The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...) comprehend the basic formal relationships that structure both reality and the ways humans perceive and communicate about reality. (shrink)

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

Peer review is a widely accepted instrument for raising the quality of science. Peer review limits the enormous unstructured influx of information and the sheer amount of dubious data, which in its absence would plunge science into chaos. In particular, peer review offers the benefit of eliminating papers that suffer from poor craftsmanship or methodological shortcomings, especially in the experimental sciences. However, we believe that peer review is not always appropriate for the evaluation of controversial hypothetical science. We argue that (...) the process of peer review can be prone to bias towards ideas that affirm the prior convictions of reviewers and against innovation and radical new ideas. Innovative hypotheses are thus highly vulnerable to being “filtered out” or made to accord with conventional wisdom by the peer review process. Consequently, having introduced peer review, the Elsevier journal Medical Hypotheses may be unable to continue its tradition as a radical journal allowing discussion of improbable or unconventional ideas. Hence we conclude by asking the publisher to consider re-introducing the system of editorial review to Medical Hypotheses. (shrink)

This lecture by Professor Werner Marx, of Freiburg University, was presented at the Moscow Hegel Convention on November 2, 1974. It is here translated for the first time by Professor James C. Risser, of Seattle University.

I argue that Ludwig Wittgenstein’s idea of the metaphysical subject sheds new light on subjective qualities of experience. In this article I draw first of all on the interpretations provided by Michael Kremer and James Conant. Subsequently, I conclude that “what is it like” means primarily “what is it like to see myself as the metaphysical subject”.

Many believe some version of all three of the following. It is strongly presumptively wrong to kill children intentionally. Modern war involves killing children intentionally. Most modern wars are morally justified. These three sentences comprise an inconsistent triad. War Realism denies 1. Just War Theory denies 2. Pragmatic or Conditional Pacifism denies 3. Scrutiny reveals that one can justify, depending on the rest of what one believes, any one of the three positions but they cannot all be true. I suggest (...) that the solution lies with pragmatic pacifism and relies upon James's sentiment of rationality. (shrink)

Jonna Vance and Preston Werner argue that humans’ mechanisms of perceptual attention tend to be sensitive to morally relevant properties. They dub this tendency “Attentional Moral Perception” (AMP) and argue that it can play all the explanatory roles that some theorists have hoped moral perception can play. In this article, I argue that, although AMP can indeed play some important explanatory roles, there are certain crucial things that AMP cannot do. Firstly, many theorists appeal to moral perception to explain (...) how moral knowledge is possible. I argue that AMP cannot put an agent in a position to acquire moral knowledge unless it is supplemented with some other capacity for becoming aware of moral properties. Secondly, theorists appeal to moral perception to explain “moral conversions”, i.e., cases in which an experience leads an agent to form a moral belief that conflicts with her pre-existing moral beliefs. I argue that AMP cannot explain this either. Due to these shortcomings, theorists should turn to emotions for a powerful and psychologically realistic account of virtuous agents’ sensitivity to the moral landscape. (shrink)

This essay is focused upon the question raised by the economic historian Andrei Znamenski: was National Socialism really socialist? I lay out his answer—that indeed it was—and explore it. I introduce the notion of neo-socialism as a way to characterize the Nazi regime, and fascist regimes more generally. I explore the key role played in the development of this ideology a number of thinkers called by Jeffrey Herf “reactionary modernists”: Ferdinand Tonnies; Werner Sombart; Hans Freyer; Martin Heidegger; Ernst Junger; (...) Carl Schmitt; and (to a lesser degree) Oswald Spengler. I conclude the essay by explaining the role of the uniquely virulent Nazi anti-Semitism—as well as the changes of the breakout of the war in 1939—played in the decision to exterminate the Jews. (shrink)

We generalize the Unstable Formula Theorem characterization of stable theories from Shelah [11], that a theory T is stable just in case any infinite indiscernible sequence in a model of T is an indiscernible set. We use a generalized form of indiscernibles from [11], in our notation, a sequence of parameters from an L-structure M, , indexed by an L′-structure I is L′-generalized indiscernible inM if qftpL′=qftpL′ implies tpL=tpL for all same-length, finite ¯,j from I. Let Tg be the theory (...) of linearly ordered graphs in the language with signature Lg={<,R}. Let Kg be the class of all finite models of Tg. We show that a theory T has NIP if and only if any Lg-generalized indiscernible in a model of T indexed by an Lg-structure with age equal to Kg is an indiscernible sequence. (shrink)

The author has previously shown that for a certain class of structures $\mathcal {I}$, $\mathcal {I}$-indexed indiscernible sets have the modeling property just in case the age of $\mathcal {I}$ is a Ramsey class. We expand this known class of structures from ordered structures in a finite relational language to ordered, locally finite structures which isolate quantifier-free types by way of quantifier-free formulas. This result is applied to give new proofs that certain classes of trees are Ramsey. To aid this (...) project we develop the logic of EM-types. (shrink)

How (Not) to Be Secular is what Jamie Smith calls "your hitchhiker's guide to the present" -- it is both a reading guide to Charles Taylor's monumental work A Secular Age and philosophical guidance on how we might learn to live in our times. Taylor's landmark book A Secular Age (2007) provides a monumental, incisive analysis of what it means to live in the post-Christian present -- a pluralist world of competing beliefs and growing unbelief. Jamie Smith's book is a (...) compact field guide to Taylor's insightful study of the secular, making that very significant but daunting work accessible to a wide array of readers. Even more, though, Smith's How (Not) to Be Secular is a practical philosophical guidebook, a kind of how-to manual on how to live in our secular age. It ultimately offers us an adventure in self-understanding and maps out a way to get our bearings in today's secular culture, no matter who "we" are -- whether believers or skeptics, devout or doubting, self-assured or puzzled and confused. This is a book for any thinking person to chew on. (shrink)

The Gifford Lectures were established in 1885 at the universities of St Andrews, Glasgow, Aberdeen and Edinburgh to promote the discussion of 'Natural Theology in the widest sense of the term - in other words, the knowledge of God', and some of the world's most influential thinkers have delivered them. The 1901–2 lectures given in Edinburgh by American philosopher William James are considered by many to be the greatest in the series. The lectures were published in book form in (...) 1902 and have been reprinted many times. James, who was educated in the United States and Europe, and spent much of his career teaching philosophy at Harvard, was very influential in the development of modern psychology, and in these twenty lectures he explores the personal experience of religion. Some of the topics include religion and neurology, 'the sick soul', saintliness, and mysticism. (shrink)

Plato's dialogues frequently criticize traditional Greek myth, yet Plato also integrates myth with his writing. Daniel S. Werner confronts this paradox through an in-depth analysis of the Phaedrus, Plato's most mythical dialogue. Werner argues that the myths of the Phaedrus serve several complex functions: they bring nonphilosophers into the philosophical life; they offer a starting point for philosophical inquiry; they unify the dialogue as a literary and dramatic whole; they draw attention to the limits of language and the (...) limits of knowledge; and they allow Plato to co-opt cultural authority as a way of defining and legitimating the practice of philosophy. Platonic myth, as a species of traditional tale, is thus both distinct from philosophical dialectic and similar to it. Ultimately, the most powerful effect of Platonic myth is the way in which it leads readers to participate in Plato's dialogues and to engage in a process of self-examination. (shrink)

Hubert Dreyfus has argued that cases of absorbed bodily coping show that there is no room for self-awareness in flow experiences of experts. In this paper, I argue against Dreyfus’ maxim of vanishing self-awareness by suggesting that awareness of agency is present in expert bodily action. First, I discuss the phenomenon of absorbed bodily coping by discussing flow experiences involved in expert bodily action: merging into the flow; immersion in the flow; emergence out of flow. I argue against the claim (...) that flow experience does not involve an awareness of agency for each of these features, while conceding that fluent agency does not involve self-awareness in the thetic sense. I challenge the assumption that the awareness of fluent agency must be understood in terms of a thetic awareness of agency. Instead, I develop an Anscombean account of the awareness of fluent agency in terms of the phenomenal character of knowing one’s aims. I respond to the challenge that if an Anscombean account of the awareness of agency is to succeed, then agents must be able to answer Anscombean questions. I consider the objection that awareness of agency is not a form of self-awareness by outlining an account of self-awareness as self-synthesis that is distinct from self-perception and self-ascription, but which makes room for self-awareness in expert bodily action. (shrink)

Do Quine and Carnap distort the social nature of inquiry by privileging individual epistemic subjects? This objection is at the heart of Donald Davidson’s claim that Quine fails to grasp the significance of the concept of truth. In Carnap’s case, the objection may be detected in Charles Morris’s call to ground scientific philosophy in semiotics, the science of signs, rather than syntax, the formal investigation of languages. Drawing out the challenge from Morris’s proposal requires examining a neglected influence on this (...) neglected philosopher: his advisor George Herbert Mead’s social theory of mind. I argue that Morris and Davidson can both be understood as demanding that scientific philosophers socialize their conception of objectivity. (shrink)

Affective congruency effects in the evaluation task can be explained by either spreading of activation or response competition. Eliminating effects of response compatibility by using other tasks (semantic categorisation, naming task) typically also eliminates affective congruency effects. However, there is no need for processing the affective information of the stimuli in these tasks either, which could be necessary for an affectively mediated spreading of activation (Spruyt et al., 2007, 2009, 2012). We introduced a new task to further test this hypothesis. (...) The valent/neutral-categorisation task does not confound affective congruency with response compatibility, but still requires a processing of the stimuli's valence. No affective congruency effect was obtained with this task in two experiments, disfavouring a conditional spreading activation account. On the other hand, a significant priming effect was found for associated word pairs in Experiment 1, providing evidence for the sensitivity of the task to detect spreading activation processes. (shrink)

We investigate the notion of a semi-retraction between two first-order structures (in typically different signatures) that was introduced by the second author as a link between the Ramsey property and generalized indiscernible sequences. We look at semi-retractions through a new lens establishing transfers of the Ramsey property and finite Ramsey degrees under quite general conditions that are optimal as demonstrated by counterexamples. Finally, we compare semi-retractions to the category theoretic notion of a pre-adjunction.

This collection broadens the scientific discussion of modularity by bringing together experts from a variety of disciplines, including artificial life, ...

This is Werner S. Pluhar's translation of Immanuel Kant's Critique of Judgment (Kritik der Urtheilskraft) for Hackett Publications (Indianapolis, Indiana). ISBN 9780872200258 (paperback).

Philosophers of science traditionally have ignored the details of scientific research, and the result has often been theories that lack relevance either to science or to philosophy in general. In this volume, leading philosophers of biology discuss the limitations of this tradition and the advantages of the "naturalistic turn"—the idea that the study of science is itself a scientific enterprise and should be conducted accordingly. This innovative book presents candid, informal debates among scholars who examine the benefits and problems of (...) studying science in the same way that scientists study the natural world. Callebaut achieves the effect of face-to-face engagement through separate interviews with participants. Contributors include William Bechtel, Robert Brandon, Richard M. Burian, Donald T. Campbell, Patricia Churchland, Jon Elster, Ronald N. Giere, David L. Hull, Philip Kitcher, Karin Knorr Cetina, Bruno Latour, Richard Levins, Richard C. Lewontin, Elisabeth Lloyd, Helen Longino, Thomas Nickles, Henry C. Plotkin, Robert J. Richards, Alexander Rosenberg, Michael Ruse, Dudley Shapere, Elliott Sober, Ryan Tweney, and William Wimsatt. "Why can't we have both theoretical ecology and natural histories, lovingly done?"—Philip Kitcher "Don't underestimate the arrogance of philosophers!"—Elisabeth Lloyd. (shrink)

The Information Artifact Ontology (IAO) was created to serve as a domain‐neutral resource for the representation of types of information content entities (ICEs) such as documents, data‐bases, and digital im‐ages. We identify a series of problems with the current version of the IAO and suggest solutions designed to advance our understanding of the relations between ICEs and associated cognitive representations in the minds of human subjects. This requires embedding IAO in a larger framework of ontologies, including most importantly the Mental (...) Func‐tioning Ontology (MFO). It also requires a careful treatment of the aboutness relations between ICEs and associated cognitive representa‐tions and their targets in reality, which implies in turn a new treatment of the relation of truthmaking. (shrink)

Big data biology—bioinformatics, computational biology, systems biology (including ‘omics’), and synthetic biology—raises a number of issues for the philosophy of science. This article deals with several such: Is data-intensive biology a new kind of science, presumably post-reductionistic? To what extent is big data biology data-driven? Can data ‘speak for themselves?’ I discuss these issues by way of a reflection on Carl Woese’s worry that “a society that permits biology to become an engineering discipline, that allows that science to slip into (...) the role of changing the living world without trying to understand it, is a danger to itself.” And I argue that scientific perspectivism, a philosophical stance represented prominently by Giere, Van Fraassen, and Wimsatt, according to which science cannot as a matter of principle transcend our human perspective, provides the best resources currently at our disposal to tackle many of the philosophical issues implied in the modeling of complex, multilevel/multiscale phenomena. (shrink)

There are many things that philosophy of biology might be. But, given the existence of a professional philosophy of biology that is arguably a progressive research program and, as such, unrivaled, it makes sense to define philosophy of biology more narrowly than the totality of intersecting concerns biologists and philosophers (let alone other scholars) might have. The reasons for the success of the “new” philosophy of biology remain poorly understood. I reflect on what Dutch and Flemish, and, more generally, European (...) philosophers of biology could do to improve the situation of their discipline locally, regionally, and internationally, paying particular attention to the lessons to be learned from the “Science Wars.”. (shrink)

The goal of referent tracking is to create an ever-growing pool of data relating to the entities existing in concrete spatiotemporal reality. In the context of Electronic Healthcare Records (EHRs) the relevant concrete entities are not only particular patients but also their parts, diseases, therapies, lesions, and so forth, insofar as these are salient to diagnosis and treatment. Within a referent tracking system, all such entities are referred to directly and explicitly, something which cannot be achieved when familiar concept-based systems (...) are used in what is called “clinical coding”. In this paper we describe the components of a referent tracking system in an informal way and we outline the procedures that would have to be followed by healthcare personnel in using such a system. We argue that the referent tracking paradigm can be introduced with only minor – though nevertheless ontologically important – technical changes to existing EHR infrastructures, but that it will require a radically different mindset on the part of those involved in clinical coding and terminology development from that which has prevailed hitherto. (shrink)

We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...) of problems that have been observed in other biomedical terminologies. For its further development, we recommend the use of a more principled approach that allows the Thesaurus to be tested not just for internal consistency but also for its degree of correspondence to that part of reality which it is designed to represent. (shrink)

INTRODUCTION WERNER ABRAHAM, LACI MARÁCZ, SJAAK DE MEY & WIM SCHERPENISSE University of Groningen The Groningen Conference on Topic, ...

This article explores Adorno’s negative dialectics as a critical social theory of economic objectivity. It rejects the conventional view that Adorno does not offer a critique of the economic forms of capitalist society. The article holds that negative dialectics is a dialectics of the social world in the form of the economic object, one that is governed by the movement of economic quantities, that is, real economic abstractions. Negative dialectics refuses to accept the constituted economic categories as categories of economic (...) nature. Instead, the article argues, it amounts to a conceptualized social praxis [ begriffene Praxis] of the capitalistically constituted social relations, which manifest themselves in the form of seemingly independent economic categories. Economic nature is a socially constituted nature, which entails the class antagonism in its concept. The article concludes that for negative dialectics the explanation of real economic abstractions lies in the understanding of the class-divided nature of human practice. (shrink)

While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...) We here present a view of mental disease that is based on ontological realism and which follows the principles embodied in Basic Formal Ontology and in the application of BFO in the Ontology of General Medical Science. We analyzed statements about what counts as a mental disease provided in the research agenda for the DSM-V, and in Pies' model. The results were used to assess whether the representational units of BFO and OGMS were adequate as foundations for a formal representation of the entities in reality that these statements attempt to describe. We then analyzed the representational units specific to mental disease and provided corresponding definitions. Our key contributions lie in the identification of confusions and conflations in the existing terminology of mental disease and in providing what we believe is a framework for the sort of clear and unambiguous reference to entities on the side of the patient that is needed in order to avoid these confusions in the future. (shrink)

We study the preservation of certain properties under products of classes of finite structures. In particular, we examine indivisibility, definable self-similarity, the amalgamation property, and the disjoint n-amalgamation property. We explore how each of these properties interacts with the lexicographic product, full product, and free superposition of classes of structures. Additionally, we consider the classes of theories which admit configurations indexed by these products. In particular, we show that, under mild assumptions, the products considered in this article do not yield (...) new classes of theories. (shrink)