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.

Critics have often misunderstood the higher-order theory (HOT) of consciousness. Here we clarify its position on several issues, and distinguish it from other views such as the global The higher-order theory (HOT) of consciousness has often been misunderstood by critics. Here we clarify its position on several issues, and distinguish it from other views such as the global workspace theory (GWT) and early sensory models (e.g. first-order local recurrency theories). For example, HOT has been criticized for over-intellectualizing consciousness. We show (...) that while higher-order states are cognitively assembled, the requirements are actually considerably less than often presumed. In this sense HOT may be viewed as an intermediate position between GWT and early sensory views. Also, we clarify that most proponents of HOT do not stipulate consciousness as equivalent to metacognition or confidence. Further, compared to other existing theories, HOT can arguably account better for complex everyday experiences, such as of emotions and episodic memories. This makes HOT particularly useful as a framework for conceptualizing pathological mental states. (shrink)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

Bracket out the wrong of committing a wrong, or conspiring or colluding or conniving with others in their committing one. Suppose you have done none of those things, and you find yourself merely benefiting from a wrong committed wholly by someone else. What, if anything, is wrong with that? What, if any, duties follow from it? If straightforward restitution were possible — if you could just ‘give back’ what you received as a result of the wrongdoing to its rightful owner (...) — then matters are morally more straightforward. But in real-world cases that is often impossible, and questions of ‘how much, from whom and to whom?’ become far more vexing. The beneficiary disgorging all benefits of the wrong is part of the story, but where that is not possible or will not suffice to compensate the victim of wrongdoing we discuss various ways of allocating the cost of making the victim whole, including supplementation from public coffers. (shrink)

Having an agreed-upon definition of character education would be useful for both researchers and practitioners in the field. However, even experts in character education disagree on how they would define it. We attempted to achieve greater conceptual clarity on this issue through a prototype analysis in which the features perceived as most central to character education were identified. In Study 1 (N = 77), we asked character education experts to enumerate features of character education. Based on these lists, we identified (...) 30 features. In Study 2 (N = 101), experts assessed which features were central to character education through a categorization task. In Study 3 (N = 166), we assessed the extent of centrality using scalar items. We conclude by offering practical advice for the development of future character education studies and programs rooted in what is deemed central to such programs. (shrink)

Die bahnbrechenden wissenschaftlichen Ergebnisse der letzten Jahre erzwingen eine neue philosophische Auseinandersetzung mit den Grundkategorien der Biologie und der benachbarten Disziplinen. Insbesondere die Anwendung neuer informationstechnischer Mittel in der biomedizinischen Forschung und die damit verbundene, kontinuierlich zunehmende Datenflut sowie die Notwendigkeit, ihrer Herr zu werden, erfordern ein konsequentes Nachdenken darüber, wie biologische Daten systematisiert und klassifiziert werden können. Dafür wiederum bedarf es robuster Theorien von Grundbegriffen wie Art, Spezies, Teil, Ganzes, Funktion, Prozess, Fragment, Sequenz, Expression, Grenze, Locus, Umwelt, System usw. (...) Solche Begriffe gehören zum impliziten Wissen jedes Biologen. Sie spiegeln einerseits eine Dimension der biologischen Wirklichkeit wider, die auch vor dem Hintergrund der biologischen Evolution unverändert bleibt. Andererseits verlangt deren theoretische Behandlung nach zeitgemäßen Analoga der in der traditionellen aristotelischen Metaphysik entwickelten Methoden. Zugleich können so die explizit formulierten Theorien und Definitionen bereitgestellt werden, die für computergestützte Informationssysteme unabdingbar sind. Das Entwickeln derartiger Theorien und Definitionen ist eine Aufgabe der Philosophie, die in diesem Sinne herausgefordert ist, zwischen Biologie und Informatik zu vermitteln. (shrink)

This paper explores the cosmology of St Maximus the Confessor and its relevance for contemporary ethics. It takes as it’s starting point two papers on Maximus’ cosmology and environmental ethics (Bordeianu, 2009; Munteanu, 2010) and from there argues that we can not consider environmental ethics in isolation from other ethical issues. This, as both Ware and Keselopoulos have also pointed out, is because the environmental crisis is actually a crisis in the human heart and in human attitudes toward everything about (...) us. The paper goes through some key areas in Maximus’ cosmology according to his own formula of creation – movement – rest and considers at each stage the implications of this theology for the way the human should be living and treating other beings. The main sources for this exploration are Ambiguum 7, Ambiguum 41, and The Mystagogia with especial focus on the doctrine of the logoi and the divisions of nature. The paper concludes that Bordeianu and Munteanu are right to consider Maximus’ theology to be of ecological relevance, but that this relevance comes from the radical ethical statement being made about human activity. Maximus’ theology points the human toward becoming in the likeness of Christ who unites heaven and earth through love. The love of Christ when considered in an ethical context stands as a formidable challenge to current attitudes and institutions that advocate the exploitation and destruction of human or non-human creation. (shrink)

In this paper we propose a formal theory of partitions (ways of dividing up or sorting or mapping reality) and we show how the theory can be applied in the geospatial domain. We characterize partitions at two levels: as systems of cells (theory A), and in terms of their projective relation to reality (theory B). We lay down conditions of well-formedness for partitions and we define what it means for partitions to project truly onto reality. We continue by classifying well-formed (...) partitions along three axes: (a) degree of correspondence between partition cells and objects in reality; (b) degree to which a partition represents the mereological structure of the domain it is projected onto; and (c) degree of completeness and exhaustiveness with which a partition represents reality. This classification is used to characterize three types of partitions that play an important role in spatial information science: cadastral partitions, categorical coverages, and the partitions involved in folk categorizations of the geospatial domain. (shrink)

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

This chapter describes the potential far‐reaching consequences of contemplative higher education for the fields of science and medicine.

Driving licenses, identity cards, passports, boarding passes, credit cards, ATM cards – all of these are examples of credentials. Credentials are documents that play a fundamental role in all modern societies. However, philosophers and social ontologists have not yet addressed the analysis of their nature and function. This paper aims to fill this gap through a review of the essential characteristics of credentials, as documents whose primary purpose is to certify the identity and institutional status of the bearer, for example (...) as being the bearer of specific rights. However, credentials also allow their holders the concrete exercise of their rights, as when exercising a right concretely (e.g., crossing a border) requires the possession of a particular credential. The authors distinguish the different types of credentials and describe their functions and the various kinds of acts that are performable with their aid. (shrink)

One of the primary concerns in animal research is ensuring the welfare of laboratory animals. Modern views on animal welfare emphasize the role of animal sentience, i.e. the capacity to experience subjective states such as pleasure or suffering, as a central component of welfare. The increasing official recognition of animal sentience has had large effects on laboratory animal research. The Cambridge Declaration on Consciousness (Low et al., University of Cambridge, 2012) marked an official scientific recognition of the presence of sentience (...) in mammals, birds, and cephalopods. Animal sentience has furthermore been recognized in legislation in the European Union, UK, New Zealand and parts of Australia, with discussions underway in other parts of the world to follow suit. In this paper, we analyze this shift towards recognition of sentience in the regulation and practice in the treatment of laboratory animals and its effects on animal welfare and use. (shrink)

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

Aims: The Research Diagnostic Criteria for Temporomandi¬bular Disorders (RDC/TMD) Axis I diagnostic algorithms were demonstrated to be reliable but below target sensitivity and specificity. Empirical data supported Axis I algorithm revisions that were valid. Axis II instruments were shown to be both reliable and valid. An international consensus workshop was convened to obtain recommendations and finalization of new Axis I diagnostic algorithms and new Axis II instruments. Methods: A comprehensive search of published TMD diagnostic literature was followed by review and (...) consensus via a formal structured process by a panel of experts for revision of the RDC/TMD. Results: The recommended Diagnostic Criteria for TMD (DC/TMD) Axis I protocol includes both a valid screener for pain diagnoses and valid criteria for the most common pain-related TMDs and for one intra-articular disorder. The Axis II protocol retains selected RDC/TMD screening instruments augmented with new instruments to better assess the interactions between pain and psychosocial functioning. A comprehensive classification system is also presented. Conclusion: The recommended evidence-based DC/TMD protocol is appropriate for use in both the clinical and research settings. Simple Axis I and II screening tests augmented by validated Axis I and Axis II instruments allow for identification of simple to complex TMD patients. (shrink)

Per Husserl, come per Bolzano, la logica e una dottrina della sdenza. Husserl prende pero piu sul serio l'idea che le teorie scientifiche siano costituite dagli atti mentali di soggetti conoscenti. Quella che segue e un' esposizione della concezione husserliana della logica e della scienza, fondata appunto sugli atti; essa approdera a una delineazione dell'idea husserliana di «ontologia formale».

The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the corresponding (...) speech act varieties. The present paper is an attempt to apply this idea of standard and modified instances of ontological structures to the realm of judgement and cognition, and thereby to develop a Reinachian theory of how intentionality is mediated through language in acts of thinking and speaking. (shrink)

Decision theory and folk psychology both purport to represent the same phenomena: our belief-like and desire- and preference-like states. They also purport to do the same work with these representations: explain and predict our actions. But they do so with different sets of concepts. There's much at stake in whether one of these two sets of concepts can be accounted for with the other. Without such an account, we'd have two competing representations and systems of prediction and explanation, a dubious (...) dualism. Folk psychology structures our daily lives and has proven fruitful in the study of mind and ethics, while decision theory is pervasive in various disciplines, including the quantitative social sciences, especially economics, and philosophy. My interest is in accounting for folk psychology with decision theory -- in particular, for believe and wanting, which decision theory omits. Many have attempted this task for belief. (The Lockean Thesis says that there is such an account.) I take up the parallel task for wanting, which has received far less attention. I propose necessary and sufficient conditions, stated in terms of decision theory, for when you're truly said to want; I give an analogue of the Lockean Thesis for wanting. My account is an alternative to orthodox accounts that link wanting to preference (e.g. Stalnaker (1984), Lewis (1986)), which I argue are false. I argue further that want ascriptions are context-sensitive. My account explains this context-sensitivity, makes sense of conflicting desires, and accommodates phenomena that motivate traditional theses on which 'want' has multiple senses (e.g. all-things-considered vs. pro tanto). (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)

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)

L'articolo usa la teoria delle parti, del tutto e dei contomi per elaborare alcune relazioni cruciali tra la «psicologia ecologica» di J.J. Gibson e la fenomenologia di Husserl. Presenta, inoltre, una teoria ontologica dei contomi spaziali e delle entita spazialmente estese, applicandola al cam po visivo, qui concepito come un' entita spazialmente estesa dipendente dal soggetto che percepisce. Su questa base e possibile formulare un nuovo tipo di definizione teoretico-correspondentista della verita per gli enunciati del linguaggio naturale.

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

The 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)

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)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Meet Tega. Blue, fluffy, and AI-enabled, Tega is a relational robot: a robot designed to form relationships with humans. Created to aid in early childhood education, Tega talks with children, plays educational games with them, solves puzzles, and helps in creative activities like making up stories and drawing. Children are drawn to Tega, describing him as a friend, and attributing thoughts and feelings to him ("he's kind," "if you just left him here and nobody came to play with him, he (...) might be sad"). Scholars and members of the public alike have raised the alarm about relational robots, worrying that the relationships that people, and especially children, form with such robots are objectionably inauthentic. We, members of an interdisciplinary team that developed and studies Tega, make this inauthenticity worry precise and offer practical recommendations for addressing it. We distinguish two kinds of (in)authenticity -- inauthenticity as unreality, and inauthenticity as deception -- arguing that neither is just what others have thought it is. With our distinction in hand, we argue that the authenticity concern can be met only through co-design methods -- methods that give stakeholders of all kinds (e.g. parents, educators, and children themselves) a genuine say in how relational robots are built. (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)

Recent work in formal philosophy has concentrated over-whelmingly on the logical problems pertaining to epistemic shortfall - which is to say on the various ways in which partial and sometimes incorrect information may be stored and processed. A directly depicting language, in contrast, would reflect a condition of epistemic perfection. It would enable us to construct representations not of our knowledge but of the structures of reality itself, in much the way that chemical diagrams allow the representation (at a certain (...) level of abstractness) of the structures of molecules of different sorts. A diagram of such a language would be true if that which it sets out to depict exists in reality, i.e. if the structural relations between the names (and other bits and pieces in the diagram) map structural relations among the corresponding objects in the world. Otherwise it would be false. All of this should, of course, be perfectly familiar. (See, for example, Aristotle, Metaphysics, 1027 b 22, 1051 b 32ff.) The present paper seeks to go further than its predecessors, however, in offering a detailed account of the syntax of a working universal characteristic and of the ways in which it might be used. (shrink)

The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...) and skin. (shrink)

The theory of speech acts put forward by Adolf Reinach in his "The A Priori Foundations of the Civil Law" of 1913 rests on a systematic account of the ontological structures associated with various different sorts of language use. One of the most original features of Reinach's account lies in hIs demonstration of how the ontological structure of, say, an action of promising or of commanding, may be modified in different ways, yielding different sorts of non-standard instances of the corresponding (...) speech act varieties. The present paper is an attempt to apply this idea of standard and modified instances of ontological structures to the realm of judgement and cognition, and thereby to develop a Reinachian theory of how intentionality is mediated through language in acts of thinking and speaking. (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)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (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)

Amongst the entities making up social reality, are there necessary relations whose necessity is not a mere reflection of the logical connections between corresponding concepts? We distinguish three main groups of answers to this question, associated with Hume and Adolf Reinach at opposite extremes, and with Searle who occupies a position somewhere in the middle. We first set forth Reinach’s views on what he calls ‘material necessities’ in the realm of social entities. We then attempt to show that Searle has (...) not identified a sustainable position somewhere between the Humean and the Reinachian extremes. This is because Searle’s position is threatened by circularity, and to steer clear of that danger it must incorporate at least some elements of Reinach’s essentialism. (shrink)

Mathematical objects are divided into (1) those which are autonomous, i.e., not dependent for their existence upon mathematicians’ conscious acts, and (2) intentional objects, which are so dependent. Platonist philosophy of mathematics argues that all objects belong to group (1), Brouwer’s intuitionism argues that all belong to group (2). Here we attempt to develop a dualist ontology of mathematics (implicit in the work of, e.g., Hilbert), exploiting the theories of Meinong, Husserl and Ingarden on the relations between autonomous and intentional (...) objects. In particular we develop a phenomenology of mathematical works, which has the stratified intentional structure discovered by Ingarden in his study of the literary work. (shrink)

It will be the thesis of this paper that there are among our mental acts some which fall into the category of real material relations. That is: some acts are necessarily such as to involve a plurality of objects as their relata or fundamenta. Suppose Bruno walks into his study and sees a cat. To describe the seeing, here, as a relation, is to affirm that it serves somehow to tie Bruno to the cat. Bruno's act of seeing, unlike his (...) feeling depressed, his putative thinking-about-Santa-Claus or his musing, abstractedly, about the tallest spy, has at least two fundamenta: it is, as a matter of necessity, dependent for its existence upon both Bruno himself and the cat that he sees. This idea will naturally raise echoes of Russell's doctrine of knowledge by acquaintance. 'I am acquainted with an object', Russell tells us, 'when I have a direct cognitive relation to that object, i. e. when I am directly aware of the object itself' (1918, p. 209). And indeed a distinction in many ways like that between acquaintance and description will find a place within the theory here projected, but there are crucial differences. (shrink)

Since antiquity, scholars have observed a structural tension within Plato’s Phaedrus. The dialogue demands order in every linguistic composition, yet it presents itself as a disordered composition. Accordingly, one of the key problems of the Phaedrus is determining which—if any—aspect of the dialogue can supply a unifying thread for the dialogue’s major themes (love, rhetoric, writing, myth, philosophy, etc.). My dissertation argues that “soul-leading” (psuchagōgia)—a rare and ambiguous term used to define the innate power of words—resolves the dialogue’s structural tension. (...) I clarify the conceptual and dramatic features of soul-leading by focusing on the dialogue’s uniquely prevalent use of the semantic network of “leading” and “following.” By continuing to foreground the language and drama of leading and following, I offer a new interpretation of the dialogue as a whole: the Phaedrus is Plato’s articulation of how the soul can be led into communion with reality. Chapter 1 discusses scholarly disputes about the unity of the Phaedrus and proposes that soul-leading adequately satisfies the criteria put forward for what would count as a unifying element. I argue that soul-leading unifies the dialogue both thematically and non-thematically; moreover, soul-leading is a theme capacious enough to account for the other principal contenders for unity put forward. Chapter 2 develops the ambiguous character of soul-leading by examining how the dialogue showcases dangerous forms thereof. Love and language are dangerous when they lead the soul toward goods which can never truly fulfill it. In order to clarify how love and language can mislead the soul, Socrates develops a set of accounts of how the soul is led, both internally and externally, in the three speeches on love. If the soul is to be led into communion with reality (the proper end of soul-leading), it must be led internally by the right part of the soul and externally by the right object of desire. Chapter 3 argues that all souls can, in principle, be harmonized and directed in the way that Chapter 2 requires. I show that Plato’s view of philosophy is neither elitist (i.e., some are intrinsically incapable of philosophy) nor naively essentialist. All can come into communion with reality because all are by nature equipped to do so. While Plato recognizes that there are forces which tend to prohibit one from exercising one’s capability of being rightly led, none of them are intrinsic to human nature. Chapter 4 argues that successful soul-leading require neither the leader nor the follower to be already well-disposed to what’s ultimate in order for the pair to come to a communion with what’s ultimate. Plato’s depiction of soul-leading love shows that love can itself promote the formation needed for both leader and follower to come into contact with reality. Love can do so because it is always already bound up reality in its responsiveness to beauty. Beauty itself calls the lover to itself by shining through the beautiful beloved, who acts as a reminder of transcendent Beauty. The lover mediates this same experience for the beloved. Each comes to desire the other as well as Beauty itself. Chapter 5 argues that the drama of the lovers’ formation mythically depicted in the Palinode (Chapter 4) is written into the drama of the dialogue as a whole. In the relationship between Socrates and Phaedrus, we see an enactment of love’s formative role. Likewise, in the relationship between Phaedrus and Lysias, we see an enactment of the dangerous soul-leading discussed in Chapter 2. My focus on leading and following also allows me to show the thematic significance of the drama’s setting. Chapter 6 articulates the metaphysical conditions under which one can be led into communion with reality. Transcendent Beauty invites us into communion with itself and makes possible our ascent by providing us with divine guides and images which can transport us from our ordinary experiences to the true beings. Beauty accomplishes its work—leading us in a “divine dance” where we follow the gods up to Beauty and back down to each other—through images. When we handle images of reality rightly, they lead our souls into communion with reality. Further, when we have come into communion, we’ll be inspired to be co-workers of Beauty’s soul-leading work. When we articulate reality in language, we create new images that can serve to lead others toward reality. (shrink)

It is reasonably well accepted that the explanation of intentional action is teleological explanation. Very roughly, an explanation of some event, E, is teleological only if it explains E by citing some goal or purpose or reason that produced E. Alternatively, teleological explanations of intentional action explain “by citing the state of affairs toward which the behavior was directed” thereby answering questions like “To what end was the agent’s behavior directed?” Causalism—advocated by causalists—is the thesis that explanations of intentional action (...) are both causal and teleological. By contrast, non-causalism—advocated by non-causalists—is the thesis that explanations of intentional action are teleological but not causal. Familiarly, the problem of causal deviance plagues causalism. But while some have supposed that the problem is grave enough that causalism is bound to suffer a global breakdown, the rumors of causalism’s demise are greatly exaggerated. In what follows, I note that every instance of causal deviance is also an instance of teleological deviance and that teleological deviance is a problem for causalist and non-causalist alike, a problem that causalists may be better able to deal with. Or so I argue. (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)

La ricerca medica è afflitta da un problema di comunicazione. Comunità distinte di ricercatori si servono di terminologie diverse e spesso incompatibili per esprimere i risultati del loro lavoro, generando in questo modo problemi di integrazione tra database ogniqualvolta si presenti la necessità di inserire i dati medici nei computer. In un primo momento i problemi di integrazione tra database venivano risolti caso per caso, in seguito si è fatta strada l’idea di realizzare un’unica tassonomia di riferimento in cui tradurre, (...) una volta soltanto, tutti i vari sistemi di classificazione. Funzionando come una sorta di lingua franca, questa tassonomia di riferimento avrebbe automaticamente garantito ad ogni database calibrato su di essa la compatibilità con tutti gli altri. È curioso come gli informatici abbiano chiamato il sistema centrale di classificazione che stavano proponendo un’ontologia, riconoscendo così l’esistenza di più di un’affinità tra il lavoro di costruzione che un simile sistema comportava e la vecchia metafisica. Il presente articolo descrive un tentativo di sfruttare le risorse della filosofia per risolvere problemi che sorgono, in particolar modo, nel campo dell’integrazione delle terminologie mediche. Vengono delineati in particolare i contorni di un’iniziativa che è il frutto della collaborazione tra l’Istituto di Ontologia Formale e Informatica Medica e la società di software belga Language and Computing, iniziativa che prevede la messa alla prova di un’ontologia fondata su solidi principi filosofici nel contesto di potenti strumenti software per l’elaborazione di testo medico. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

Die zeitgenössischen Philosophen haben zwar der Sprache, die wir verwenden, um die Welt der alltäglichen Erfahrung zu beschreiben oder um uns in dieser Welt zurechtzufinden, große Aufmerksamkeit geschenkt, sie haben sich jedoch – von einigen Ausnahmen abgesehen – geweigert, diese Welt selbst als passendes Objekt theoretischer Betrachtungen anzusehen. Im folgenden werde ich versuchen zu zeigen, wie es möglich ist, die Common-Sense-Welt als ontologisch eigenständiges Untersuchungsobjekt zu verstehen. Gleichzeitig werde ich mich bemühen, deutlich zu zeigen, wie eine solch eigenständige Behandlung uns (...) möglicherweise hilft, die Strukturen sowohl der physikalischen Welt als auch der menschlichen Erkenntnis philosophisch besser zu verstehen. (shrink)

From the point of view of Brentano’s philosophy, contemporary philosophy of mind presupposes an over-crude theory of the internal structures of mental acts and states and of the corresponding types of parts, unity and dependence. We here describe Brentano’s own account of the part-whole structures obtaining in the mental sphere, and show how it opens up new possibilities for mereological investigation. One feature of Brentano’s view is that the objects of experience are themselves parts of mind, so that there is (...) a sense in which for him (as e.g. for Leibniz) ontology is a proper part of rational or descriptive psychology. (shrink)

In un articolo comparso sul Wall Street Journal del 13 novembre 2oi:n viene descritto il modo in cui i computer potrebbero essere utilizzati al fine di allertare i responsabili della salute pubblica in relazione ad eventuali problemi provocati dal bioterrorismo. L'autore nota come gli attacchi biologici sarebbero probabilmente contraddistinti da picchi statistici negli acquisti senza ricetta medica di rimedi per specifici disturbi di tipo comune e come i dati che riguardano tali acquisti possano essere resi disponibili immediatamente grazie agli inventari (...) computerizzati dei rivenditori. (shrink)

Introduction to the Scientific Proof of the Natural Moral Law This paper proves that Aquinas has a means of demonstrating and deriving both moral goodness and the natural moral law from human nature alone. Aquinas scientifically proves the existence of the natural moral law as the natural rule of human operations from human nature alone. The distinction between moral goodness and transcendental goodness is affirmed. This provides the intellectual tools to refute the G.E. Moore (Principles of Ethics) attack against the (...) natural law as committing a "naturalistic fallacy". This article proves that instead Moore commits the fallacy of equivocation between moral goodness and transcendental goodness in his very assertion of a "naturalistic fallacy" by the proponents of the natural moral law. In the process the new deontological/kantian theory of natural law as articulated by John Finnis, Robert George, and Germain Grisez is false historically and philosophically. Ethical naturalism is affirmed as a result. (shrink)

Common sense is on the one hand a certain set of processes of natural cognition – of speaking, reasoning, seeing, and so on. On the other hand common sense is a system of beliefs (of folk physics, folk psychology and so on). Over against both of these is the world of common sense, the world of objects to which the processes of natural cognition and the corresponding belief-contents standardly relate. What are the structures of this world? How does the scientific (...) treatment of this world relate to traditional and contemporary metaphysics and formal ontology? Can we embrace a thesis of common-sense realism to the effect that the world of common sense exists uniquely? Or must we adopt instead a position of cultural relativism which would assign distinct worlds of common sense to each group and epoch? The present paper draws on recent work in computer science (especially in the fields of naive and qualitative physics), in perceptual and developmental psychology, and in cognitive anthropology, in order to consider in a new light these and related questions and to draw conclusions for the methodology and philosophical foundations of the cognitive sciences. (shrink)

Provides a survey of the development of speech act theory from Aristotle through Reid and Peirce to Edmund Husserl, Anton Marty, Johannes Daubert, Adolf Reinach, and finally to Austin and Searle. A special role is played by Husserl's theory of objectifying acts (meaning, roughly, acts of naming or stating) and of the efforts by his followers to extend this theory to cover phenomena such as questioning and commanding. These efforts culminated in the work of Adolf Reinach, who developed the first (...) systematic theory of speech acts in connection with his monograph of 1913 on “The A Priori Foundations of the Civil Law”. (shrink)

Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...) they belong to the domain of epistemology). We analyze terms from several biomedical vocabularies in order to throw light on the interactions between ontological and epistemological components of these terminologies. We identify four cases: 1) terms containing classification criteria, 2) terms reflecting detectability, modality, uncertainty, and vagueness, 3) terms created in order to obtain a complete partition of a given domain, and 4) terms reflecting mere fiat boundaries. We show that epistemology-loaded terms are pervasive in biomedical vocabularies, that the “classes” they name often do not comply with sound classification principles, and that they are therefore likely to cause problems in the evolution and alignment of terminologies and associated ontologies. (shrink)

Propomos uma tipologia dos artefatos de representação para as áreas de saúde e ciências biológicas, e a associação dessa tipologia com diferentes tipos de ontologia formal e lógica, chegando a conclusões quanto aos pontos fortes e limitações da ontologia de diferentes tipos de recursos lógicos, enquanto mantemos o foco na lógica descritiva. Consideramos quatro tipos de representação de área: (i) representação léxico-semântica, (ii) representação de tipos de entidades, (iii) representação de conhecimento prévio, e (iv) representação de indivíduos. Defendemos uma clara (...) distinção entre os quatro tipos de representação, de forma a oferecer uma base mais racional para o uso das ontologias e artefatos relacionados no avanço da integração de dados e interoperabilidade de sistemas de raciocínio associados. Destacamos que apenas uma pequena porção de fatos cientificamente relevantes em áreas como a biomedicina pode ser adequadamente representada por ontologias formais, quando estas últimas são concebidas como representações de tipos de entidades. Particularmente, a tentativa de codificar conhecimento padrão ou probabilístico pela utilização de ontologias assim concebidas é fadada à produção de modelos não intencionais e errôneos. (shrink)