Fusion genes formed by chromosomal rearrangements are common drivers of cancer. Recent innovations in the field of next‐generation sequencing (NGS) have seen a dynamic shift from traditional fusion detection approaches, such as visual characterization by fluorescence, to more precise multiplexed methods. There are many different NGS‐based approaches to fusion gene detection and deciding on the most appropriate method can be difficult. Beyond the experimental approach, consideration needs to be given to factors such as the ease of implementation, processing time, associated (...) costs, and the level of expertise required for data analysis. Here, the different NGS‐based methods for fusion gene detection, the basic principles underlying the techniques, and the benefits and limitations of each approach are reviewed. This article concludes with a discussion of how NGS will impact fusion gene detection in a clinical context and from where the next innovations are evolving. (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)

In their simplest form, hybrid languages are propositional modal languages which can refer to states. They were introduced by Arthur Prior, the inventor of tense logic, and played an important role in his work: because they make reference to specific times possible, they remove the most serious obstacle to developing modal approaches to temporal representation and reasoning. However very little is known about the computational complexity of hybrid temporal logics.In this paper we analyze the complexity of the satisfiability problem of (...) a number of hybrid temporal logics: the basic hybrid language over transitive trees; nominal Until logic; and referential interval logic. We discuss the effects of including nominals, the @ operator, the somewhere modality E, and the difference operator D. Adding nominals to tense logic leads for several frame-classes to an increase in complexity of the satisfiability problem from PSPACE to EXPTIME. On transitive trees, however, the satisfiability problem for this language can be decided in PSPACE. Along the way we make a detour through hybrid propositional dynamic logic: we establish upper bounds for a number of temporal logics by generalizing results due to Passy and Tinchev [29] and De Giacomo [16]. We conclude with some remarks on the relevance of our results to description logic, and draw attention to the utility of the spypoint technique for proving upper and lower bounds. (shrink)

Este artigo canta uma canção — uma canção criada ao unir o trabalho de quatro grandes nomes na história da lógica: Hans Reichenbach, Arthur Prior, Richard Montague, e Leon Henkin. Embora a obra dos primeiros três desses autores tenha sido previamente combinada, acrescentar as ideias de Leon Henkin é o acréscimo requerido para fazer com que essa combinação funcione no nível lógico. Mas o presente trabalho não se concentra nas tecnicalidades subjacentes (que podem ser encontradas em Areces, Blackburn, Huertas, (...) e Manzano [no prelo]), e sim nos instrumentos subjacentes e no modo como trabalham em conjunto. Esperamos que o leitor fique tentado a cantar junto. DOI:10.5007/1808-1711.2011v15n2p225. (shrink)

Expressivism is the view that the function of normative sentences is not to represent a kind of fact, but to avow attitudes, prescribe behavior, or the like. The idea can be found in David Hume. In the 20th century, G.E. Moore’s Open Question Argument provided important support for the view. Elizabeth Anscombe introduced the notion of “direction of fit,” which helped distinguish expressivism from a kind of naive subjectivism. The central advantage of expressivism is that it easily explains the motivational (...) force of moral conviction. Its chief problem is it has difficulty explaining the “realist surface” of moralizing. Quasi-realism is a strategy for explaining the realist surface without abandoning the underlying ideas of expressivism. It aims to explain moral error as well as deal with the so-called Frege-Geach problem. This chapter explains quasi-realism, and evaluates it by comparison with its chief rivals: Aristotelian approaches, Kantian approaches, realist moral naturalism, and fictionalism. (shrink)

This collection of previously unpublished essays addresses a number of issues arising out of philosophical controversies over the possibility of genuine moral dilemmas. Issues addressed include the form of a moral dilemma; the paradoxes a moral dilemma is said to entail; the question of whether a moral dilemma must exhibit inconsistency; the role of intractable circumstances in occasioning moral dilemmas; and the plausibility of supposing that there might be rational ways of addressing moral dilemmas in practice. The contributors, writing from (...) a number of widely differing points of view, include Simon Blackburn, Ruth Barcan Marcus, Alan Donagan, Terrance McConnell, Walter Sinnott-Armstrong, Mary Mothersill, Norman Dahl, David Brink, Peter Railton, Thomas E. Hill, Jr., Christopher Gowans, and H.E. Mason. (shrink)

The title of this rich, wide-ranging, and rewarding book alludes both to the idea that passions rule, and to the thought that we rule our passions. Blackburn offers a conception of both, one broadly in the spirit of Hume and Adam Smith.

The title of this rich, wide-ranging, and rewarding book alludes both to the idea that passions rule, and to the thought that we rule our passions. Blackburn offers a conception of both, one broadly in the spirit of Hume and Adam Smith.

Se è un difetto della ragione essere incapaci di adottare certi mezzi, allo stesso modo è un difetto della ragione essere incapaci di adottare certi fini, dicono i kantiani. Secondo Blackburn questa tesi non-strumentalista deve la sua apparente validità ad una fallacia modale. Dal condizionale «Se si adotta il fine X, è necessario adottare il mezzo Y», si deriva il conseguente «Si deve adottare il mezzo Y», ci si interroga sulla natura del modale che occorre nel conseguente, poi si (...) ricostruisce l’antecedente come «E’ necessario adottare il fine X» e infine si ricostruisce il condizionale come «Se è necessario adottare il fine X, è necessario adottare il mezzo Y». Il non-strumentalista è così portato a credere che la stessa normatività che è contenuta nel principio strumentalista deve essere derivata dalla normatività dei fini (p. 242). (shrink)

Blackburn’s dilemma (as commonly understood) is that in explaining truths of the form ‘Necessarily-P’ we have to appeal either to a necessary truth, in which case we don’t seem to make the right kind of progress, or to a contingent truth, in which case we seem to undermine the necessity we were meant to be explaining. This paper advances two claims. First, it is argued that the dilemma is wider in scope than usually supposed. The standard assumption (evident also (...) in Black-burn’s original paper (1993)) is that the dilemma applies to explanations of truths of the form ‘Necessarily-P’. I argue that the real problem identified by Blackburn doesn’t just apply to explanations of truths of this form, but to explanations of necessary truths in general (e.g. truths of logic, mathematics, etc.). In the course of this argument it also transpires that the real problem on the necessity horn is rather different—and rather less susceptible to obvious objections—than it is usually taken to be. It concerns the antinaturalistic core of necessity. Second, it is argued that there is an escape from the antinaturalistic core on the contingency horn. In the footsteps of Wright (1985), the claim is that the contingency horn is tenable for those who believe that the necessary truth in question is analytic, i.e. follows from its meaning. (shrink)

Expressionism, holism, and deflationism are central concepts in Blackburn quasi-realistic metaethics. The paper deals with these in order to evaluate the general tenability of Blackburn’s version of non-cognitivism.

Abstract In this piece I take issue with Bernard Williams's interpretation of Herodotus as lacking something of our conception of time. I claim that there is nothing so unusual in the interleaving of myth or fiction and history that Williams finds in Herodotus. I also reflect on the difficulty of separating acceptance of truth from acceptance of myth, metaphor, and model, not only in history but also in science.

In this note we show that the classical modal technology of Sahlqvist formulas gives quick proofs of the completeness theorems in [8] (D. Gregory, Completeness and decidability results for some propositional modal logics containing “actually” operators, Journal of Philosophical Logic 30(1): 57–78, 2001) and vastly generalizes them. Moreover, as a corollary, interpolation theorems for the logics considered in [8] are obtained. We then compare Gregory's modal language enriched with an “actually” operator with the work of Arthur Prior now known under (...) the name of hybrid logic. This analysis relates the “actually” axioms to standard hybrid axioms, yields the decidability results in [8], and provides a number of complexity results. Finally, we use a bisimulation argument to show that the hybrid language is strictly more expressive than Gregory's language. (shrink)

Pragmatists have traditionally been enemies of representationalism but friends of naturalism, when naturalism is understood to pertain to human subjects, in the sense of Hume and Nietzsche. In this volume Huw Price presents his distinctive version of this traditional combination, as delivered in his René Descartes Lectures at Tilburg University in 2008. Price contrasts his view with other contemporary forms of philosophical naturalism, comparing it with other pragmatist and neo-pragmatist views such as those of Robert Brandom and Simon Blackburn. (...) Linking their different 'expressivist' programmes, Price argues for a radical global expressivism that combines key elements from both. With Paul Horwich and Michael Williams, Brandom and Blackburn respond to Price in new essays. Price replies in the closing essay, emphasising links between his views and those of Wilfrid Sellars. The volume will be of great interest to advanced students of philosophy of language and metaphysics. (shrink)

A modal logic is developed to deal with finite ordered binary trees a they are used in linguistics. A modal language is introduced with operators for the ‘mother of’, ‘first daughter of’ and ‘second daughter of’ relations together with their transitive reflexive closures. The relevant class of tree models is defined and three linguistic applications of this language are discussed: context free grammars, command relations, and trees decorated with feature structures. An axiomatic proof system is given for which completeness is (...) shown with respect to the class of finite ordered binary trees. A number of decidability results follow. (shrink)

The article challenges conventional assumptions regarding the question of incest survival within contemporary discourses. A textual analysis of Kathryn Harrison's autobiographical novel tracing her consensual sexual relationship with her father is used to address the issue of failed or unresolved mourning as a prototypically ‘modern’ cultural phenomenon. Psychoanalytically informed feminist literary criticism is used to explore the parallels between the cultural construction of femininity and failed or postponed mourning in western historical and philosophical traditions. Following the work of Juliana Schiesari (...) and Kathleen Woodward, the article contends that melancholia is a gendered discourse that has historically privileged male theorists and film-makers, such as Barthes and Fassbinder. The article suggests that contemporary women writers, such as Harrison, are engaged in a revisionary approach to the construction of loss within their writing. By situating themselves at the heart of the contemporary family narrative, instead of the ‘melancholic’ margins, they are able to produce a counter-discourse that dispels the conventional dynamics of the traditional family romance. By using the ‘writing cure’ to overcome ideological loss, the desiring daughter is able to challenge misogynist constructions of femininity within contemporary literature. (shrink)

The idea of combining logics, structures, and theories has recently been attracting interest in areas as diverse as constraint logic programming, theorem proving, verification, computational linguistics, artificial intelligence and indeed, various branches of logic itself. It would be an exaggeration to claim that these (scattered, and by-and-large independent) investigations have crystallized into an enterprise meriting the title "combined methods"; nonetheless, a number of interesting themes are emerging. This introduction notes some prominent ones and relates them to the papers in this (...) special issue. (shrink)

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

Within a year of each other, three one-volume general dictionaries of philosophy have recently appeared; when our future colleagues in philosophy look back on the 1990s they may well think of it as the decade of reference works. But however productive these years may prove to be in this genre, clearly visible somewhere around the top of the heap will be this handy, useful, entertaining, and instructive contribution from Simon Blackburn. Its two immediate competitors are the Cambridge Dictionary of (...) Philosophy, edited by Robert Audi, and the Oxford Companion to Philosophy, edited by Ted Honderich. No detailed comparison will be attempted here, but two points stand out as obviously giving Blackburn’s dictionary a rather different use and flavor from the others: while containing a closely comparable number of entries, it is distinctly shorter and handier in format; and it has all been written by a single author. (shrink)

Provides a comprehensive introduction to the major philosophical theories attempting to explain the workings of language.

Simon Blackburn puts forward a compelling original philosophy of human motivation and morality. He maintains that we cannot get clear about ethics until we get clear about human nature. So these are the sorts of questions he addresses: Why do we behave as we do? Can we improve? Is our ethics at war with our passions, or is it an upshot of those passions? Blackburn seeks the answers in an exploration of guilt, shame, disgust, and other moral emotions; (...) he draws also on game theory and cognitive science in his account of the structures of human motivation. Many philosophers have wanted a naturalistic ethics a theory that integrates our understanding of human morality with the rest of our understanding of the world we live in. What is special about Blackburn's naturalistic ethics is that it does not debunk the ethical by reducing it to the non-ethical. At the same time he banishes the spectres of scepticism and relativism that have haunted recent moral philosophy. Ruling Passions sets ethics in the context of human nature: it offers a solution to the puzzle of how ethics can maintain its authority even though it is rooted in the very emotions and motivations that it exists to control. (shrink)

This volume collects some influential essays in which Simon Blackburn, one of our leading philosophers, explores one of the most profound and fertile of philosophical problems: the way in which our judgments relate to the world. This debate has centered on realism, or the view that what we say is validated by the way things stand in the world, and a variety of oppositions to it. Prominent among the latter are expressive and projective theories, but also a relaxed pluralism (...) that discourages the view that there are substantial issues at stake. The figure of the "quasi-realist" dramatizes the difficulty of conducting these debates. Typically philosophers thinking of themselves as realists will believe that they alone can give a proper or literal account of some of our attachments--to truth, to facts, to the independent world, to knowledge and certainty. The quasi-realist challenge, developed by Blackburn in this volume, is that we can have those attachments without any metaphysic that deserves to be called realism, so that the metaphysical picture that goes with our practices is quite idle. The cases treated here include the theories of value and knowledge, modality, probability, causation, intentionality and rule-following, and explanation. A substantial new introduction has been added, drawing together some of the central themes. The essays articulate a fresh alternative to a primitive realist/anti-realist opposition, and their cumulative effect is to yield a new appreciation of the delicacy of the debate in these central areas. (shrink)