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)

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)

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)

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.

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 modern, advanced textbook reviews modal logic, a field which caught the attention of computer scientists in the late 1970's.

This modern, advanced textbook reviews modal logic, a field which caught the attention of computer scientists in the late 1970's.

Ruling Passions is about human nature. It is an invitation to see human nature a certain way. It defends this way of looking at ourselves against competitors, including rational choice theory, modern Kantianism, various applications of evolutionary psychology, views that enchant our natures, and those that disenchant them in the direction of relativism or nihilism. It is a story centred upon a view of human ethical nature, which it places amongst other facets of human nature, as just one of the (...) elements which give us the manifold objects of our concerns and cares. (shrink)

The author of the highly popular book Think, which Time magazine hailed as "the one book every smart person should read to understand, and even enjoy, the key questions of philosophy," Simon Blackburn is that rara avis--an eminent thinker who is able to explain philosophy to the general reader. Now Blackburn offers a tour de force exploration of what he calls "the most exciting and engaging issue in the whole of philosophy"--the age-old war over truth. The front lines (...) of this war are well defined. On one side are those who believe in plain, unvarnished facts, rock-solid truths that can be found through reason and objectivity--that science leads to truth, for instance. Their opponents mock this idea. They see the dark forces of language, culture, power, gender, class, ideology and desire--all subverting our perceptions of the world, and clouding our judgement with false notions of absolute truth. Beginning with an early skirmish in the war--when Socrates confronted the sophists in ancient Athens--Blackburn offers a penetrating look at the longstanding battle these two groups have waged, examining the philosophical battles fought by Plato, Protagoras, William James, David Hume, Hans-Georg Gadamer, Jacques Derrida, Michel Foucault, Richard Rorty, and many others, with a particularly fascinating look at Nietzsche. Among the questions Blackburn considers are: is science mere opinion, can historians understand another historical period, and indeed can one culture ever truly understand another. Blackburn concludes that both sides have merit, and that neither has exclusive ownership of truth. What is important is that, whichever side we embrace, we should know where we stand and what is to be said for our opponents. (shrink)

The classic approaches -- Correspondence -- Coherence -- Pragmatism -- Deflationism -- Tarski and the semantic theory of truth -- Summary of part I -- Varieties of enquiry -- Truths of taste; truth in art -- Truth in ethics -- Reason -- Religion and truth -- Interpretations.

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)

This is a very short introduction to ethics. It divides into three parts: first, introducing and discussing reasons for skepticism about ethics; second introducing themes of birth, death, happiness, desire and freedom to show how deeply our lives are interwoven with ethics; third, introducing attempts to found ethics, due to Aristotle, Kant, and the contractarian tradition.

Is what's true ultimately relative to your point of view? So that what's true as viewed from over here might be false if viewed from over there? In this article, Simon Blackburn grapples with the suggestion that what's true is ultimately just a matter of perspective.