A realist theory of truth for a class of sentences holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar, we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core of our theory is the (...) account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. In contrast to this, we uphold the mutual independence of logical and ontological complexity, and the authors outline formal principles of truthmaking taking account of both kinds of complexity. (shrink)

Philosophy in the West divides into three parts: Analytic Philosophy (AP), Continental Philosophy (CP), and History of Philosophy (HP). But all three parts are in a bad way. AP is sceptical about the claim that philosophy can be a science, and hence is uninterested in the real world. CP is never pursued in a properly theoretical way, and its practice is tailor-made for particular political and ethical conclusions. HP is mostly developed on a regionalist basis: what is studied is determined (...) by the nation or culture to which a philosopher belongs, rather than by the objective value of that philosopher’s work. Progress in philosophy can only be attained by avoiding these pitfalls. (shrink)

Simon Blackburn has not shied away from the use of vivid imagery in developing, over a long and prolific career, a large-scale philosophical vision. Here one might think, for instance, of ‘Practical Tortoise Raising’ or ‘Ramsey's Ladder’ or ‘Frege's Abyss’. Blackburn develops a ‘quasi-realist’ account of many of our philosophical and everyday commitments, both theoretical (e.g., modality and causation) and practical (e.g., moral judgement and normative reasons). Quasi-realism aims to provide a naturalistic treatment of its targeted phenomena while earning (...) the right to deploy all of the ‘trappings’ of realism—i.e., while eschewing any idea that our normal thought and talk about such phenomena are pervasively in error. The quasi-realist project is that of explaining how (as Huw Price puts it here) ‘the folk come to “talk the realist talk” without committing ourselves—us theorists, as it were—to “walking the metaphysical walk”’ (p. 136). Quasi-realism, too, can speak of truth, facts, properties, belief, knowledge, and so on. The imagery in this collection also abounds, though, in capturing a different view of quasi-realism: No fewer than three of the contributors picture Blackburn as wanting to have his cake and eat it too (Louise Antony asking, in addition, ‘Who doesn't? It's cake’ [p. 19]). (shrink)

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

Als zu Beginn des Jahrhunderts der Realismus wieder ernst genommen wurde, gab es viele Philosophen, die sich mit der Ontologie der Wahrheit befaßten. Unabhängig von der Bestimmung der Wahrheit als Korrespondenzbeziehung wollten sie herausfinden, inwieweit zur Erklärung der Wahrheit von Sätzen besondere Entitäten herangezogen werden müssen. Einige dieser Entitäten, so zum Beispiel Bolzanos ‘Sätze an sich’, Freges ‘Gedanken’ oder die ‘propositions’ von Russell und Moore, wurden als Träger der Eigenschaften Wahrheit und Falschheit aufgefaßt. Einige Philosophen jedoch, wie Russell, Wittgenstein im (...) ›Tractatus‹ und Husserl in den ›Logischen Untersuchungen‹, argumentierten, zusätzlich zu den Wahrheitsträgern bzw. an ihrer Stelle müßten Entitäten angenommen werden, auf Grund deren Sätze und/oder ‘Propositionen’ wahr sind. Solchen Entitäten gab man verschiedene Namen, insbesondere ‘fact’, ‘Tatsache’, ‘state of affairs’ und ‘Sachverhalt’. 1 Wir wollen einer Entscheidung über die Angebrachtheit dieser Ausdrücke nicht vorgreifen und daher zunächst eine neutralere Terminologie verwenden: Alle Entitäten, die für diese zweite Rolle in Frage kommen, wollen wir ‘Wahrmacher’ nennen. (shrink)

French translation of "Truth-Makers" (1984). A realist theory of truth for a class of sentence holds that there are entities in virtue of which these sentences are true or false. We call such entities ‘truthmakers’ and contend that those for a wide range of sentences about the real world are moments (dependent particulars). Since moments are unfamiliar we provide a definition and a brief philosophical history, anchoring them in our ontology by showing that they are objects of perception. The core (...) of our theory is the account of truthmaking for atomic sentences, in which we expose a pervasive ‘dogma of logical form’, which says that atomic sentences cannot have more than one truthmaker. The authors uphold the mutual independence of logical and ontological complexity. The theory is compared with that of Wittgenstein’s Tractatus, and the authors outline formal principles of truthmaking taking account of both kinds of complexity and suggesting how to overcome Wittgenstein’s problem of negation. (shrink)

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

This paper is a fresh attempt to articulate the role of a theory of truthmakers. We argue that truthmaker theory constitutes a cornerstone of good methodology in metaphysics, but that a conflation of truthmaker theory with the theory of truth has been responsible for certain excesses associated with truthmaker-based approaches in the recent literature. If truthmaker theory is not a component of a theory of truth, then truthmaker maximalism – the view that every truth has a truthmaker – loses its (...) primary motivation. More generally, if the task of truthmaker theory is not to provide a definition or account of truth in truthmaker terms, there is no pressing need for hard, a priori principles stating which truths have truthmakers and which do not. (shrink)

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

A letter to The Times of London, May 9, 1992 protesting the Cambridge University proposal to award an honorary degree to M. Jacques Derrida.

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

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

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

The three young philosophers Kevin Mulligan, Peter Simons and Barry Smith have become well-known in the last few years especially in German-speaking analytical philosophy and phenomenology circles. This is on the one hand as a result of their historical and systematic philosophical work; but it is also because of the provocative way in which they represent their philosophy. Because they often appear in threes, they have become known as the "gang of three" or "three musketeers" or even – and (...) this in an admiring sense – "mafiosi" (Rescher). They are known primarily for the small workshops they have been organizing in uncomplicated Anglo-Saxon manner all over Europe. Their goal has been to show that analytic philosophy as it has been pursued up to now is in need of reform and also that the history of scientific philosophizing is not identical to the history of Anglo-Saxon analytic philosophy. Above all, they have tried to make more well known the Austrian tradition of scientific philosophy, and they can be given credit for having done much to promote the current interest in this tradition, which means: the history of Austrian philosophy of the 19th and early 20th centuries and its historical context in the Austro-Hungarian Empire. (shrink)

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

Experimental philosophers have gathered impressive evidence for the surprising conclusion that philosophers' intuitions are out of step with those of the folk. As a result, many argue that philosophers' intuitions are unreliable. Focusing on the Knobe Effect, a leading finding of experimental philosophy, we defend traditional philosophy against this conclusion. Our key premise relies on experiments we conducted which indicate that judgments of the folk elicited under higher quality cognitive or epistemic conditions are more likely to resemble those of the (...) philosopher. We end by showing how our experimental findings can help us better understand the Knobe Effect. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

The traditional use of conventional media by businesses for audience targeting has shifted with the rise of influencer marketing, notably on platforms like TikTok, posing challenges in content adaptation and technological adaptation. Albert Bandura's Social Cognitive Theory examines factors shaping purchasing behavior, particularly relevant for young professionals. A quantitative correlational study focused on young professionals engaging with TikTok and influenced by Filipino TikTok creators, revealing education level as a key determinant of purchasing behavior. Extended TikTok engagement positively correlates with increased (...) purchasing likelihood. Filipino TikTok influencers significantly impact young professionals' purchasing decisions, emphasizing the need for tailored marketing strategies targeting this demographic. Recommendations were provided for effective influencer and digital marketing strategies targeting young professionals. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

Autobiographical survey of interactions between the author and Barry Smith, especially as concerns the background and influence of the Seminar for Austro-German Philosophy and work on the relevance of Adolf Reinach, Roman Ingarden and other Central-European thinkers to contemporary analytic philosophy.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

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

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Medicine is often thought of as a science of the body, but it is also a science of data. In some contexts, it can even be asserted that data drive health. This article focuses on a key piece of data technology central to contemporary practices of medicine: the medical record. By situating the medical record in the perspective of its history, we inquire into how the kinds of data that are kept at sites of clinical encounter often depend on informational (...) requirements that originate well outside of the clinic, in particular in health insurance records systems. Although this dependency of today's electronic medical records on billing requirements is widely lamented by clinical providers, its history remains little studied. Following the archaeology of medicine developed by Michel Foucault in The Birth of the Clinic and expanding his methodology in light of more recent contributions to the field of media archaeology, this article excavates some of the underexplored technological conditions that help constitute today's electronic medical record. If in some contexts, it is true that data drive health, then an archaeology of medical records helps reveal how health insurance records often impact clinical care and, by extension, health and disease. (shrink)

A collection of material on Husserl's Logical Investigations, and specifically on Husserl's formal theory of parts, wholes and dependence and its influence in ontology, logic and psychology. Includes translations of classic works by Adolf Reinach and Eugenie Ginsberg, as well as original contributions by Wolfgang Künne, Kevin Mulligan, Gilbert Null, Barry Smith, Peter M. Simons, Roger A. Simons and Dallas Willard. Documents work on Husserl's ontology arising out of early meetings of the Seminar for Austro-German Philosophy.

This essay is an investigation into the sense of ‘able’ relevant to free will, where free will is understood as requiring the ability to do otherwise. I argue that van Inwagen's recent functional specification of the relevant sense of ‘able’ is flawed, and that explicating the powers involved in free will shall likely require paying detailed attention to the semantics and pragmatics of ‘can’ and ‘able’. Further, I argue that van Inwagen's promise-level ability requirement on free will is too strong. (...) I also argue that Mele's conjecture that the strength of the ability to perform the ‘alternative’ action be no higher than the strength of the ability exercised in performing an action is mistaken. I suggest there is an asymmetry in the strengths of the abilities which make up the n-way power that comprises free will, and that this looks to have some interesting consequences for the connection between the abilities required for free will and, e.g. the ‘up to us’ locution. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

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.

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.

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)

This book is a survey of the most important developments in Austrian philosophy in its classical period from the 1870s to the Anschluss in 1938. Thus it is intended as a contribution to the history of philosophy. But I hope that it will be seen also as a contribution to philosophy in its own right as an attempt to philosophize in the spirit of those, above all Roderick Chisholm, Rudolf Haller, Kevin Mulligan and Peter Simons, who have done so much (...) to demonstrate the continued fertility of the ideas and methods of the Austrian philosophers in our own day. For some time now, historians of philosophy have been gradually coming to terms with the idea that post-Kantian philosophy in the German-speaking world ought properly to be divided into two distinct traditions which we might refer to as the German and Austrian traditions, respectively. The main line of the first consists in a list of personages beginning with Kant, Fichte, Hegel and Schelling and ending with Heidegger, Adorno and Bloch. The main line of the second may be picked out similarly by means of a list beginning with Bolzano, Mach and Meinong, and ending with Wittgenstein, Neurath and Popper. As should be clear, it is the Austrian tradition that has contributed most to the contemporary mainstream of philosophical thinking in the Anglo-Saxon world. For while there are of course German thinkers who have made crucial contributions to the development of exact or analytic philosophy, such thinkers were outsiders when seen from the perspective of native German philosophical culture, and in fact a number of them found their philosophical home precisely in Vienna. When, in contrast, we examine the influence of the Austrian line, we encounter a whole series of familiar and unfamiliar links to the characteristic concerns of more recent philosophy of the analytic sort. As Michael Dummett points out in his Origins of Analytic Philosophy, the newly fashionable habit of referring to analytic philosophy as "Anglo-American" is in this light a "grave historical distortion". If, he says, we take into account the historical context in which analytic philosophy developed, then such philosophy "could at least as well be called "Anglo-Austrian" (1988, p. 7). Much valuable scholarly work has been done on the thinking of Husserl and Wittgenstein, Mach and the Vienna Circle. The central axis of Austrian philosophy, however, which as I hope to show in what follows is constituted by the work of Brentano and his school, is still rather poorly understood. Work on Meinong or Twardowski by contemporary philosophers still standardly rests upon simplified and often confused renderings of a few favoured theses taken out of context. Little attention is paid to original sources, and little effort is devoted to establishing what the problems were by which the Austrian philosophers in general were exercised -- in spite of the fact that many of these same problems have once more become important as a result of the contemporary burgeoning of interest on the part of philosophers in problems in the field of cognitive science. (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)

A preliminary statement of the formal theory of the truthmaker relation advanced in the paper “Truth-makers” (Mulligan, Simons and Smith) in 1984. Correspondence theories of truth have. I give a brief account of some more or less obvious formal characteristics of this almost forgotten basic truthmaker relation. I then attempt to show how this account may be extended to provide elements of a theory of truth which is in keeping with the spirit of Wittgenstein’s Tractatus.

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)

(For English, scroll down) Der Text präsentiert drei miteinander verbundene Thesen. (1) Philosophie der Musik modifiziert philosophische Grundbegriffe. (2) Eine gemeinsame Eigenschaft in der Vielfalt der Musikformen liegt im Effekt einer Wahrnehmungsveränderung: oft subtil, unterschwellig und zuweilen als ekstatisch erlebte Selbst- und Welt-Transformation. (3) Strenggenommen nehmen wir nicht Töne wahr, sondern a) unsere Hör-Physiologie wandelt Schwingungsfrequenzen ab circa 18 Hz in Tonhöhen um und damit Zeit-Organisation in ein Raum-Äquivalent. (Musik mit tiefen Tönen an der Grenze zur Wahrnehmung, etwa mittels großer (...) Orgelpfeifen in Kathedralen oder Ton-Anlagen in Nachtclubs, inszeniert genau diesen physiologischen Umschlag, mit potentiellen Transzendenz-Effekten.) b) Wir nehmen einfache Frequenzverhältnisse wie 1:2, 2:3 etc. als (relativ) konsonant wahr, komplexere Verhältnisse als (relativ) dissonant. Die Folge: c) Musikhören verbindet uns mit physikalischem Verhalten von Materie, einschließlich unserer selbst. Hierin gründen rare, musikalisch herausgehobene Eindrücke von Erkenntnis und Enthüllung: das Universum betreffend und unsere Stellung in ihm. -/- The text presents three related claims. (1) Music as a topic of philosophy alters key philosophical concepts; (2) In spite of their vast cultural, historical and contextual differences, all forms of music share the effect of a transformation of perception: ranging from subtle and subliminal to the (rare) experience of ecstatic world- and self-transformations; (3) Strictly speaking, we do not perceive sounds. Rather, a) our hearing-physiology translates frequencies (impulses) of more than 18 Hz into pitch and thus temporal events into quasi-spatial perceptions. Compositions containing very deep sounds (e.g. in cathedrals or in night-clubs) stage exactly this physiological conversion: with potentially ‘transcendence’-like effects. b) We hear simple frequency-ratios such as 1:2, 2:3, 3:4 etc. as (relative) consonances and more complex ones as (relative) dissonances. Thus, c) musical compositions make laws of physical behaviour of matter affectively perceptible. This allows for the occasional impression of musical revelations: regarding the universe, its laws, and our place in it. -/- . (shrink)

Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.

Is the brain really a computer? In particular, is our intelligence a computational achievement: is it because our brains are computers that we get on in the world as well as we do? In this paper I will evaluate an ambitious new argument to the contrary, developed in Landgrebe and Smith (2021a, 2022). Landgrebe and Smith begin with the fact that many dynamical systems in the world are difficult or impossible to model accurately (inter alia, because it is (...) intractable to find exact solutions to the differential equations that describe them—meaning we have to approximate—but at the same time they are such that small differences in starting conditions lead to big differences in final conditions, thwarting accurate approximation). Yet we manage to survive and thrive in a world full of such systems. Landgrebe and Smith argue from these premises that it is not because our brains are computers that we get on as well as we do: instead it is because of the various ways that we dynamically couple with such systems, these couplings themselves impossible to model well enough to emulate in silico. Landgrebe and Smith thus defend a dynamical systems model in the lineage of Gibson (1979), Van Gelder (1995), and Thompson (2007), though their focus is on decisively refuting the computationalist alternatives rather than developing the positive account. Here I will defend the claim that human intelligence is genuinely computational (and that whole brain emulation and others forms of AGI may be possible) against this argument. (shrink)

Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...) future persons, and to current persons in low-lying and developing countries, by way of their impacts on climate change. When it comes to such large-scale harms, it's easy for the individual to feel helpless. Even if she sincerely wishes things were otherwise, she may wonder what she could possibly do to make them so. In this paper I briefly explore several promising avenues for generating duties in individuals to consume ethically, and develop one in particular: that an individual ought to signal her commitments to others, as a first step in collectivizing to act against unjust global labour practices. (shrink)

Of all twentieth century philosophers, it is Gilles Deleuze whose work agitates most forcefully for a worldview privileging becoming over being, difference over sameness; the world as a complex, open set of multiplicities. Nevertheless, Deleuze remains singular in enlisting mathematical resources to underpin and inform such a position, refusing the hackneyed opposition between ‘static’ mathematical logic versus ‘dynamic’ physical world. This is an international collection of work commissioned from foremost philosophers, mathematicians and philosophers of science, to address the wide range (...) of problematics and influences in this most important strand of Deleuze’s thinking. Contributors are Charles Alunni, Alain Badiou, Gilles Châtelet, Manuel DeLanda, Simon Duffy, Robin Durie, Aden Evens, Arkady Plotnitsky, Jean-Michel Salanskis, Daniel Smith and David Webb. (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)

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain and the (...) relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

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

While there has been significant discussion in the health sciences and ethics literatures about problems associated with publication practices (e.g., ghost- and gift-authorship, conflicts of interest), there has been relatively little practical guidance developed to help researchers determine how they should fairly allocate credit for multi-authored publications. Fair allocation of credit requires that participating authors be acknowledged for their contribution and responsibilities, but it is not obvious what contributions should warrant authorship, nor who should be responsible for the quality and (...) content of the scientific research findings presented in a publication. In this paper, we review arguments presented in the ethics and health science literatures, and the policies or guidelines proposed by learned societies and journals, in order to explore the link between author contribution and responsibility in multi-author multidisciplinary health science publications. We then critically examine the various procedures used in the field to help researchers fairly allocate authorship. (shrink)

I argue for the thesis (UL) that there are certain logical abilities that any rational creature must have. Opposition to UL comes from naturalized epistemologists who hold that it is a purely empirical question which logical abilities a rational creature has. I provide arguments that any creatures meeting certain conditions—plausible necessary conditions on rationality—must have certain specific logical concepts and be able to use them in certain specific ways. For example, I argue that any creature able to grasp theories must (...) have a concept of conjunction subject to the usual introduction and elimination rules. I also deal with disjunction, conditionality and negation. Finally, I put UL to work in showing how it could be used to define a notion of logical obviousness that would be well suited to certain contexts—e.g. radical translation and epistemic logic—in which a concept of obviousness is often invoked. (shrink)

The paper investigates the role played by ethical deliberation and ethical judgment in Wittgenstein's early thought in the light of twentieth?century German legal philosophy. In particular the theories of the phenomenologists Adolf Reinach, Wilhelm Schapp, and Gerhart Husserl are singled out, as resting on ontologies which are structurally similar to that of the Tractatus: in each case it is actual and possible Sachverhalte which constitute the prime ontological category. The study of the relationship between the states of affairs depicted, e.g., (...) in the sentences of a legal trial and prior fact?complexes to which these may correspond suggests one possible connecting link between the logical and ontological sections of the Tractatus and the ethical reflections appearing at the end. It is argued that the latter can best be understood in terms of the idea of a ?last judgment? (with its associated ethical rewards and punishments) which would relate to the world as a whole as a penal trial relates to individual complexes of facts. (shrink)