Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

We describe a strategy that is being used for the horizontal integration of warfighter intelligence data within the framework of the US Army’s Distributed Common Ground System Standard Cloud (DSC) initiative. The strategy rests on the development of a set of ontologies that are being incrementally applied to bring about what we call the ‘semantic enhancement’ of data models used within each intelligence discipline. We show how the strategy can help to overcome familiar tendencies to stovepiping of intelligence data, and (...) describe how it can be applied in an agile fashion to new data resources in ways that address immediate needs of intelligence analysts. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

The magisterial analyses of logic and meaning advanced in Husserl's Logical Investigations of 1900/01 have for a number of reasons been neglected by analytical philosophers in subsequent decades. This state of affairs has to do, in part, with the history of the editions and translations of Husserl's writings. Findlay's readable but imperfect translation appeared seventy years after the work itself was first published, and the editors and translators and expositors of Husserl's works have reflected the prevailing philosophical atmosphere on the (...) Continent by concentration their energies on Husserl's later writings. Now, however, over eighty years after the appearance of Husserl's one true masterpiece, a critical edition of the work is at last available in completed form. We here analyze the structure and content of this new edition, published as part of the Husserliana series by the Husserl Archive in Louvain. (shrink)

Samuel Butler is usually remembered for Erewhon, widely considered among the best English satires. He also contributed to philosophical biology in works that collectively compose the nineteenth century's finest statement of the evolutionary argument associated with the name of Lamarck. In writing on evolution, Butler was not presenting science for a popular audience but deliberately intervening in the scientific argument about Darwinism. Surprised by the success of his first venture in philosophical biology, Life and Habit, Butler committed himself to the (...) project of developing an alternative to Darwinism, which he did in three additional volumes, and these are the works canvassed in this “delayed book review.”. (shrink)

It is regrettably common for theorists to attempt to characterize the Humean dictum that one can’t get an ‘ought’ from an ‘is’ just in broadly logical terms. We here address an important new class of such approaches which appeal to model-theoretic machinery. Our complaint about these recent attempts is that they interfere with substantive debates about the nature of the ethical. This problem, developed in detail for Daniel Singer’s and Gillian Russell and Greg Restall’s accounts of Hume’s dictum, is of (...) a general type arising for the use of model-theoretic structures in cashing out substantive philosophical claims: the question of whether an abstract model-theoretic structure successfully interprets something often involves taking a stand on non-trivial issues surrounding the thing. In the particular case of Hume’s dictum, given reasonable conceptual or metaphysical claims about the ethical, Singer’s and Russell and Restall’s accounts treat obviously ethical claims as descriptive and vice versa. Consequently, their model-theoretic characterizations of Hume’s dictum are not metaethically neutral. This encourages skepticism about whether model-theoretic machinery suffices to provide an illuminating distinction between the ethical and the descriptive. (shrink)

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

This paper is a study of Brentano’s ontology, and more specifically of his theory of substance and accident as put forward toward the end of his life in the materials collected together as the Kategorienlehre or Theory of Categories. Here Brentano presents an auditious (re-)interpretation of Aristotle’s theory of substance and accidence. We show that on the Brentano initially defends, it is space which serves as the single substance upon which all other entities depend as accidents of space. In an (...) appendix, however, Brentano puts forward an even more radical suggestion, inspired by the physics of Kelvin. According to this final view, space itself is an accident of a deeper substance: the present time. (shrink)

This paper is a contribution to the historical roots of the analytical tradition. As Michael Dummett points out in his Origins of Analytic Philosophy, many tendencies in Central European thought contributed to the early development of analytic philosophy. Dummett himself concentrates on just one aspect of this historical complex, namely on the relationship between the theories of meaning and reference developed by Frege and by Husserl in the years around the turn of the century. It is to this specific issue (...) that the present essay is devoted, though we attempt a more sympathetic reading of Husserl's views on these matters than is to be found in Dummett’s work. Topics covered include Husserl’s theory of intentionality, his view of meanings as types or essences of mental acts, of the relation between meaning and expression, of states of affairs, and of indexicality. (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)

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.

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

We argue that a modified version of Mill’s method of agreement can strongly confirm causal generalizations. This mode of causal inference implicates the explanatory virtues of mechanism, analogy, consilience, and simplicity, and we identify it as a species of Inference to the Best Explanation (IBE). Since rational causal inference provides normative guidance, IBE is not a heuristic for Bayesian rationality. We give it an objective Bayesian formalization, one that has no need of principles of indifference and yields responses to the (...) Voltaire objection, van Fraassen’s Bad Lot objection, and John Norton’s recent objection to IBE. (shrink)

Frank Cabrera argues that informational explanatory virtues—specifically, mechanism, precision, and explanatory scope—cannot be confirmational virtues, since hypotheses that possess them must have a lower probability than less virtuous, entailed hypotheses. We argue against Cabrera’s characterization of confirmational virtue and for an alternative on which the informational virtues clearly are confirmational virtues. Our illustration of their confirmational virtuousness appeals to aspects of causal inference, suggesting that causal inference has a role for the explanatory virtues. We briefly explore this possibility, delineating a (...) path from Mill’s method of agreement to Inference to the Best Explanation (IBE). (shrink)

Simple random sampling resolutions of the raven paradox relevantly diverge from scientific practice. We develop a stratified random sampling model, yielding a better fit and apparently rehabilitating simple random sampling as a legitimate idealization. However, neither accommodates a second concern, the objection from potential bias. We develop a third model that crucially invokes causal considerations, yielding a novel resolution that handles both concerns. This approach resembles Inference to the Best Explanation (IBE) and relates the generalization’s confirmation to confirmation of an (...) associated law. We give it an objective Bayesian formalization and discuss the compatibility of Bayesianism and IBE. (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)

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (shrink)

The Matrix exposes us to the uncomfortable worries of philosophical skepticism in an especially compelling way. However, with a bit more reflection, we can see why we need not share the skeptic’s doubts about the existence of the world. Such doubts are appropriate only in the very special context of the philosophical seminar. When we return to normal life we see immediately that they are groundless. Furthermore, we see also the drastic mistake that Cypher commits in turning his back upon (...) reality and re-entering the matrix. Not only does reason compel us to admit the existence of the external world, it also requires us to face this world, to build for ourselves meaningful lives within it, and to engage, as adults, in the serious business of living. (shrink)

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

The book’s core argument is that an artificial intelligence that could equal or exceed human intelligence—sometimes called artificial general intelligence (AGI)—is for mathematical reasons impossible. It offers two specific reasons for this claim: Human intelligence is a capability of a complex dynamic system—the human brain and central nervous system. Systems of this sort cannot be modelled mathematically in a way that allows them to operate inside a computer. In supporting their claim, the authors, Jobst Landgrebe and Barry Smith, marshal (...) evidence from mathematics, physics, computer science, philosophy, linguistics, and biology, setting up their book around three central questions: What are the essential marks of human intelligence? What is it that researchers try to do when they attempt to achieve "artificial intelligence" (AI)? And why, after more than 50 years, are our most common interactions with AI, for example with our bank’s computers, still so unsatisfactory? Landgrebe and Smith show how a widespread fear about AI’s potential to bring about radical changes in the nature of human beings and in the human social order is founded on an error. There is still, as they demonstrate in a final chapter, a great deal that AI can achieve which will benefit humanity. But these benefits will be achieved without the aid of systems that are more powerful than humans, which are as impossible as AI systems that are intrinsically "evil" or able to "will" a takeover of human society. (shrink)

COVID-19 often manifests with different outcomes in different patients, highlighting the complexity of the host-pathogen interactions involved in manifestations of the disease at the molecular and cellular levels. In this paper, we propose a set of postulates and a framework for systematically understanding complex molecular host-pathogen interaction networks. Specifically, we first propose four host-pathogen interaction (HPI) postulates as the basis for understanding molecular and cellular host-pathogen interactions and their relations to disease outcomes. These four postulates cover the evolutionary dispositions involved (...) in HPIs, the dynamic nature of HPI outcomes, roles that HPI components may occupy leading to such outcomes, and HPI checkpoints that are critical for specific disease outcomes. Based on these postulates, an HPI Postulate and Ontology (HPIPO) framework is proposed to apply interoperable ontologies to systematically model and represent various granular details and knowledge within the scope of the HPI postulates, in a way that will support AI-ready data standardization, sharing, integration, and analysis. As a demonstration, the HPI postulates and the HPIPO framework were applied to study COVID-19 with the Coronavirus Infectious Disease Ontology (CIDO), leading to a novel approach to rational design of drug/vaccine cocktails aimed at interrupting processes occurring at critical host-coronavirus interaction checkpoints. Furthermore, the host-coronavirus protein-protein interactions (PPIs) relevant to COVID-19 were predicted and evaluated based on prior knowledge of curated PPIs and domain-domain interactions, and how such studies can be further explored with the HPI postulates and the HPIPO framework is discussed. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, pathogenesis, diagnosis, (...) prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

Ernst Mach's atomistic theory of sensation faces problems in doing justice to our ability to perceive and remember complex phenomena such as melodies and shapes. Christian von Ehrenfels attempted to solve these problems with his theory of "Gestalt qualities", which he sees as entities depending one-sidedly on the corresponding simple objects of sensation. We explore the theory of dependence relations advanced by Ehrenfels and show how it relates to the views on the objects of perception advanced by Husserl and by (...) the Gestalt psychologists. (shrink)

This process is the transformation of the self, even to the extent that we no longer recognize ourselves although, oddly, something in us will then recognize our ‘new’ self as being what we really are, or at least what we started out to be. Then, in a way, we are like the seedling of some wonderful tree which has been overtaken by a parasitic plant until very little of the original tree is recognizable – it may have become dwarfed, hollowed (...) out or even killed by the parasite, which is our egoic mask. With meticulous pruning and therapy, the tree can be uncovered and possibly healed, but then it will be a test of the tree’s original nature and soil to see whether it will endure and grow straight and tall, with roots that will hold against adversity. For this purpose, I have assembled twelve steps to describe the transformational process (consider it coincidental that the alcoholic recovery program also has twelve steps but there is, inevitably, some correspondence between the two systems). Although I describe these steps here as if they were a progression, you’ll find that they really work in parallel or in stages wherein first one line will seem emphasized, and then another at a different point in your evolution. These steps induce a gradual change in our psychic shape (the way that we fit with each other and with our circumstances), and also they are an alchemic progression, in that each prepares our neurochemical apparatus to attune to the next stage more readily. (shrink)

We outline Brentano’s theory of boundaries, for instance between two neighboring subregions within a larger region of space. Does every such pair of regions contain points in common where they meet? Or is the boundary at which they meet somehow pointless? On Brentano’s view, two such subregions do not overlap; rather, along the line where they meet there are two sets of points which are not identical but rather spatially coincident. We outline Brentano’s theory of coincidence, and show how he (...) uses it to resolve a number of Zeno-like paradoxes. (shrink)

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

Some defenders of so-called `artificial intelligence' believe that machines can understand language. In particular, Søgaard has argued in his "Understanding models understanding language" (2022) for a thesis of this sort. His idea is that (1) where there is semantics there is also understanding and (2) machines are not only capable of what he calls `inferential semantics', but even that they can (with the help of inputs from sensors) `learn' referential semantics. We show that he goes wrong because he pays insufficient (...) attention to the difference between language as used by humans and the sequences of inert symbols which arise when language is stored on hard drives or in books in libraries. (shrink)

We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A (...) problem arises for this theory for cases involving 'free-standing Y terms', as for example in the case of money in a computerized bank account. Here there is no physical X to which a status function might be attached. We conclude by arguing that Searle's response to this problem creates difficulties for his naturalistic framework. (shrink)

In his The Meaning of Disgust, Colin McGinn employs elements of the phenomenological theory of disgust advanced by Aurel Kolnai in 1929. Kolnai’s treatment of what he calls “material” disgust and of its primary elicitors—putrefying organic matter, bodily wastes and secretions, sticky contaminants, vermin—anticipates more recent scientific treatments of this emotion as a mode of protective recoil. While Nina Strohminger charges McGinn with neglecting such scientific studies, we here attempt to show how Kolnai goes beyond experimental findings in his careful (...) description of the phenomenological differences between disgust and other emotions of forceful disapproval. (shrink)

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

Ingarden’s puzzle is: how can we come to know what is essentially involved in an act of knowing? As starting point he takes what he holds to be a particular good candidate example of such an act, namely an act of perceiving an apple. Here we have act and object standing in a certain first-level relation to each other. We now in a second level act of reflection, make this first-level relation into an object, and strive to apprehend this object (...) as an instantiation of the essence knowledge. But how, on this basis, could we ever establish that we had indeed grasped this essence, and that this is indeed the appropriate essence? Surely, through some third-level act of reflection on this second-level act. We expound from an ontological point of view Ingarden's idea as to how this regress can be avoided. (shrink)

In manuscripts of 1930-1 Johannes Daubert, principal member of the Munich board of realist phenomenologists, put forward a series of detailed criticisms of the idealism of Husserl’s Ideas I. The paper provides a sketch of these criticisms and of Daubert’s own alternative conceptions of consciousness and reality, as also of Daubert’s views on perception, similar, in many respects, to those of J. J. Gibson.

The paper [which is in German] seeks to show how Weininger’s interpretations of Kant and Schopenhauer help us to understand some of the peculiar reflections on the will, on happiness and unhappiness, and on the problems of life, which are to be found in Wittgenstein's Notebooks. It seeks to explain, above all, why Wittgenstein should wish to reject the basic ethical axiom of “love thy neighbor.” There follows a sketch of one possible Kantian interpretation of the Tractatus along Weiningerian lines. (...) The conclusion is drawn, however, that, while in the Notebooks many of Weininger’s views are still accepted, by the time of the Tractatus Wittgenstein has moved to a position in which a thinker like Weininger must be conceived as propounding so much more “ethical nonsense.” Wittgenstein adopts in the Tractatus a wholly new conception of the ethical, a form of logical individualism or quietism. (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)

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)

Even though there are many views on consciousness theory in the pertinent literature, there remains a need for a unifying framework for specifying the features of specific states of consciousness. In order to know what kinds of experiences conscious states have in common, researchers need to elicit testimony that is more direct and finer-grained than has been previously available. This dissertation endeavors to fill a gap in current research by addressing concepts and methods for making requisite distinctions and illuminates the (...) question of whether specific states of consciousness can be reliably and validly distinguished from each other. In order to do this, 41 individuals were invited to be interviewed. The interview was designed as a conversational-type synthesis of 5 well-known questionnaires pertinent to states of consciousness, but without their explicit and implicit assumptions; that is, the volunteers’ responses would not conform to predetermined questions. Encoding their responses allowed me to develop a model that helped to answer the research question (“Are there identifiable features that can reliably and validly distinguish among states of consciousness thought to be distinct from each other?”) by formulating a model in which any given conscious state can be catalogued in terms of its component factors (background, resistances, setting, induction, tradition, energies, and breakthrough events). The results of this study provide much-needed insights into people’s internal experiences of their various states, thus forming a basis for improved treatments and analyses. Better understanding of these states can be an impetus for social change by allowing for more incisive analyses and treatments, as well as fostering improved interpersonal communications. (shrink)

La présente étude utilise les outils du domaine de la méréotopologie (la théorie des parts, ensembles et frontières) pour élaborer les implications de certaines analogies entre la 'psychologie écologique' de J.J.Gibson et la phénoménologie de Edmund Husserl. On présentera une théorie ontologique de frontières spatiales et des entités possédant une extension spatiale. S'en rapportant aux exemples de la sphère de géographie, on démontre qu'aussi bien les frontières que les entités à extension spatiale appartiennent à deux vastes catégories: des objets qui (...) existent indépendamment de nos actes cognitifs (par exemple: la planète Terre, sa surface extérieure); et des objets qui existent seulement grâce à ces actes (par exemple: l'équateur, la Mer du Nord). Le champ visuel, lui aussi, peut être conçu comme un exemple d'une entité à extension spatiale qui est dépendante dans le sens proposé ci-dessus. L'étude présente suggère une extension de cette analogie en postulant les entités qui, pour les vrais jugements, seraient ce que le champ visuel est pour les actes de perception visuelle. Le champ de jugement est défini plus précisément comme une entité étendue complexe, contenant toutes les entités essentielles pour la vérité d'un (vrai) jugement donné. Il est possible de démontrer que le travail des linguistes cognitifs tel Talmy ou Langacker, si l'on l'interprète convenablement, produit une explication détaillée des structures des champs de jugement correspondant aux phrases de sortes différentes. Un genre nouveau de définition de la vérité en tant que correspondance pour les expressions de la langue naturelle peut donc être formulé sur cette base. (shrink)

Ernst Mach's atomistic theory of sensation faces problems in doing justice to our ability to perceive and remember complex phenomena such as melodies and shapes. Christian von Ehrenfels attempted to solve these problems with his theory of "Gestalt qualities", which he sees as entities depending one-sidedly on the corresponding simple objects of sensation. We explore the theory of dependence relations advanced by Ehrenfels and show how it relates to the views on the objects of perception advanced by Husserl and by (...) the Gestalt psychologists. (shrink)

Stephan Witasek was a student and follow of Meinong, who applied Meinong's ideas on the ontology of the non-existent to the working out of a theory of aesthetic phenomena in his Grundzüge der allgemeinen Ästhetik of 1904. Witasek shows how our feelings undergo certain sorts of structural modifications when they are directed towards what does not exist. He draws a distinction between genuine mental phenomena and what he calls ‘phantasy-material’, asserting that ‘the job of the aesthetic object, whether it is (...) a work of art or a product of nature, is to excite and support the actualisation of phantasy-material in the experiencing subject’. (shrink)

Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be (...) constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. (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)

Part 1 of this exchange consists in a critique by Smith of Searle’s The Construction of Social Reality focusing on Searle’s use of the formula ‘X counts as Y in context C’. Smith argues that this formula works well for social objects such as dollar bills and presidents where the corresponding X terms (pieces of paper, human beings) are easy to identify. In cases such as debts and prices and money in a bank's computers, however, the formula fails, because these (...) are cases of what he calls ‘free-standing Y terms’, since there is here no X which can count as the corresponding Y. In his response in Part 2, Searle argues that Smith’s critique rests on three misunderstandings: 1. in wrongly presupposing that Searle is trying to analyze the nature of what he calls “social objects”, rather than of social facts; 2. in thinking that the counts as formula is intended as a definition, rather than as a mere mnemonic; and 3. in neglecting the naturalism of Searle’s account. (shrink)

We take as our starting point a thesis to the effect that, at least for true judgments of many varieties, there are parts of reality which make such judgments are true. We argue that two distinct components are involved in this truthmaker relation. On the one hand is the relation of necessitation, which holds between an object x and a judgment p when the existence of x entails the truth of p. On the other hand is the dual notion of (...) projection, which holds between a judgment p and an object x when the truth of p entails the existence of x. A truthmaker for a judgment p is then a necessitator for p which satisfies the further constraint that it is part of p’s projection. We offer a formal theory of the truthmaker relation thus defined, exploiting ontological tools of basic mereology and the theory of dependence. We then apply the theory to a range of problems connected with generic expressions, ellipsis, vagueness, and indexical and perceptual judgments. (shrink)

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

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)

The paper is a contribution to formal ontology. It seeks to use topological means in order to derive ontological laws pertaining to the boundaries and interiors of wholes, to relations of contact and connectedness, to the concepts of surface, point, neighbourhood, and so on. The basis of the theory is mereology, the formal theory of part and whole, a theory which is shown to have a number of advantages, for ontological purposes, over standard treatments of topology in set-theoretic terms. One (...) central goal of the paper is to provide a rigorous formulation of Brentano's thesis to the effect that a boundary can exist as a matter of necessity only as part of a whole of higher dimension which it is the boundary of. It concludes with a brief survey of current applications of mereotopology in areas such as natural-language analysis, geographic information systems, machine vision, naive physics, and database and knowledge engineering. (shrink)

A survey of theories of part, whole and dependence from Aristotle to the Gestalt psychologists, with special attention to Husserl’s Third Logical Investigation “On the Theory of Parts and Wholes”.

The aim of this volume is to present Kafka not as a writer, or not only as a writer, but as a philosopher. However, even after narrowing the scope of our interest down, there will still be several Kafka’s left on the table. Themes treated in the volume include: the so-called Brentano School in Prague, Kafka’s affiliation to the Louvre Circle, Kafka and existentialist philosophy, Kafka’s Jewish heritage, his love of Nietzsche and Meister Eckhart and—last but not least, since he (...) was such an exceptional writer—his aesthetics. (shrink)

We provide an overview of Searle's contributions to speech act theory and the ontology of social reality, focusing on his theory of constitutive rules. In early versions of this theory, Searle proposed that all such rules have the form 'X counts as Y in context C' formula – as for example when Barack Obama (X) counts as President of the United States (Y) in the context of US political affairs. Crucially, the X and the Y terms are here identical. A (...) problem arises for this theory for cases involving 'free-standing Y terms', as for example in the case of money in a computerized bank account. Here there is no physical X to which a status function might be attached. We conclude by arguing that Searle's response to this problem creates difficulties for his naturalistic framework. (shrink)

The theory of document acts is an extension of the more traditional theory of speech acts advanced by Austin and Searle. It is designed to do justice to the ways in which documents can be used to bring about a variety of effects in virtue of the fact that, where speech is evanescent, documents are continuant entities. This means that documents can be preserved in such a way that they can be inspected and modified at successive points in time and (...) grouped together into enduring document complexes. We outline some components of a theory of document acts, and show how it can throw light on certain problems in Searle’s ontology of social reality. (shrink)