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)

Mental and behavioral disorders represent a significant portion of the public health burden in all countries. The human cost of these disorders is immense, yet treatment options for sufferers are currently limited, with many patients failing to respond sufficiently to available interventions and drugs. High quality ontologies facilitate data aggregation and comparison across different disciplines, and may therefore speed up the translation of primary research into novel therapeutics. Realism-based ontologies describe entities in reality and the relationships between them in such (...) a way that – once formulated in a suitable formal language – the ontologies can be used for sophisticated automated reasoning applications. Reference ontologies can be applied across different contexts in which different, and often mutually incompatible, domain-specific vocabularies have traditionally been used. In this contribution we describe the Mental Functioning Ontology (MF) and Mental Disease Ontology (MD), two realism-based ontologies currently under development for the description of humanmental functioning and disease. We describe the structure and upper levels of the ontologies and preliminary application scenarios, and identify some open questions. (shrink)

In 1890 Christian von Ehrenfels published his classic paper "Über 'Gestaltqualitäten'", the first systematic investigation of the philosophy and psychology of Gestalt. Ehrenfels thereby issued an important challenge to the psychological atomism that was still predominant in his day. His paper not only exerted a powerful influence on the philosophy of the Meinong school, it also marked the beginning of the Gestalt tradition in psychology, later associated with the work of Wertheimer, Köhler and Koffka in Berlin. Includes papers by C. (...) Von Ehrenfels, Kurt Grelling and Paul Oppenheim and contributions by K. Mulligan, P.M. Simons and Barry Smith. (shrink)

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

We propose as a UCGIS research priority the topic of “Ontological Foundations for Geographic Information.” Under this umbrella we unify several interrelated research subfields, each of which deals with different perspectives on geospatial ontologies and their roles in geographic information science. While each of these subfields could be addressed separately, we believe it is important to address ontological research in a unitary, systematic fashion, embracing conceptual issues concerning what would be required to establish an exhaustive ontology of the geospatial domain, (...) issues relating to the choice of appropriate methods for formalizing ontologies, and considerations regarding the design of ontology-driven information systems. This integrated approach is necessary, because there is a strong dependency between the methods used to specify an ontology, and the conceptual richness, robustness and tractability of the ontology itself. Likewise, information system implementations are needed as testbeds of the usefulness of every aspect of an exhaustive ontology of the geospatial domain. None of the current UCGIS research priorities provides such an integrative perspective, and therefore the topic of “Ontological Foundations for Geographic Information Science” is unique. (shrink)

Techniques from behavioral economics—nudges—may help physicians increase pediatric vaccine compliance, but critics have objected that nudges can undermine autonomy. Since autonomy is a centrally important value in healthcare decision-making contexts, it counts against pediatric vaccination nudges if they undermine parental autonomy. Advocates for healthcare nudges have resisted the charge that nudges undermine autonomy, and the recent bioethics literature illustrates the current intractability of this debate. This article rejects a principle to which parties on both sides of this debate sometimes seem (...) committed: that nudges are morally permissible only if they are consistent with autonomy. Instead, I argue that, at least in the case of pediatric vaccination, some autonomy-undermining nudges may be morally justified. This is because parental autonomy in pediatric decision-making is not as morally valuable as the autonomy of adult patients, and because the interests of both the vaccinated child and other members of the community can sometimes be weighty enough to justify autonomy-infringing pediatric vaccination nudges. This article concludes with a set of worries about the effect of pediatric vaccination nudges on parent-physician relationships, and it calls on the American Academy of Pediatrics to draw on scientific and bioethics research to develop guidelines for the use of nudges in pediatric practice and, in particular, for the use of pediatric vaccination nudges. (shrink)

Many advocate practices of ‘local food’ or ‘locavorism’ as a partial solution to the injustices and unsustainability of contemporary food systems. I think that there is much to be said in favor of local food movements, but these virtues are insufficient to immunize locavorism from criticism. In particular, three duties of international ethics—beneficence, repair and fairness—may provide reasons for constraining the developed world’s permissible pursuit of local food. A complete account of why (and how) the fulfillment of these duties constrains (...) locavorism will require extensive empirical evidence about the relationship between agricultural demand-led industrialization, international trade (rules), and local food practices. In this paper I can only gesture at some of this evidence and, for that reason, my policy prescriptions are merely provisional. Instead, the upshot of this paper is that advocates of locavorism ought to be attentive to the empirical-dependence of the moral permissibility of their projects. As local food ‘scales up’—and comes to be embraced as a goal of political communities—these concerns should receive even greater attention. (shrink)

In this paper we argue that Socrates is a cognitivist about emotions, but then ask how the beliefs that constitute emotions can come into being, and why those beliefs seem more resistant to change through rational persuasion than other beliefs.

The paper has two complementary objectives. First, it sustains an analysis of the concept of ‘coloniality’ that accounts for the epistemic imbalance in the modern world, demonstrating precisely how Africa is adversely affected, having been caught up in the throes of coloniality and its epistemic implications. Second – and complementarily – the paper attempts to bring this very concept of ‘coloniality’ into the discourse on Africa’s emigration crisis, arguing that Africa’s emigration crisis is traceable, inter alia, to the epistemic imbalance (...) in the very structure of modernity. This imbalance results from the stifling of Africa’s epistemic resources under Western epistemic hegemony. Epistemic coloniality, of course interacting with some material factors, creates a sufficient condition for emigration. It is further theorized that the apparent lack of epistemic will on the part of Africans to mobilize some surviving epistemic resources to address some problems on their own is also a function of coloniality. (shrink)

The work argues that engaging Africa's cultural and epistemic resources as social imaginaries, and not as metaphysical or ontological “essences,” could help practitioners of African philosophy overcome the cluster of shortcomings and undesirable features associated with “ethnophilosophy.” A number of points are outlined to buttress this claim. First, the framework of social imaginaries does not operate with the false assumption that Africa's cultural forms and epistemic resources are static and immutable. Second, this framework does not lend itself to sweeping generalizations (...) about Africa or large swathes of it. Third, the framework of social imaginaries remedies ethnophilosophy's problem of collectivism. Fourth, unlike ethnophilosophy, it does not romanticize and canonize a supposedly “idyllic” African past, which militates against a realistic and forward‐looking philosophizing. Finally, with the framework of social imaginaries, Africa's indigenous cultural and epistemic resources become amenable to being engaged with critical philosophical rigor. This not only enhances their potential for cross‐cultural philosophical conversation but also enhances their usefulness for addressing current sociopolitical issues affecting Africa. The discussion in this paper somewhat touches upon the question of method in African philosophy, using the ethnophilosophy problem to navigate the vast gamut of issues involved. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

Pojęcie niszy (otoczenia, kontekstu, siedliska, środowiska) nie cieszy się specjalnym zainteresowaniem ontologów, mimo że ma szerokie zastosowanie w rozmaitych dyscyplinach, od biologii ewolucyjnej po ekonomię. Niniejszy artykuł zawiera pierwszą teorię formalną tego pojęcia — teorię relacji pomiędzy przedmiotami a ich niszami. Teoria ta opiera się na istniejącym dorobku mereologii, topologii i teorii lokalizacji przestrzennej, które są narzędziami ontologii formalnej. Jest ona tutaj ilustrowana głównie za pomocą prostych przykładów z biologii, ale pojęcie niszy należy rozumieć — podobnie jak pojęcia części, granicy (...) i położenia — jako pojęcie strukturalne, znajdujące zastosowanie w obszernym zakresie różnych dziedzin. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

The central argument of this article is that there is a remarkable conceptual parallel between Hegel’s famous notion of the “cunning of Reason” and the philosophically profound concept of Chi in Igbo metaphysics. By way of establishing this parallel, the article advances the following subsidiary but complementary points: Chi is also “cunning” in its dynamics; both principles (i.e. Chi and Reason/Spirit) are non-deterministic because they try to maintain a dialectic balance between destiny and individual responsibility; both possess divine attributes; and (...) community serves as an invaluable medium of operation for both. The scholarly significance of the article lies in its attempt not only to systematise the Igbo thought on Chi by eliminating the vestiges of discredited “ethno-philosophy”, but also to open up a constructive dialogue between Hegel and elements of African philosophy, using Igbo metaphysics as a placeholder. This is against the backdrop of certain discontents generated by Hegel’s famous uncomplimentary and racist remarks on Africa. Seen in this light, the article may well be an exercise in “rapprochement”. (shrink)

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

The sense of interconnectedness is perhaps one of the most celebrated features of African thought. It has been theorized under different philosophical idi- oms among African philosophers. It has appeared variously as African metaphysics, ontology, socialism and even religion—all in a bid to underline the basic idea that aspects of reality are inextricably interconnected and mutually impact one another in a seemingly universal web of interaction. While each of the idioms used to express this idea has some merits, the article (...) privileges the epistemic idiom. To support this move, I make two mutually reinforcing arguments. First, it is appropriate to describe the sense of interconnectedness in epistemic terms because it is primarily a mode of knowing/perceiving the world. Second, and more importantly, the epistemic idiom is useful for the formulation of emancipatory demands and formation of epistemic alliances against the subjugation of African and non-Western knowledges by mecha- nisms of coloniality. (shrink)

Since it is only five years since the publication of our paper, "Geographical categories: An ontological investigation" (Smith and Mark 2001), it seems somewhat strange to be making retrospective comments on the piece. Nevertheless, the field is moving quickly, and much has happened since the article appeared. A large number of papers have already cited the work, which suggests that there is a seam here that people find worthy of being mined. In this short essay, we first review (...) the paper and attempt to assess its significance from the perspective of our current work. We then put the paper in the context of our individual and joint works, which led up to it, and summarize our research trajectories since the paper appeared, pointing out what some of this reveals about spatial ontology in general. We conclude with some remarks on the future of ontological research in geographical information science. (shrink)

Long-standing neglect of the chemical senses in the philosophy of perception is due, mostly, to their being regarded as ‘lower’ senses. Smell, taste, and chemically irritated touch are thought to produce mere bodily sensations. However, empirically informed theories of perception can show how these senses lead to perception of objective properties, and why they cannot be treated as special cases of perception modelled on vision. The senses of taste, touch, and smell also combine to create unified perceptions of flavour. The (...) nature of these multimodal experiences and the character of our awareness of them puts pressure on the traditional idea that each episode of perception goes one or other of the five senses. Thus, the chemical senses, far from being peripheral to the concerns of the philosophy of perception, may hold important clues to the multisensory nature of perception in general. (shrink)

Do mountains exist? The answer to this question is surely: yes. In fact, ‘mountain’ is the example of a kind of geographic feature or thing most commonly cited by English speakers (Mark, et al., 1999; Smith and Mark 2001), and this result may hold across many languages and cultures. But whether they are considered as individuals (tokens) or as kinds (types), mountains do not exist in quite the same unequivocal sense as do such prototypical everyday objects as (...) chairs or people. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

There is a basic distinction, in the realm of spatial boundaries, between bona fide boundaries on the one hand, and fiat boundaries on the other. The former are just the physical boundaries of old. The latter are exemplified especially by boundaries induced through human demarcation, for example in the geographic domain. The classical problems connected with the notions of adjacency, contact, separation and division can be resolved in an intuitive way by recognizing this two-sorted ontology of boundaries. Bona fide boundaries (...) yield a notion of contact that is effectively modeled by classical topology; the analogue of contact involving fiat boundaries calls, however, for a different account, based on the intuition that fiat boundaries do not support the open/closed distinction on which classical topology is based. In the presence of this two-sorted ontology it then transpires that mereotopology—topology erected on a mereological basis—is more than a trivial formal variant of classical point-set topology. (shrink)

Cognitive categories in the geographic realm appear to manifest certain special features as contrasted with categories for objects at surveyable scales. We have argued that these features reflect specific ontological characteristics of geographic objects. This paper presents hypotheses as to the nature of the features mentioned, reviews previous empirical work on geographic categories, and presents the results of pilot experiments that used English-speaking subjects to test our hypotheses. Our experiments show geographic categories to be similar to their non-geographic counterparts in (...) the ways in which they generate instances of different relative frequencies at different levels. Other tests, however, provide preliminary evidence for the existence of important differences in subjects’ categorizations of geographic and non-geographic objects, and suggest further experimental work especially with regard to the role in cognitive categorization of different types of object-boundaries at different scales. (shrink)

Ontology, since Aristotle, has been conceived as a sort of highly general physics, a science of the types of entities in reality, of the objects, properties, categories and relations which make up the world. At the same time ontology has been for some two thousand years a speculative enterprise. It has rested methodologically on introspection and on the construction and analysis of elaborate world-models and of abstract formal-ontological theories. In the work of Quine and others this ontological theorizing in abstract (...) fashion about the world was supplemented by the study, based on the use of logical methods, of the ontological commitments or presuppositions embodied in scientific theories. In recent years both types of ontological study have found application in the world of information systems, for example in the construction of frameworks for knowledge representation and in database design and translation. As ontology is in this way drawn closer to the domain of real-world applications, the question arises as to whether it is possible to use empirical methods in studying ontological theories. More specifically: can we use empirical methods to test the ontological theories embodied in human cognition? We set forth the outlines of a framework for the formulation and testing of such theories as they relate to the specific domain of geographic objects and categories. (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)

The concept of niche (setting, context, habitat, environment) has been little studied by ontologists, in spite of its wide application in a variety of disciplines from evolutionary biology to economics. What follows is a first formal theory of this concept, a theory of the relations between objects and their niches. The theory builds upon existing work on mereology, topology, and the theory of spatial location as tools of formal ontology. It will be illustrated above all by means of simple biological (...) examples, but the concept of niche should be understood as being, like concepts such as part, boundary, and location, a structural concept that is applicable in principle to a wide range of different domains. (shrink)

We rely on language to know the minds of others, but does language have a role to play in knowing our own minds? To suppose it does is to look for a connection between mastery of a language and the epistemic relation we bear to our inner lives. What could such a connection consist in? To explore this, I shall examine strategies for explaining self-knowledge in terms of the use we make of language to express and report our mental states. (...) Success in these strategies will depend on the view we take of speakers' understanding of the words they use to speak their minds. The key is to avoid circularity in the account of how they know what they mean; for if knowing what one is saying in speaking a language provides a means of knowing one's own mind, it cannot simply be a part of it. I shall look at ways in which we might proceed here, and examine whether the strategy can make room for a genuinely first-person point of view. But first let me try to motivate the problem of self-knowledge. (shrink)

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

Human cognitive acts are directed towards objects extended in space of a wide range of different types. What follows is a new proposal for bringing order into this typological clutter. The theory of spatially extended objects should make room not only for the objects of physics but also for objects at higher levels, including the objects of geography and of related disciplines. It should leave room for different types of boundaries, including both the bona fide boundaries which we find in (...) the physical world and the fiat (or human-demarcation-induced) boundaries with which much of geography has to deal. Two distinct axiomatic theories of boundaries are accordingly presented, and the need for both is examined in some detail. The resultant dual framework is shown to have application above all for our understanding of issues involving contact, division, and separation, issues which have posed serious difficulties for the ontological theories of boundaries that have been proposed hitherto. (shrink)

In his latest book, Michael Devitt rejects Chomsky’s mentalist conception of linguistics. The case against Chomsky is based on two principal claims. First, that we can separate the study of linguistic competence from the study of its outputs: only the latter belongs to linguistic inquiry. Second, Chomsky’s account of a speaker’s competence as consisiting in the mental representation of rules of a grammar for his language is mistaken. I shall argue, first, that Devitt fails to make a case for separating (...) the study of outputs from the study of competence, and second, that Devitt mis-characterises Chomsky’s account of competence, and so his objections miss their target. Chomsky’s own views come close to a denial that speaker’s have knowledge of their language. But a satisfactory account of what speakers are able to do will need to ascribe them linguistic knowledge that they use to speak and understand. I shall explore a conception of speaker’s knowledge of language that confirrns Chomsky’s mentalist view of linguistics but which is immune to Devitt’s criticism. (shrink)

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

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

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

The history of evolution is a history of development from less to more complex organisms. This growth in complexity of organisms goes hand in hand with a concurrent growth in complexity of environments and of organism-environment relations. It is a concern with this latter aspect of evolutionary development that motivates the present paper. We begin by outlining a theory of organism-environment relations. We then show that the theory can be applied to a range of different sorts of cases, both biological (...) and non-biological, in which objects are lodged or housed within specific environments, or niches. Biological science is interested in types—for example in genotypes, phenotypes, and environment types—in regularities that can serve as the basis for the formulation of laws or general principles. Types, however, can exist only through their corresponding tokens. Our theory of token environments is meant to plug this gap and to provide a first step towards a general theory of causally relevant spatial volumes. (shrink)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis. Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato’s dialogues, is sfounded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then show (...) how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato’s dialogues by date, more general challenges to historicist interpretations of Plato’s dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

In uttering a sentence we are often take to assert more than its literal meaning - though sometimes we assert less. This phenomenon is taken by many to show that what is said or asserted by a speaker on an occasion is a contextually enriched or developed version of the semantic content of the words uttered. I argue that we can resist this conclusion by recognizing that what we think we are asserting, or take others to assert, involves selective attention (...) to just one of the ways a sentence could be true and neglects others. In most conversations people converge in their selective attention and communication is not impaired. Though in the case of sentences involving predicates of personal taste, people's attention to aspects of what is claimed differs and this can lead to intractable disputes. I offer a diagnosis of such disputes where speakers can disagree about the same claim and both be right. (shrink)

John Searle’s The Construction of Social Reality and Hernando de Soto’s The Mystery of Capital shifted the focus of current thought on capital and economic development to the cultural and conceptual ideas that underpin market economies and that are taken for granted in developed nations. This collection of essays assembles 21 philosophers, economists, and political scientists to help readers understand these exciting new theories.

The shape of the Earth's surface, its topography, is a fundamental dimension of the environment, shaping or mediating many other environmental flows or functions. But there is a major divergence in the way that topography is conceptualized in different domains. Topographic cartographers, information scientists, geomorphologists and environmental modelers typically conceptualize topographic variability as a continuous field of elevations or as some discrete approximation to such a field. Pilots, explorers, anthropologists, ecologists, hikers, and archeologists, on the other hand, typically conceptualize this (...) same variability in terms of hills and valleys, mountains and plains, barrows and trenches, that is, as (special sorts of) objects, with locations, shapes, and often names of their own. In this chapter, we sketch an approach to bridging this fundamental gap in geographic information infrastructure. (shrink)

Information may be defined as the conceptual or communicable part of the content of mental acts. The content of mental acts includes sensory data as well as concepts, particular as well as general information. An information system is an external (non-mental) system designed to store such content. Information systems afford indirect transmission of content between people, some of whom may put information into the system and others who are among those who use the system. In order for communication to happen, (...) the conceptual systems of the originators and users of the information must be sufficiently similar. A formal conceptual framework that can provide the basis for exchange of information is termed an ontology. In its most fundamental form, ontology studies the most basic constituents of reality. Traditionally, ontology seeks to reflects structures that are independent of thought and cognition. The term ontology is used more broadly in artificial intelligence and software engineering, to refer to the conceptual basis for an information system. (shrink)

We propose the beginnings of a general theory of environments, of the parts or regions of space in which organisms live and move. We draw on two sources: on the one hand on recent work on the ontology of space; and on the other hand on work by ecological scientists on concepts such as territory, habitat, and niche. An environment is in first approximation a volume of space; it is a specific habitat, location, or site that is suitable or adequate (...) for given purposes (of foraging, resting, hunting, breeding, nesting, grooming) in the life of an organism or group of organisms. This spatial notion of environment can be drawn closer to biological and ecological science by taking account of the pertinent physical attributes realized within given spatial regions. (shrink)

Translation of Mark Sainsbury: Paradoxes (Cambridge University Press 1988).

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

This is an informal presentation of the theory of niches understood as ecological contexts. The first part sets out the basic conceptual background. The second part outlines the main principles of the theory and addresses the question of how the theory can be extended to aid our thinking in relation to the special types of causal integrity that characterize niches and niched entities.

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

Revised version published as Barry Smith and Achille Varzi, “Fiat and Bona Fide Boundaries”, Philosophy and Phenomenological Research, 60: 2 (March 2000), 401–420.