideology, alienation, and praxis; 13.6. Schopenhauer on compassion; 13.7. Kierkegaard on faith beyond ethics. -/- XIV Followers of the Enlightenment: intuitionists and utilitarian 14.1 Whewell‘s criticism of utilitarianism; 14.2 Whewell on morality and the philosophy of morality; 14.3 Whewell on the Supreme Norm; 14.4 Whewell on the conflict between duties; 14.5 Mill and the proof of the principle of utility; 14.6 Mill’s eudemonistic utilitarianism; 14.7 Mill on rules -/- XV Followers of the Enlightenment: neo-Kantians and positivists 15.1. French spiritualism; 15.2. Neo-Kantians: the Marburg school; 15.3. Neo-Kantians: the Marburg school; 15.4. Comte’s positivism and the invention of altruism; 15.5. Social Darwinism; 15.6. Wundt and an ethic of humankind -/- XVI Post-enlighteners: Sidgwick 16.1. Criticism of intuitionism; 16.2. On ethical egoism; 16.3. Criticism of utilitarianism -/- XVII Post-enlighteners: Durkheim 17.1. Sociology as physics of customs; 17.2. Morality as physics of customs and as practical science; 17.3. On Kantian ethics and utilitarianism; 17.4. The variability of moralities;17.5. Social solidarity as end and justification of morality; 17.6. Secular morality as “sociodicy”; XVIII Post-enlighteners: Nietzsche 18.1. On the Dionysian; 18.2. On the deconstruction of the world of values 18.3 On the twofold genealogy of moralities; 18.4. On ascetics and nihilism; 18.5. Normative ethics of self-fulfilment -/- Bibliography / Index of names / Index of concepts -/- . (shrink)

I discuss Hume's views about whether simplicity and generality are positive features of explanations. In criticizing Hobbes and others who base their systems of morality on self interest, Hume diagnoses their errors as resulting from a "love of simplicity". These worries about whether simplicity is a positive feature of explanations emerge in Hume's thinking over time. But Hume does not completely reject the idea that it's good to seek simple explanations. What Hume thinks we need is good judgment about when (...) we are going too far in our search for simple explanations. These worries about simplicity are not unique to Hume. We can see versions of them in the work of Hutcheson, Smith, and Reid. (shrink)

This essay falls into three parts. Section 1 describes how Politics Book I, which includes Aristotle’s famous claims that the human being is by nature a political animal (politikon zōon) and that the polis (city-state) is natural and naturally prior to the individual, and his infamous claim that it is just to enslave those who are slaves by nature, may be connected with the rest of the Politics, which is about politeiai (constitutions). Section 2 examines Aristotle’s ideal politeia in Politics (...) VII-VIII in the light of his criticisms of other politeiai in Book II. Section 3 discusses non-ideal constitutions in Politics III-VI. (shrink)

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)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

The term ‘intelligence’ as used in this paper refers to items of knowledge collected for the sake of assessing and maintaining national security. The intelligence community (IC) of the United States (US) is a community of organizations that collaborate in collecting and processing intelligence for the US. The IC relies on human-machine-based analytic strategies that 1) access and integrate vast amounts of information from disparate sources, 2) continuously process this information, so that, 3) a maximally comprehensive understanding of world actors (...) and their behaviors can be developed and updated. Herein we describe an approach to utilizing outcomes-based learning (OBL) to support these efforts that is based on an ontology of the cognitive processes performed by intelligence analysts. Of particular importance to the Cognitive Process Ontology is the class Representation that is Warranted. Such a representation is descriptive in nature and deserving of trust in its veridicality. The latter is because a Representation that is Warranted is always produced by a process that was vetted (or successfully designed) to reliably produce veridical representations. As such, Representations that are Warranted are what in other contexts we might refer to as ‘items of knowledge’. (shrink)

Elon Musk famously predicted that an artificial intelligence superior to the smartest individual human would arrive by the year 2025. In response, Gary Marcus offered Musk a $1 million bet to the effect that he would be proved wrong. In specifying the conditions of this bet (which Musk did not take) Marcus lists the following ‘tasks that ordinary people can perform’ which, he claimed, AI will not be able to perform by the end of 2025. • Reliably drive a car (...) in a novel location that they haven’t previously encountered, even in the face of unusual circumstances like hand lettered signs, without the assistance of other humans. • Learn to ride a mountain bike off-road through forest trails. • Babysit children in an unfamiliar home and keep them safe. • Tend to the physical and psychological needs of an elderly or infirm person. Each of these tasks involves the application of practical or tacit knowledge, or what is also called ‘knowing how’, which is to say knowledge of a sort that is captured not by means of sentences or propositions or explicit rules, but rather through the expertise demonstrated in human actions. The talk addresses the puzzle that nowhere in the AI literature do we find a discussion of knowing how as a feature of human intelligence. (shrink)

A diagnostic process is an investigative process that takes a clinical picture as input and outputs a diagnosis. We propose a method for distinguishing diagnoses that are warranted from those that are not, based on the cognitive processes of which they are the outputs. Processes designed and vetted to reliably produce correct diagnoses will output what we shall call ‘warranted diagnoses’. The latter are diagnoses that should be trusted even if they later turn out to have been wrong. Our work (...) is based on the recently developed Cognitive Process Ontology and further develops the Ontology of General Medical Science. It also has applications in fields such as intelligence, forensics, and predictive maintenance, all of which rely on vetted processes designed to secure the reliability of their outputs. (shrink)

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. Description: The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data (...) relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term ‘adverse event’ denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. (shrink)

Batı’da teorik felsefe; Analitik Felsefe (AF), Kıta Felsefesi (KF) ve Felsefe Tarihi (FT) olmak üzere üçe ayrılır. Fakat üçünde de işler yolunda değildir. AF, felsefenin bir bilim olabileceği iddiasından kuşku duyduğu için gerçek dünyayla ilgilenmiyorken başından beri uygun bir teorik yöntem izlemeyen Kıta Felsefesinin uygulanışı, belirli politik ve etik yargılara hizmet edecek şekilde özelleştirilmiştir. FT çalışmalarının gidişatı ise eldeki eserin nesnel değerinden daha çok ilgili filozofun ait olduğu ulus veya kültüre göre bölgesel bir temelde gelişmiştir. Felsefede ilerleme sağlanacaksa bu ancak (...) bahsi geçen tuzaklardan kaçınılarak gerçekleşebilir. (shrink)

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

When people now talk about a relationship as being “Platonic”, they mean that the relationship is a non-sexual friendship. But what did Plato himself say about different kinds of relationship, and how did his name come to be associated with non-sexual relationships? While Plato’s Symposium has been the center of attention for his views on love, I argue that the Phaedrus and Laws VIII provide a much clearer account of Plato’s views. In these dialogues, Plato distinguishes between two kinds of (...) love and three kinds of lover. The two kinds of love are fundamentally oriented towards different objects: one kind of love is focused on the body of the beloved and seeks to extract as much bodily pleasure from them as possible, whereas the other kind of love is focused on the soul and seeks to benefit the beloved by improving their character. There is a lover for each kind of love, and a third kind of lover who is torn between these two opposing objects of love. Notably, in the kind of love directed towards the soul, the lovers will not engage in sexual activity. I argue that this is because Plato thinks that the natural function of sex is the procreation of good children and that engaging in such an intensely pleasurable activity risks making the lovers intemperate and lacking in self-control. Thus Plato thinks that the best kind of relationship is one of love (and not just friendship) but is nonetheless non-sexual. (shrink)

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)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

We propose capability as a universal or type intermediate between function and disposition. A capability is, broadly speaking, a disposition that is of a type whose instances can be evaluated on the basis of how well they are realized. A function, on the view we are proposing, is a capability the possession of which is the rationale for the existence of its bearer. To say for example that a water pump has the function to pump water is to say that (...) the pump exists because something was needed that would pump water. A water pump may have many capabilities, including: to be weatherproof, to run without lubricant, to be transportable, and so forth. But its function is to pump water. We focus here on capabilities possessed by humans – such as piano playing or language using – and we explore the relation between capabilities of these sorts and structures in the brain. (shrink)

Current COVID-19 pandemic and previous SARS/MERS outbreaks have caused a series of major crises to global public health. We must integrate the large and exponentially growing amount of heterogeneous coronavirus data to better understand coronaviruses and associated disease mechanisms, in the interest of developing effective and safe vaccines and drugs. Ontologies have emerged to play an important role in standard knowledge and data representation, integration, sharing, and analysis. We have initiated the development of the community-based Coronavirus Infectious Disease Ontology (CIDO). (...) As an Open Biomedical Ontology (OBO) library ontology, CIDO is an open source and interoperable with other existing OBO ontologies. In this article, the general architecture and the design patterns of the CIDO are introduced, CIDO representation of coronaviruses, phenotypes, anti-coronavirus drugs and medical devices (e.g. ventilators) are illustrated, and an application of CIDO implemented to identify repurposable drug candidates for effective and safe COVID-19 treatment is presented. (shrink)

The 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)

We propose a definition of capability as a class intermediate between function and disposition as the latter are defined in Basic Formal Ontology (BFO). A disposition inheres in a material entity and is realized in a certain kind of process. An example is the disposition of a glass to break when struck, which is realized when it shatters. A function is a disposition which is (simply put) the rationale for the existence of its bearer. To say for example that a (...) water pump has the function to pump water is to say that the pump exists because something was needed that would pump water. Capabilities are a special sort of disposition in that that, like functions, they can be evaluated on the basis of how well they are realized. They differ from functions in that their realizations are not the rationale – not the primary reason – for the existence of their bearers. Thus, a water pump may have many capabilities, including to be weatherproof, to run without lubricant, and so forth, but only one function. All functions are capabilities on the view we defend, but not all capabilities are functions. We develop a series of axioms to distinguish capabilities formally from both dispositions and functions and provide examples of the use of ‘capability’ in a variety of domains. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

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

In “Toward an Ontology of Commercial Exchange” [11], we proposed human readable definitions for terms that are central to an ontology of commercial exchange. This paper furthers that project in two ways. First, the definitions have been modified to be compatible with the Common Core Ontologies (CCO). CCO is used in a wide variety of domains including the industrial and military domains. Having a commerce ontology compatible with CCO allows data about the exchange of goods relevant to those domains to (...) be tagged with compatible ontologies. Second, we propose preliminary formalizations of these definitions, with the aim of informing the creation of an ontology which can be used to assist in reasoning over businessrelated data. (shrink)

Applied ontologies have been used more and more frequently to enhance systems engineering. In this paper, we argue that adopting principles of ontological realism can increase the benefits that ontologies have already been shown to provide to the systems engineering process. Moreover, adopting Basic Formal Ontology (BFO), an ISO standard for top-level ontologies from which more domain specific ontologies are constructed, can lead to benefits in four distinct areas of systems engineering: (1) interoperability, (2) standardization, (3) testing, and (4) data (...) exploitation. Reaping these benefits in a model-based systems engineering (MBSE) context requires utilizing an ontology’s vocabulary when modeling systems and entities within those systems. If the chosen ontology abides by the principles of ontological realism, a semantic standard capable of uniting distinct domains, using BFO as a hub, can be leveraged to promote greater interoperability among systems. As interoperability and standardization increase, so does the ability to collect data during the testing and implementation of systems. These data can then be reasoned over by computational reasoners using the logical axioms within the ontology. This, in turn, generates new data that would have been impossible or too inefficient to generate without the aid of computational reasoners. (shrink)

Recent years have seen rapid progress in the development of ontologies as semantic models intended to capture and represent aspects of the real world. There is, however, great variation in the quality of ontologies. If ontologies are to become progressively better in the future, more rigorously developed, and more appropriately compared, then a systematic discipline of ontology evaluation must be created to ensure quality of content and methodology. Systematic methods for ontology evaluation will take into account representation of individual ontologies, (...) performance (in terms of accuracy, domain coverage and the efficiency and quality of automated reasoning using the ontologies) on tasks for which the ontology is designed and used, degree of alignment with other ontologies and their compatibility with automated reasoning. A sound and systematic approach to ontology evaluation is required to transform ontology engineering into a true scientific and engineering discipline. This chapter discusses issues and problems in ontology evaluation, describes some current strategies, and suggests some approaches that might be useful in the future. (shrink)

The article re-visits the different scholarly approaches to Hegel's end-of-art scenario, and then proposes a new reading whereby ending and finitude are presented as essential features of beautiful art. The first and most determinant of art's endings is the death of the Christly art object, not representations of Christ, but the actual death of (the son of) God himself as the last classical artwork. The death of God represents the last word in Greco-Roman art, the accomplishment of the beautiful individuality (...) and its failure to present the Absolute in a singular, naturally infected, lively, human (made) form. The ending of art brings about a new form of the sacred: the representational language of revelatory religion. The ongoing production of modern artistic forms is a feature of actuality ("Wirklichkeit") and as such is condemned to an infinite approximation of what has been. Such actuality nonetheless "ends" in the ironic discourse of contemporary artistic expression, which Hegel qualifies as a "Vereitelung". The final realization of the beautiful art form, as a human-informed singularity embodying absolute content, may well be the Encyclopedia of Philosophical Sciences, whose performative iteration takes place in the form of "worship" practiced in the modern, state university. (shrink)

Driven by the use cases of PubChemRDF and SCAIView, we have developed a first community-based clinical trial ontology (CTO) by following the OBO Foundry principles. CTO uses the Basic Formal Ontology (BFO) as the top level ontology and reuses many terms from existing ontologies. CTO has also defined many clinical trial-specific terms. The general CTO design pattern is based on the PICO framework together with two applications. First, the PubChemRDF use case demonstrates how a drug Gleevec is linked to multiple (...) clinical trials investigating Gleevec’s related chemical compounds. Second, the SCAIView text mining engine shows how the use of CTO terms in its search algorithm can identify publications referring to COVID-19-related clinical trials. Future opportunities and challenges are discussed. (shrink)

The organic trope is a popular way of accepting the systematicity of Hegelian science. It allows for diversity and difference within the living whole, where each organ contributes to the life of the holistic "one", which, in turn, ensures the vitality of each organ. For example, in the Philosophy of Right, the organic state maintains itself in relation to the various institutions and corporations that constitute its organs. However, one element of the organic trope remains largely ignored: excretion. Briefly, if (...) we take Hegel's system as organic, then what does it excrete? What constitutes its excrement? This book chapter examines Hegel's philosophical, syllogistic interpretation of animal digestion and excretion in the Philosophy of Nature and then attempts to apply it to the organic system of science, as an individual, purposive life form whose subjectivity arises through the excretion of what is deemed superfluous. (shrink)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

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)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

Plato is often acknowledged as the first philosophical critic of democracy and his Republic is regularly taken as a paradigm of an anti-democratic work. While it is true that Plato objected to much about the democracy of his own time, Plato’s political theorizing also reveals an interest in improving democratic institutions. This chapter explores three themes in Plato’s thinking about democracy: firstly, Plato's insistence that rulers should be knowledgeable and his claim that most people are politically incompetent (§1); secondly, Plato's (...) criticisms of oratory and the corrupting effects of public rhetoric (§2); thirdly, Plato's use of democratic institutions in the Laws (§3). Once we appreciate these different evaluations of democratic practices, we can see that Plato was not simply ‘anti-democratic’ or ‘pro-democratic’ but thought some democratic practices should be abandoned, some reformed, and some adopted. (shrink)

Biomedical research is increasingly a matter of the navigation through large computerized information resources deriving from functional genomics or from the biochemistry of disease pathways. To make such navigation possible, controlled vocabularies are needed in terms of which data from different sources can be unified. One of the most influential developments in this regard is the so-called Gene Ontology, which consists of controlled vocabularies of terms used by biologists to describe cellular constituents, biological processes and molecular functions, organized into hierarchies (...) via the relation of class subsumption. Here we seek to provide a rigorous account of the logic of classification that underlies GO and similar biomedical ontologies. Drawing on Aristotle, we develop a system of axioms and definitions for the treatment of biological classes and instances. (shrink)

This paper examines the Hegelian moment of the for-another in its negative relation to the other moment of particularity: the for-itself. I identify the dissolving, fluidifying action of the for-another by examining figures within the Philosophy of Nature, particularly comets and moons, but also Hegel’s physics of light and sound. The dissolution of the lunar for-itself at the hands of the cometary for-another illustrates how the dynamic relation between the two moments of particularity participates in the presentation of essence, within (...) the Hegelian syllogism, i.e. as mediating between the universal and the singular. The dynamic action of cometary negativity occurs throughout the Philosophy of Nature and therefore should be pivotal to how the work is read. (shrink)

Did Plato intend the laws of the Laws to change? While most scholars agree that there is to be legal change in Magnesia, I contend that this issue has been clouded by confusing three distinct questions: (1) whether there are legal mechanisms for changing the law in Magnesia, (2) what the attitudes of Magnesian citizens towards innovation and legal change are, and (3) whether Plato thinks the law is always the ultimate political authority. Once we separate these issues and look (...) at the relevant texts more closely, we see that the Athenian Visitor is primarily concerned with supplementing the original lawgiver’s laws and that any innovation that occurs should be consistent with this lawcode. This does not settle the question about whether it is always right to act in accordance with the existing laws, though it does provide a valuable framework for understanding a central aspect of Platonic political philosophy. Thus, although Plato’s ideal places knowledge above the law, in practice the laws of Magnesia will be fixed and authoritative for those people living under them. (shrink)

According to a captivating picture, epistemic justification is essentially a matter of epistemic or evidential likelihood. While certain problems for this view are well known, it is motivated by a very natural thought—if justification can fall short of epistemic certainty, then what else could it possibly be? In this paper I shall develop an alternative way of thinking about epistemic justification. On this conception, the difference between justification and likelihood turns out to be akin to the more widely recognised difference (...) between ceteris paribus laws and brute statistical generalisations. I go on to discuss, in light of this suggestion, issues such as classical and lottery-driven scepticism as well as the lottery and preface paradoxes. (shrink)

Some random processes, like a series of coin flips, can produce outcomes that seem particularly remarkable or striking. This paper explores an epistemic puzzle that arises when thinking about these outcomes and asking what, if anything, we can justifiably believe about them. The puzzle has no obvious solution, and any theory of epistemic justification will need to contend with it sooner or later. The puzzle proves especially useful for bringing out the differences between three prominent theories; the probabilist theory, the (...) normic theory and a theory recently defended by Goodman and Salow. (shrink)

In her seminal article ‘Modern Moral Philosophy’ (1958) Elizabeth Anscombe argued that we need a new ethics, one that uses virtue terms to generate absolute prohibitions against certain act-types. Leading contemporary virtue ethicists have not taken up Anscombe's challenge in justifying absolute prohibitions and have generally downplayed the role of rule-following in their normative theories. That they have not done so is primarily because contemporary virtue ethicists have focused on what is sufficient for characterizing the deliberation and action of the (...) fully virtuous person, and rule-following is inadequate for this task. In this article, I take up Anscombe's challenge by showing that rule-following is necessary for virtuous agency, and that virtue ethics can justify absolute prohibitions. First, I offer a possibility proof by showing how virtue ethics can generate absolute prohibitions in three ways: by considering actions that directly manifest vice or that cannot be performed virtuously; actions that are prohibited by one's institutional roles and practical identities; and actions that are prohibited by the prescriptions of the wise. I then seek to show why virtue ethicists should incorporate rule-following and absolute prohibitions into their theories. I emphasize the central role that rules have in the development of virtue, then motivate the stronger view that fully virtuous agents follow moral rules by considering the importance of hope, uncertainty about consequences, and taking responsibility for what eventuates. Finally, I provide an account of what Anscombe called a ‘corrupt mind’, explaining how our understanding of virtue is corrupted if we think that virtue may require us to do vicious actions. (shrink)

Husserl’s philosophy, by the usual account, evolved through three stages: 1. development of an anti-psychologistic, objective foundation of logic and mathematics, rooted in Brentanian descriptive psychology; 2. development of a new discipline of "phenomenology" founded on a metaphysical position dubbed "transcendental idealism"; transformation of phenomenology from a form of methodological solipsism into a phenomenology of intersubjectivity and ultimately (in his Crisis of 1936) into an ontology of the life-world, embracing the social worlds of culture and history. We show that this (...) story of three revolutions can provide at best a preliminary orientation, and that Husserl was constantly expanding and revising his philosophical system, integrating views in phenomenology, ontology, epistemology and logic with views on the nature and tasks of philosophy and science as well as on the nature of culture and the world in ways that reveal more common elements than violent shifts of direction. We argue further that Husserl is a seminal figure in the evolution from traditional philosophy to the characteristic philosophical concerns of the late twentieth century: concerns with representation and intentionality and with problems at the borderlines of the philosophy of mind, ontology, and cognitive science. (shrink)

In this paper I investigate whether there are any cases in which it is rational for a person to hold inconsistent beliefs and, if there are, just what implications this might have for the theory of epistemic justification. A number of issues will crop up along the way – including the relation between justification and rationality, the nature of defeat, the possibility of epistemic dilemmas, the importance of positive epistemic duties, and the distinction between transitional and terminal attitudes.