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)

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.

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)

According to the principle of Conjunction Closure, if one has justification for believing each of a set of propositions, one has justification for believing their conjunction. The lottery and preface paradoxes can both be seen as posing challenges for Closure, but leave open familiar strategies for preserving the principle. While this is all relatively well-trodden ground, a new Closure-challenging paradox has recently emerged, in two somewhat different forms, due to Backes :3773–3787, 2019a) and Praolini :715–726, 2019). This paradox synthesises elements (...) of the lottery and the preface and is designed to close off the familiar Closure-preserving strategies. By appealing to a normic theory of justification, I will defend Closure in the face of this new paradox. Along the way I will draw more general conclusions about justification, normalcy and defeat, which bear upon what Backes :2877–2895, 2019b) has dubbed the ‘easy defeat’ problem for the normic theory. (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)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (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)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (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)

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

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)

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)

What can Stoicism offer to contemporary debates about forgiveness? Given their outright rejection of a reactive attitudes framework for responding to wrongdoing and their bold suggestions of how to revise our moral practices, the Stoics provide a valuable lens through which to re-evaluate various central claims in the debates about forgiveness. In this chapter, I highlight four common assumptions that the Stoics would consider problematic: firstly, that forgiveness is opposed to justice; secondly, that anger and resentment are necessary for registering (...) wrongdoing; thirdly, that anger and resentment are generally reliable at tracking the severity of wrongdoing; fourthly, that reconciliation with wrongdoers is an option rather than an imperative of virtue. Insofar as the Stoics provide defensible and often compelling alternatives to these positions, Stoicism offers a number of philosophical resources to re-conceptualize the way we think about forgiveness and suggests ways in which forgiveness might be better integrated into a virtue ethical framework. (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)

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

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

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (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)

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

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)

In this paper I respond to Marcello Di Bello’s criticisms of the ‘normic account’ of the criminal standard of proof. In so doing, I further elaborate on what the normic account predicts about certain significant legal categories of evidence, including DNA and fingerprint evidence and eyewitness identifications.

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: We present (...) computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (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)

Kate Crawford presents AI as “both reflecting and producing social relations and understandings of the world”; or again, as “a form of exercising power, and a way of seeing… as a manifestation of highly organized capital backed by vast systems of extraction and logistics, with supply chains that wrap around the entire planet”. I interpret these material insights through a Marxist understanding of ideology, with reference to Marx/Engels, Guy Debord and Louis Althusser. In the German Ideology, Marx and Engels present (...) ideology as the alienated and alienating discourse of exchange, dissimulating the material forces of production and its science. Guy Debord presents the spectacle as the further representation of capital. The spectacle is a total Weltanschauung, pure appearance, where “whatever appears is good and where what is good, appears.” Above all, the spectacle is ideology, representing “the impoverishment, enslavement and negation of real life”. Louis Althusser presents ideology as essential for the reproduction of labor-power and capital. His notion of “interpellation” explains the subjective uptake of ideology, how we respond, “yes!” to its call. The algorithms of AI are enactments of surplus value generating capital as data. The AI data-world is the spectacle, “the autonomous movement of non-life” (Debord) where the proletariat/consumer is the producer of their own ideological subjection. Is resistance possible? What form might it take? And if AI is understood as ideology, i.e. as a language that obscures the true conditions of real life, then what are those true conditions? What is “real life”? (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)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (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)

Every domain-specific ontology must use as a framework some upper-level ontology which describes the most general, domain-independent categories of reality. In the present paper we sketch a new type of upper-level ontology, which is intended to be the basis of a knowledge modelling language GOL (for: 'General Ontological Language'). It turns out that the upper- level ontology underlying standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. Set theory has considerable mathematical power and (...) great flexibility as a framework for modelling different sorts of structures. At the same time it has the disadvantage that sets are abstract entities (entities existing outside the realm of time, space and causality), and thus a set-theoretical framework should be supplemented by some other machinery if it is to support applications in the ripe, messy world of concrete objects. In the present paper we partition the entities of the real world into sets and urelements, and then we introduce several new ontological relations between these urelements. In contrast to standard modelling and representation formalisms, the concepts of GOL provide a machinery for representing and analysing such ontologically basic relations. (shrink)

Examining the historical development of scientific concepts is important for understanding the structured routines within which these concepts are currently used as goal-directed tools in experiments. To illustrate this claim, I will outline how the concepts of mental imagery and hallucinations each draw on an older interdependent set of associations that, although nominally-discarded, continues to structure their current independent uses for pursuing discrete experimental goals. In doing so, I will highlight how three strands of literature offer mutually instructive insights for (...) understanding how the uses of our current scientific concepts contribute to experimental practices. The first strand of literature includes recent scholarship examining how the uses of scientific concepts can enable scientific practices (e.g., Boon 2012; Brigandt 2012; Feest 2010; Steinle 2012). In this context, scientific concepts have been described as tools that function in ways that contribute to empirical knowledge; contributions that extend beyond their traditionally recognized roles in mental and linguistic representation. The second strand of literature can be glimpsed within the technoscientific studies focus on non-human agency; a focus that supports an account of the disciplined routines within which concepts are used as acting in analogous ways to the routinized participation of machines in experiments (Pickering 1995). The third strand of the literature draws attention to how the functions of concepts are grounded by the set of historically-contingent experimental practices (e.g., Canguilhem 2008; Tiles 1984). Although maintaining valuable differences, the focus of these three strands of literature are mutually instructive. Together, they offer a view of the uses of concepts as taken-for-granted tools that function within networks of subterranean associations; associations that are grounded by historically contingent experimental practices that structure how they act (in concert with human and material participants) within the temporally dynamic processes of scientific practice. Through examples drawn from a comparison of the concepts of mental imagery and hallucinations, I aim to demonstrate the value that the converging insights of these three strands of literature offer for studying the role of scientific concepts in experimental practices. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

A brief introduction to Thomas Reid's philosophy on language.

Hegel reads the poet Novalis as an expression of terminal irony, a pathological case of Gemüt, where the conscious mind is alienated from reality and turns its negativity inwards on the contents of its own natural soul. The condition of self-feeling, presented in Hegel’s “Anthropology”, is a self-consumption that manifests itself somatically in the physical disease (consumption) from which Novalis dies. The poet’s literary production represents a pathological fixation that impedes the dynamic organicity of Hegelian Science. As such, Novalis’s mental (...) illness and death constitute an expression of romantic irony and an ongoing threat to Hegel’s philosophy. (shrink)

I begin by defending Heinrich Gustav Hotho’s foundational edition of the Lectures on Aesthetics (LA) contra Gethmann-Siebert and others who argue for a non-systematic view of Hegel’s aesthetics generally and music specifically. I defend Hegel against the common conceit that his comprehension of music was somehow deficient and introduce the Hegelian idea of absolute agency as performative in art and music. Reference to Kant’s transcendental aesthetics then allows us to grasp how, in Hegel, meaningful tones arise from the vibratory oscillation (...) between selfhood’s presiding unity and its temporal self-positing. I then trace back further elements of musical architecture, such as rhythm, harmony and melody to the temporal oscillation arising from within selfhood. The fundamental ambiguity within temporal oscillation is the source of meaningfulness in music, the feeling that its experience is meaningful without telling us exactly what that meaning is. Meaningfulness forms the absolute Ur-Ton of beautiful music, which arises as determinate tones within selfhood and resonates into the soul of the listener. The temporal vanishing of musical tones within a compositional framework is a pre-linguistic expression of meaning, performative of the ambiguous oscillation between the human and the divine. (shrink)

It is not mere coincidence that several of Plato’s dialogues are set in gymnasia and palaistrai (wrestling schools), employ the gymnastic language of stripping, wrestling, tripping, even helping opponents to their feet, and imitate in argumentative form the athletic contests (agōnes) commonly associated with that place. The main explanation for this is, of course, historical. Sophists, orators, and intellectuals of all stripes, including the historical Socrates, really did frequent Athens’ gymnasia and palaistrai in search of ready audiences and potential students. (...) Perhaps they were following the example of Pythagoras, who may have been a boxing coach (gymnastēs) and was, in any case, associated with the extraordinary Olympic success of athletes from his adopted Croton—success so great it generated the saying that the last of the Crotonites was the first among all other Greeks. After his visit to Western Greece, Plato famously established his school in or adjacent to the Academy gymnasium in Athens, and he may have held the public office of Gymnasiarch there. In this essay, I would like to argue that there are also symbolic reasons for Plato setting some of his dialogues in gymnasia. These dialogues function as virtual gymnasia in which readers are coached by the character of Socrates toward an innovative ideal of aretē (virtue, excellence). (shrink)

Reading the Phenomenology onto-grammatically means interpreting its constitutive forms of consciousness as grammatical iterations of the speculative proposition, where the subject-object relations can be read as dialogical encounters between subject and predicate, where the predicate “talks back”, creating a discursive space of hermeneutical ambiguity and openness, at play in the copula. The article begins with a brief presentation of Hegel’s general theory of language, as it pertains to the distinction between the linguistic sign (Zeichen) and the word (Wort), drawn from (...) his later writings, before applying these grammatical terms to the ontological reading of the speculative sentence, as presented in the Preface to the Phenomenology and discussed by Jere Surber. Then, the article puts its dialogical insights into practice, examining how the onto-grammatical reading of the speculative sentence plays out in the Phenomenology’s famous "lordship and bondage" (aka "master/slave") dialectic. (shrink)

Research on research ethics—regarding both the governance and practice of the ethical review of human subjects research—has a tumultuous history in North America and Europe. Much of the academic literature focuses on issues to do with regulating the conduct and quality of ethics review of research protocols by ethics committees (research ethics boards (REBs) in Canada and institutional review boards (IRBs) in the United States). In addition, some of the literature attends to issues particular to the review of qualitative research, (...) and still other literature addresses the challenges posed by and the need for research on REBs/IRBs. It is this third group of literature within which our article is situated. (shrink)

Credentials play an important role in all modern societies, but the analysis of their nature and function has thus far been neglected by social philosophers. We present a view according to which the function of credentials is certify the identity and the institutional status (including the rights) of individuals. More importantly, credentials enable rights-holders to exercise their rights, so that for a particular right to be exercisable the right-holder should possess, carry and sometimes show to an authority (or QR code (...) scanner) a document of a specific kind. Driving licenses, identity cards, passports, boarding passes, library passes, credit cards, ATM cards, health insurance cards are all examples of credentials in this sense. Credentials have in every case a bearer, and the bearer should be able to carry them easily on his or her person. Credentials should also be inspectable – not least because credentials can be forged. The authors analyse several historical and contemporary examples of credentials, focusing on the credentials carried by the pilgrims of the Way of Saint James. (shrink)

Maintaining systems of military plans is critical for military effectiveness, but is also challenging. Plans will become obsolete as the world diverges from the assumptions on which they rest. If too many ad hoc changes are made to intermeshed plans, the ensemble may no longer lead to well-synchronized and coordinated operations, resulting in the system of plans becoming itself incoherent. We describe in what follows an Adaptive Planning process that we are developing on behalf of the Air Force Research Laboratory (...) (Rome) with the goal of addressing problems of these sorts through cyclical collaborative plan review and maintenance. The interactions of world state, blue force status and associated plans are too complex for manual adaptive processes, and computer-aided plan review and maintenance is thus indispensable. We argue that appropriate semantic technology can 1) provide richer representation of plan-related data and semantics, 2) allow for flexible, non-disruptive, agile, scalable, and coordinated changes in plans, and 3) support more intelligent analytical querying of plan-related data. (shrink)