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 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)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

Building Information Modelling (BIM) is a process for managing construction project information in such a way as to provide a basis for enhanced decision-making and for collaboration in a construction supply chain. One impediment to the uptake of BIM is the limited interoperability of different BIM systems. To overcome this problem, a set of Industry Foundation Classes (IFC) has been proposed as a standard for the construction industry. Building on IFC, the ifcOWL ontology was developed in order to facilitate representation (...) of building data in a consistent fashion across the Web by using the Web Ontology Language (OWL). This study presents a critical analysis of the ifcOWL ontology and of the associated interoperability issues. It shows how these issues can be resolved by using Basic Formal Ontology (ISO/IEC 21838-2) as top-level architecture. A set of competency questions is used as the basis for comparison of the original ifcOWL with the enhanced ontology, and the latter is used to align with a second ontology – the ontology for building intelligent environments (DOGONT) – in order to demonstrate the added value derived from BFO by showing how querying the enhanced ifcOWL yields useful additional information. (shrink)

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

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)

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

As so often with his published texts, the experience of reading Nietzsche’s notebooks is at once mesmerising and infuriating. One is in the presence of a thinker who, on the one hand, meditates deeply on fundamental issues in philosophy and psychology but who, on the other, refuses to be pinned down. The fact that Nietzsche’s style is so elusive can account for the enormously disparate interpretations of his work and it is no surprise that his notebooks have been read in (...) the most extreme fashion. The notebooks have a chequered history having been variously touted as the crowning achievement of his philosophy, and as not repaying the effort of reading. (shrink)

While representation learning techniques have shown great promise in application to a number of different NLP tasks, they have had little impact on the problem of ontology matching. Unlike past work that has focused on feature engineering, we present a novel representation learning approach that is tailored to the ontology matching task. Our approach is based on embedding ontological terms in a high-dimensional Euclidean space. This embedding is derived on the basis of a novel phrase retrofitting strategy through which semantic (...) similarity information becomes inscribed onto fields of pre-trained word vectors. The resulting framework also incorporates a novel outlier detection mechanism based on a denoising autoencoder that is shown to improve performance. An ontology matching system derived using the proposed framework achieved an F-score of 94% on an alignment scenario involving the Adult Mouse Anatomical Dictionary and the Foundational Model of Anatomy ontology (FMA) as targets. This compares favorably with the best performing systems on the Ontology Alignment Evaluation Initiative anatomy challenge. We performed additional experiments on aligning FMA to NCI Thesaurus and to SNOMED CT based on a reference alignment extracted from the UMLS Metathesaurus. Our system obtained overall F-scores of 93.2% and 89.2% for these experiments, thus achieving state-of-the-art results. (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)

Analytical philosophy of the last one hundred years has been heavily influenced by a doctrine to the effect that one can arrive at a correct ontology by paying attention to certain superficial (syntactic) features of first-order predicate logic as conceived by Frege and Russell. More specifically, it is a doctrine to the effect that the key to the ontological structure of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of first-order logic, where ‘F’ (...) stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects), the relation between these two kinds of entity being revealed in the predicate-argument structure of atomic formulas in first-order logic. (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, and we outline an associated knowledge modelling language called GOL – for: General Ontological Language. It turns out that the upper-level ontology underlying well-known standard modelling languages such as KIF, F-Logic and CycL is restricted to the ontology of sets. In a set theory which allows Urelements, however, there (...) will be ontological relations between these Urelements which the set-theoretic machinery cannot capture. In contrast to standard modelling and representation formalisms, GOL provides a machinery for representing and analysing such ontologically basic relations. GOL is thus a genuine extension of KIF and of similar languages. In GOL entities are divided into sets and Urelements, the latter being divided in their turn into individuals and universals. Foremost among the individuals are things or substances, tropes or moments, and situoids: entities containing facts as components. (shrink)

This paper traces how media representations encouraged enthusiasts, youth and skilled volunteers to participate actively in science and technology during the twentieth century. It assesses how distinctive discourses about scientific amateurs positioned them with respect to professionals in shifting political and cultural environments. In particular, the account assesses the seminal role of a periodical, Scientific American magazine, in shaping and championing an enduring vision of autonomous scientific enthusiasms. Between the 1920s and 1970s, editors Albert G. Ingalls and Clair L. Stong (...) shepherded generations of adult ‘amateur scientists’. Their columns and books popularized a vision of independent nonprofessional research that celebrated the frugal ingenuity and skills of inveterate tinkerers. Some of these attributes have found more recent expression in present-day ‘maker culture’. The topic consequently is relevant to the historiography of scientific practice, science popularization and science education. Its focus on independent nonprofessionals highlights political dimensions of agency and autonomy that have often been implicit for such historical (and contemporary) actors. The paper argues that the Scientific American template of adult scientific amateurism contrasted with other representations: those promoted by earlier periodicals and by a science education organization, Science Service, and by the national demands for recruiting scientific labour during and after the Second World War. The evidence indicates that advocates of the alternative models had distinctive goals and adapted their narrative tactics to reach their intended audiences, which typically were conceived as young persons requiring instruction or mentoring. By contrast, the monthly Scientific American columns established a long-lived and stable image of the independent lay scientist. (shrink)

The Report presents insights which illuminates the intertwinements of European regulatory policies and global governance arrangements. By pinning down the exact nature of the interaction between these two levels, the EU’s dilemma becomes obvious: On the one hand, stronger global governance can be a chance, through which the EU can clarify its own raison d’être of increased integration to the wider world. On the other hand, the design of the European project is being challenged by more assertive global structures. This (...) is especially the case in relation to the WTO regime, which is constraining the decisional autonomy of the EU, regarding the appropriateness of its content and its external effects. Thus, the regulation of services in the EU and the WTO are discussed in the first section of this report. Section two focuses on labour standards, which are analysed from different angles in order to clarify the functions of the WTO and the ILO, multinational companies as well as other private actors within this specific field. The final section deals with the legitimacy problematic of transnational governance. Table of contents: Introduction Christian Joerges and Poul F. Kjaer Section One: Freedom of Services Chapter 1 The Multiple Understandings of Conflict between Trade in Services and Labour Protection Alexia Herwig Chapter 2 Competing in Markets, not Rules: The Conflict over the Single Services Market Susanne K. Schmidt Chapter 3 Competitiveness and Labour Protection: A Comment Markus Krajewski Section Two: Labour Standards Chapter 4 WTO and ILO: Can Social Responsibility be maintained in International Trade? Josef Falke Chapter 5 Reframing RECON: Perspectives on Transnationalisation and Post-national Democracy from Labour Law Claire Methven O’Brien Chapter 6 Transnational Governance and Human Rights: The Obligations of Private Actors in the Global Context Regina Kreide Section Three: The Legitimacy of Transnational Governance Chapter 7 Legitimacy through Precaution in European Regulation of GMOs? From the Standpoint of Governance as Analytical Perspective Maria Weimer Chapter 8 The Justice Deficit of the EU and other International Organisations Jürgen Neyer Chapter 9 Towards Normative Legitimacy of the World Trade Order Alexia Herwig and Thorsten Hüller Chapter 10 From Utopia to Apology – The Return to Inter-state Justice in Normative IR Scholarship: Comments on Neyer and Herwig & Hüller Jens Steffek. (shrink)

Why do average Americans recall the wise words of their politicians (e.g., John F. Kennedy’s “Ask not what your country can do for you. . .”) but forget those of their political philosophers (e.g., John Rawls’s two principles of justice)? Notably absent from Sandel’s list is Benjamin Franklin, the author, printer, scientist, and statesman who led the United States through a tumultuous period of colonial politics, a revolutionary war, and its momentous, though no less precarious, founding as a nation. Lorraine (...) Smith Pangle’s new book on Franklin seeks to remedy another glaring omission, namely, “that while so much attention has been paid to Franklin’s life, so little has hitherto been given to his political thought.". (shrink)

Automated Influence is the use of Artificial Intelligence to collect, integrate, and analyse people’s data in order to deliver targeted interventions that shape their behaviour. We consider three central objections against Automated Influence, focusing on privacy, exploitation, and manipulation, showing in each case how a structural version of that objection has more purchase than its interactional counterpart. By rejecting the interactional focus of “AI Ethics” in favour of a more structural, political philosophy of AI, we show that the real problem (...) with Automated Influence is the crisis of legitimacy that it precipitates. (shrink)

A familiar part of debates about supererogatory actions concerns the role that cost should play. Two camps have emerged: one claiming that extreme cost is a necessary condition for when an action is supererogatory, while the other denies that it should be part of our definition of supererogation. In this paper, I propose an alternative position. I argue that it is comparative cost that is central to the supererogatory and that it is needed to explain a feature that all accounts (...) agree is central to the very notion of supererogation: optionality. Perhaps because of this agreement on its importance, few attempts have been made to clarify and explain the notion of optionality. I argue that giving an account of the optionality of supererogatory requires drawing a line between doing the bare minimum permissible and going beyond the bare minimum and that this line ought to be drawn based on comparative cost of alternative permissible acts. Having outlined my account and motivated it, I discuss and reject two concerns that might be raised: firstly, that it is extreme cost, not comparative cost, that matters and, secondly, that in fact no cost is needed for an act to be supererogatory. (shrink)

Standing in San Marco Cathedral in Venice, you immediately notice the exquisitely decorated spandrels: the triangular spaces bounded on either side by adjoining arches and by the dome above. You would be forgiven for seeing them as the starting point from which to understand the surrounding architecture. To do so would, however, be a mistake. It is a similar mistaken inference that evolutionary biologists have been accused of making in assuming a special adaptive purpose for such biological features as fingerprints (...) and chins. I argue that a mistake of just this sort is being made by ethicists who appeal to the intrinsic value of supererogatory acts in their efforts to make space for supererogation in ethical theory. Many cases of supererogatory action are simply spandrels: by-products of uncontroversial commitments elsewhere in our moral thought. This is not to downplay their value but rather to show that their value need not be the justification for making room for the supererogatory. I demonstrate this by examining two areas: rights and the distribution of burdens among a group. My argument has significance for those who take themselves to be defends of the possibility of supererogatory actions, as well as those who are committed to the contrary and those who believe themselves to be indifferent on the matter. (shrink)

This is a contribution to a Book symposium on The Limits of Free Will: Selected Essays by Paul Russell. Russell provides replies to three critics of The Limits of Free Will. The first reply is to Robert Wallace and focuses on the question of whether there is a conflict between the core compatibilist and pessimist components of the "critical compatibilist" position that Russell has advanced. The second reply is to Angela Smith's discussion of the "narrow" interpretation of moral responsibility (...) responsibility (as defended by R. Jay Wallace) and how best to respond to it. The third and last reply is concerned with Christopher Bennett's criticism of Russell's views concerning "motivational scepticism" and the possibility of pure practical reasons. (shrink)

F-relevant respects are never precisely defined, but the intuitive idea is clear enough. Smart- relevant respects are mental abilities, Philosopher-relevant respects presumably include where one is employed, what kinds of things one writes, etc, and, most importantly for this paper, the only Tall-relevant respect is height.

There has been some debate as to whether or not it is possible to keep a promise, and thus fulfil a duty, to supererogate. In this paper, I argue, in agreement with Jason Kawall, that such promises cannot be kept. However, I disagree with Kawall’s diagnosis of the problem and provide an alternative account. In the first section, I examine the debate between Kawall and David Heyd, who rejects Kawall’s claim that promises to supererogate cannot be kept. I disagree with (...) Heyd’s argument, as it fails to get to the heart of the problem Kawall articulates. Kawall’s argument however fails to make clear the problem with promising to supererogate because his discussion relies on the plausibility of the following claim: that supererogatory actions cannot also fulfil obligations. I argue that this view is mistaken because there are clear examples of supererogatory actions that also fulfil obligations. In the final section, I give my alternative account of the problem, identifying exactly what is wrong with fulfilling a duty, and thus keeping a promise, to supererogate. My diagnosis emphasises the importance of identifying non-supererogatory actions when it comes to understanding the way in which supererogatory actions go above and beyond the call of duty. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)

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

This article examines the ways in which Adam Smith and G. W. F Hegel conceptualize the identity of workers in a market economy. Although both see human beings as shaped in and through social rela- tionships, the relation between the worker and his work is seen in different ways. For Smith, workers “have” human capital, while for Hegel workers “are” brewers, butchers or bakers;; their profession is part of their identity. This conceptual difference, which is reflected in different (...) “varieties of capitalism” today, shows that not only degrees, but also kinds of embeddedness need to be taken into account in discussions of the relation between individual and society. (shrink)

Moral theories that demand that we do what is morally best leave no room for the supererogatory. One argument against such theories is that they fail to realize the value of autonomy: supererogatory acts allow for the exercise of autonomy because their omissions are not accompanied by any threats of sanctions, unlike obligatory ones. While this argument fails, I use the distinction it draws – between omissions of obligatory and supererogatory acts in terms of appropriate sanctions – to draw a (...) parallel with psychological perfectionism. Through this parallel, I demonstrate that requiring what is morally best is in fact counter-productive. Thus, by its own lights, a theory that wants us to do what is best ought at the very least to tell us to believe that some actions are supererogatory. As the old adage goes, the best is the enemy of the good; I argue here that the supererogatory is the solution. (shrink)

Amy saves a man from drowning despite the risk to herself, because she is moved by his plight. This is a quintessentially supererogatory act: an act that goes above and beyond the call of duty. Beth, on the other hand, saves a man from drowning because she wants to get her name in the paper. On this second example, opinions differ. One view of supererogation holds that, despite being optional and good, Beth’s act is not supererogatory because she is not (...) praiseworthy; the other agrees that Beth is not praiseworthy but holds that her act is nevertheless supererogatory because, while supererogatory actions are generally performed by praiseworthy agents, an individual need not be praiseworthy for their act to be supererogatory. In this paper, I raise a problem for this latter position, which I shall call the Anti-Motivation View of supererogation. While the Anti-Motivation View rejects the claim that the agent’s motivations are important, it accepts that the agent’s intentions are. Thus, this view assumes that a clear, coherent distinction can be drawn between intentions and motivations in the context of supererogation. This distinction is often attributed to Mill; however, his original discussion reveals an inconsistency. Consider Clara, who saves a man from drowning because she wants to torture him later. According to Mill, Clara’s act is not morally good; those who follow Mill will have to accept that it is therefore not supererogatory. Mill asserts that Clara’s act differs from Amy’s and Beth’s not just in motivation but also in intention. I question this explanation and demonstrate that the distinction between motivation and intention is not as clear as the Anti-Motivation View has supposed and that the gap between the Anti-Motivation View and the alternative Praise-Based View is either much greater or much smaller than previously thought. (shrink)

This review focuses on the Ogdoas scholastica by Jacob Lorhard, published in 1606. The importance of this document turns on the fact that it contains what is almost certainly the first published occurrence of the term “ontology.” The body of the work consists in a series of diagrams called “diagraphs.” Relevant features of this compendium of diagraphs are: 1. that it does not in fact contain the word “ontology,” and 2. that Lorhard himself was not responsible for its content.

The essay constructs an ontological theory designed to capture the categories instantiated in those portions or levels of reality which are captured in our common sense conceptual scheme. It takes as its starting point an Aristotelian ontology of “substances” and “accidents”, which are treated via the instruments of mereology and topology. The theory recognizes not only individual parts of substances and accidents, including the internal and external boundaries of these, but also universal parts, such as the “humanity” which is an (...) essential part of both Tom and Dick, and also “individual relations”, such as Tom’s promise to Dick, or their current handshake. (shrink)

The Enkratic Principle enjoys something of a protected status as a requirement of rationality. I argue that this status is undeserved, at least in the epistemic domain. Compliance with the principle should not be thought of as a requirement of epistemic rationality, but rather as defeasible indication of epistemic blamelessness. To show this, I present the Puzzle of Inconsistent Requirements, and argue that the best way to solve it is to distinguish two kinds of epistemic evaluation – requirement evaluations and (...) appraisal evaluations. This allows us to solve the puzzle while accommodating traditional motivations for thinking of the Enkratic Principle as a requirement of rationality. (shrink)

Can we make mistakes about what rationality requires? A natural answer is that we can, since it is a platitude that rational belief does not require truth; it is possible for a belief to be rational and mistaken, and this holds for any subject matter at all. However, the platitude causes trouble when applied to rationality itself. The possibility of rational mistakes about what rationality requires generates a puzzle. When combined with two further plausible claims – the enkratic principle, and (...) the claim that rational requirements apply universally – we get the result that rationality generates inconsistent requirements. One popular and attractive solution to the puzzle denies that it is possible to make rational mistakes about what rationality requires. I show why (contra Titelbaum (2015b), and Littlejohn (2015)) this solution is doomed to fail. (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)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

In this paper I defend an eudaimonistic reading of Spinoza’s ethical philosophy. Eudaimonism refers to the mainstream ethical tradition of the ancient Greeks, which considers happiness a naturalistic, stable, and exclusively intrinsic good. Within this tradition, we can also draw a distinction between weak eudaimonists and strong eudaimonists. Weak eudaimonists do not ground their ethical conceptions of happiness in complete theories of metaphysics, epistemology, or psychology. Strong eudaimonists, conversely, build their conceptions of happiness around an overall philosophical system that extends (...) far beyond ethics, while nevertheless being directed at the promotion of a happy life. I will show that Spinozistic happiness is not only naturalistic, stable, and exclusively intrinsically good, but that Spinoza is also a strong eudaimonist because his ethical account of happiness is incomprehensible without appeal to metaphysical, epistemological, and psychological doctrines. As well, I will explain how the apparent subjective and relativistic features of Spinoza’s ethics do not undermine the eudaimonistic reading, because both Spinoza and the ancient eudaimonists grant that the beliefs/feelings of the subject play a necessary (but insufficient) role in happiness as the highest good. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

Is it right to convict a person of a crime on the basis of purely statistical evidence? Many who have considered this question agree that it is not, posing a direct challenge to legal probabilism – the claim that the criminal standard of proof should be understood in terms of a high probability threshold. Some defenders of legal probabilism have, however, held their ground: Schoeman (1987) argues that there are no clear epistemic or moral problems with convictions based on purely (...) statistical evidence, and speculates that our aversion to such convictions may be nothing more than an irrational bias. More recently, Hedden and Colyvan (2019, section VI) describe our reluctance to convict on the basis of purely statistical evidence as an ‘intuition’, but suggest that there may be no ‘in principle’ problem with such convictions (see also Papineau, forthcoming, section 6). In this paper, I argue that there is, in some cases, an in principle problem with a conviction based upon statistical evidence alone – namely, it commits us to a precedent which, if consistently followed through, could lead to the deliberate conviction of an innocent person. I conclude with some reflections on the idea that the criminal justice system should strive to maximise the accuracy of its verdicts – and the related idea that we should each strive to maximise the accuracy of our beliefs. (shrink)

De Re Significance accounts of moral appraisal consider an agent’s responsiveness to a particular kind of reason, normative moral reasons de re, to be of central significance for moral appraisal. Here, I argue that such accounts find it difficult to accommodate some neuroatypical agents. I offer an alternative account of how an agent’s responsiveness to normative moral reasons affects moral appraisal – the Reasonable Expectations Account. According to this account, what is significant for appraisal is not the content of the (...) reasons an agent is responsive to, but rather whether she is responsive to the reasons it is reasonable to expect her to be responsive to, irrespective of their content. I argue that this account does a better job of dealing with neuroatypical agents, while agreeing with the De Re Significance accounts on more ordinary cases. (shrink)

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

I argue that there are some situations in which it is praiseworthy to be motivated only by moral rightness de dicto, even if this results in wrongdoing. I consider a set of cases that are challenging for views that dispute this, prioritising concern for what is morally important in moral evaluation. In these cases, the agent is not concerned about what is morally important, does the wrong thing, but nevertheless seems praiseworthy rather than blameworthy. I argue that the views under (...) discussion cannot accommodate this, and should be amended to recognise that it is often praiseworthy to be motivated to do what is right. (shrink)

Those of us who see the historical figures we work on as sources of philosophical insight, rather than merely of historical interest, will sooner or later run u.

Is normative uncertainty like factual uncertainty? Should it have the same effects on our actions? Some have thought not. Those who defend an asymmetry between normative and factual uncertainty typically do so as part of the claim that our moral beliefs in general are irrelevant to both the moral value and the moral worth of our actions. Here I use the consideration of Jackson cases to challenge this view, arguing that we can explain away the apparent asymmetries between normative and (...) factual uncertainty by considering the particular features of the cases in greater detail. Such consideration shows that, in fact, normative and factual uncertainty are equally relevant to moral assessment. (shrink)

The paper is an exercise in descriptive ontology, with specific applications to problems in the geographical sphere. It presents a general typology of spatial boundaries, based in particular on an opposition between bona fide or physical boundaries on the one hand, and fiat or human-demarcation-induced boundaries on the other. Cross-cutting this opposition are further oppositions in the realm of boundaries, for example between: crisp and indeterminate, complete and incomplete, enduring and transient, symmetrical and asymmetrical. The resulting typology generates a corresponding (...) categorization of the different sorts of objects which (complete) boundaries determine or demarcate. The theory is applied first of all in the areas of geography and of administrative and property law. Indications are then given as to how the typology may be applied also in other fields where physical and fiat boundaries are at work, including the field of cognitive linguistics and the related field of the ontology of truth. (shrink)

Incoherence is usually regarded as a bad thing. Incoherence suggests irrationality, confusion, paradox. Incoherentism disagrees: incoherence is not always a bad thing, sometimes we ought to be incoherent. If correct, Incoherentism has important and controversial implications. It implies that rationality does not always require coherence. Dilemmism and Incoherentism both embrace conflict in epistemology. After identifying some important differences between these two ways of embracing conflict, I offer some reasons to prefer Incoherentism over Dilemmism. Namely, that Incoherentism allows us to deliberate (...) about what we ought to believe using ordinary epistemology, and it does a better job of accommodating the positive features of incoherence. (shrink)

I argue for the unexceptionality of evidence about what rationality requires. Specifically, I argue that, as for other topics, one’s total evidence can sometimes support false beliefs about this. Despite being prima facie innocuous, a number of philosophers have recently denied this. Some have argued that the facts about what rationality requires are highly dependent on the agent’s situation and change depending on what that situation is like. (Bradley 2019). Others have argued that a particular subset of normative truths, those (...) concerning what epistemic rationality requires, have the special property of being ‘fixed points’—it is impossible to have total evidence that supports false belief about them. (Smithies 2012; Titelbaum 2015). Each of these kinds of exceptionality permits a solution to downstream theoretical problems that arise from the possibility of evidence supporting false belief about requirements of rationality. However, as I argue here, they incur heavy explanatory burdens that we should avoid. (shrink)

That uses of language not only can, but even normally do, have the character of actions was a fact largely unrealised by those engaged in the study of language before the present century, at least in the sense that there was lacking any attempt to come to terms systematically with the action-theoretic peculiarities of language use. Where the action-character of linguistic phenomena was acknowledged, it was normally regarded as a peripheral matter, relating to derivative or nonstandard aspects of language which (...) could afford to be ignored. (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.