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)

Judith Jarvis Thomson, The Realm Of Rights Harvard University Press, 1990, viii, 383pp.

Production and comprehension have long been viewed as inseparable components of language. The study of vision, by contrast, has centered almost exclusively on comprehension. Here we investigate drawing—the most basic form of visual production. How do we convey concepts in visual form, and how does refining this skill, in turn, affect recognition? We developed an online platform for collecting large amounts of drawing and recognition data, and applied a deep convolutional neural network model of visual cortex trained only on natural (...) images to explore the hypothesis that drawing recruits the same abstract feature representations that support natural visual object recognition. Consistent with this hypothesis, higher layers of this model captured the abstract features of both drawings and natural images most important for recognition, and people learning to produce more recognizable drawings of objects exhibited enhanced recognition of those objects. These findings could explain why drawing is so effective for communicating visual concepts, they suggest novel approaches for evaluating and refining conceptual knowledge, and they highlight the potential of deep networks for understanding human learning. (shrink)

Utopian literature is fascinating but impossible to summarize. Of course it is easy to see where its charm lies. We enjoy the “play” aspect of the Utopian convention, the common certainty— essential to both the author's intentions and the reader's pleasure—that we are dealing with a supposition described as a fact. In a Utopian text, we enjoy the power we have of imagining, and especially formulating, another overall framework for human experience—a framework which is specifically defined as being different and (...) described as if it had concrete existence. This is the underlying attraction of a mode of expression which permits the author to talk of serious things in the protected and detached manner permitted by play. Why, then, are summaries of utopias so disappointing? Why does a re-transmitted utopia convey only the idea of an insipid world and an arbitrary creation? Why is it so hard to write about works of this type? (shrink)

The impetus to revisit the issues involved in readings of Genesis 2-3 came from Deborah Rooke’s article in Feminist Theology published in 2007, and in particular follows a presentation at an ‘Afternoon of Theology’ at a girls’ secondary school, where the author provided a response to the challenge set by the history of interpretation and the subsequent cultural assumptions of the meaning of the Garden of Eden narrative. The discussion proceeds partly through narrative retelling, partly through a critical commentary and (...) partly through an Eve/snake dialogue. (shrink)

Choisir un livre, c'est en exclure beaucoup d'autres, contribuer à circonscrire le cercle lumineux de l'attention, participer à une aventure dont l'enjeu est la survie; vivre dans les lettres, ce n'est pas s'installer dans un patrimoine mais l'inventer, faire du soleil et de la place, inséparablement. Rééditer ce livre dans une édition de poche, ce n'est pas seulement faire en sorte qu'il soit de nouveau disponible; c'est en prolonger le rayonnement mais aussi le déplacer, l'inscrire autrement dans l'aventure de la (...) survie. Dans sa première vie, La Mémoire des œuvres s'est imposé à quelques-uns comme un bréviaire. Écrit pour tous et pour chacun, il demande et appelle l'amitié d'un plus large public, c'est un livre ami de la mémoire, qui aide à penser et qui aide à vivre, à habiter plus librement le séjour des livres. (shrink)

Proposer une oeuvre nouvelle, developper une idee neuve ou une vision personnelle differente, c'est dire autre chose. Mais c'est aussi dire quelque chose qui n'est pas radicalement inoui et sans connexion. Impacts, emprunts, initiatives, traditions ou ruptures: ces relations d'influence traversent la vie des idees et des oeuvres, leurs rapports entre elles, leurs caracteres de famille, et ce qui les rend chacune distincte. Invention et memoire vont ensemble. Leur liaison et leur ecart organisent ce qu'il y a d'autonome et d'unique (...) dans un point de vue novateur, et ce qu'il y a de commun et de partage. (shrink)

Cet ouvrage est une réédition numérique d’un livre paru au XXe siècle, désormais indisponible dans son format d’origine.

Toute oeuvre veut tenir l'attention, la diriger et produire de l'effet. Mais l'attention et l'effet ne sont pas les memes selon que l'oeuvre en dit plus ou en dit moins c'est-a-dire selon sa densite. Le developpe ou le concis, l'emphatique ou l'elude, le riche ou l'austere ne produisent pas les memes intensites. En explorant les variations de la densite litteraire, on retrouve directement des enjeux essentiels. Que vise l'ideal du complet face a l'ideal du pur? Comment la litterature se rapporte-t-elle (...) au langage ordinaire? Quel peut etre le minimum artistique qui subsiste au bord du silence? Comment comprendre l'echec de la lecture, l'interet perdu et l'ennui? (shrink)

In his early work, the philosopher Stanley Cavell offers a sustained engagement with the threat of epistemological scepticism, shaped by the intuition that although (as the late Wittgenstein shows) ordinary language use is the practice within which alone meaning is possible (and which can thus not be further analysed or rationalised), it is also a basic human inclination to wish to escape the limitations of the ‘ordinary’. This, for Cavell, is the root of scepticism. Scepticism, on this view, thus appears (...) not primarily as an epistemological but as an (injurious) moral stance, which cannot be refuted but must be continually confronted and overcome. Vis-à-vis scepticism, ‘acknowledgement’ is the practice-based recognition of the world and other people in their continuing elusiveness, which ineluctably involves risk, but just so is the only way of knowing that is appropriate to and honours the (finite) human condition. One problematic aspect of this (very fertile) approach is that Cavell’s secular viewpoint makes it difficult for him to say both why the desire for a ‘beyond’ arises in the first place, and why its expression as denial is morally wrong (rather than merely misguided). His approach thus invites a theological ‘supplementation’ which grounds the human condition in an original and real relation to God that is meant to draw the believer, through Christ, into the divine life itself. Such a reinterpretation both elucidates the concepts of scepticism and acknowledgement, and makes these concepts available for a theological outlook that is able to accommodate Cavell’s profound insights into ‘the human’. (shrink)

Some decades ago in his intriguing book on Jonathan Edwards, Perry Miller used to great effect the device of supposing a two-fold biography of Edwards, an external one consisting of the historical record embracing the major events of his life and times, and an internal one aimed at an interpretation of the mind of Edwards and the development of his thought.

There is an undercurrent to be detected in Anselm's record of the meditative experience that issued in the Ontological Argument and, although it points to a profound and perennial problem in the interpretation of religion, this undercurrent has been largely ignored. The Argument, as is well known, moves entirely within the medium of reflective meaning focused on the idea of God and, unlike the cosmological arguments of later theologians, it makes no appeal whatever to a principle of causality or to (...) the discovery of a sufficient reason for finite existence. Anselm seems to have had his own sense of what one may call the unadulterated rationalism of the Argument when, in his own words, he wondered, ‘if perhaps it might be possible to find one single argument that for its proof required no other save itself, and that by itself would suffice to prove that God really exists’. Here we are entirely within that inner chamber of the mind so dear to the Augustinian tradition, a mind from which one is to exclude all thought save that of God. The task of the one who reflects is to penetrate the inner meaning of this thought in order to discover what it implies beyond what is evident on the surface. With such an eminently rational or logical aim occupying the centre of attention, it is quite understandable that the presence of another, and quite opposed, concern should have been overlooked - Anselm's concern, namely, to transcend, as it were, the medium of thought itself, and enter into the presence of God. The reason that this concern introduces a tension in the search for a proof is that the realization of presence would seem to render proof superfluous, while the inference in an argument - especially one moving towards existence – inevitably suggests, in some sense and to some degree, the absence of what is sought for. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

In this article I argue that evolutionary psychological strategies for making inferences about present-day human psychology are methodologically unsound. Evolutionary psychology is committed to the view that the mind has an architecture that has been conserved since the Pleistocene, and that our psychology can be fruitfully understood in terms of the original, fitness-enhancing functions of these conserved psychological mechanisms. But for evolutionary psychological explanations to succeed, practitioners must be able to show that contemporary cognitive mechanisms correspond to those that were (...) selected for in the environment of evolutionary adaptedness, that these present-day cognitive mechanisms are descended from the corresponding ancestral mechanisms, and that they have retained the functions of the ancestral mechanisms from which they are descended. I refer to the problem of demonstrating that these conditions obtain as “the matching problem,” argue that evolutionary psychology does not have the resources to address it, and conclude that evolutionary psychology, as it is currently understood, is therefore impossible. (shrink)

This paper addresses the question of what organisms are and therefore what kinds of biological entities qualify as organisms. For some time now, the concept of organismality has been eclipsed by the notion of individuality. Biological individuals are those systems that are units of selection. I develop a conception of organismality that does not rely on evolutionary considerations, but instead draws on development and ecology. On this account, organismality and individuality can come apart. Organisms, in my view, are as Godfrey- (...) class='Hi'>Smith puts it “essentially persisters.” I argue that persistence is underpinned by differentiation, integration, development, and the constitutive embeddedness of organisms in their worlds. I examine two marginal cases, the Portuguese Man O’ War and the honey bee colony, and show that both count as organisms in light of my analysis. Next, I examine the case of holobionts, hosts plus their microsymbionts, and argue that they can be counted as organisms even though they may not be biological individuals. Finally, I consider the question of whether other, less tightly integrated biological systems might also be treated as organisms. (shrink)

Avian Flu Pandemic – Flight of the Healthcare Worker? Content Type Journal Article Pages 365-385 DOI 10.1007/s10730-009-9114-9 Authors Robert B. Shabanowitz, Geisinger Medical Center, Dept. of OB/GYN 100 North Academy Avenue Danville PA 17822-2920 USA Judith E. Reardon, Geisinger Medical Center Center for Health Research 100 North Academy Avenue Danville PA 17822-3003 USA Journal HEC Forum Online ISSN 1572-8498 Print ISSN 0956-2737 Journal Volume Volume 21 Journal Issue Volume 21, Number 4.

In my contribution to this volume, I (BHS) comment on on the stultifying rhetoric of contemporary analytic moral theory as illustrated in Judith Jarvis Thomson's Tanner Lectures, with particular reference to Thomson's anxieties about the moral relativism exhibited by college freshman and to her efforts--quite strained, in my view, and inevitably unsuccessful--to demonstrate the existence of objective judgments in matters of morality and taste .

The idea of arousal as a non-specific state of activation has been implicated as an explanatory factor for many aspects of human behavior, ranging from emotional experiences to learning and memory. Critiques of this concept have highlighted that arousal is ambiguous and evidence for its role in emotion is mixed. However, contemporary emotion theories and empirical research continue to incorporate the concept of arousal in ways that fail to address its problems. Here, we review the origins of the term arousal (...) in physiology and trace how it has been translated and applied to psychology (particularly as it relates to emotion). We consider whether the construct of arousal is currently (a) consistent and (b) useful in understanding human behavior. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Jonathan Edwards's Philosophy of History: The Reenchantment of the World in the Age of EnlightenmentJohn E. SmithAvihu Zakai. Jonathan Edwards's Philosophy of History: The Reenchantment of the World in the Age of Enlightenment. Princeton: Princeton University Press, 2003. Pp. xvii + 348. Cloth, $49.95.Edwards's History of Redemption is the focus of this study by Avihu Zakai—Professor of History at the Hebrew University in Jerusalem. The History is a (...) series of thirty sermons Edwards preached on Isaiah 51:8 "... my righteousness shall be forever... my salvation from generation to generation." For him, it was a "new method in divinity... thrown into the form of a history"—a narrative showing God's sovereignty in redemption "from the fall of man to the end of the world."Zakai gives a comprehensive account of Edwards's view of history meant to highlight his struggle against modern beliefs threatening Christian faith (308; passim). The discussion is not limited to history, but includes most of Edwards's writing from 1720-1750 with emphasis on his opposition to the Enlightenment. Zakai cannot interpret so many works with the accuracy needed; he repeats old errors such as opposing the "head" and "heart" in the Affections and minimizing Edwards's respect for "common morality" in the ethical writings. Zakai is right in saying that Edwards insisted on God's authority over the world and history, but he puts it in such absolutistic terms that he often seems to abandon historical analysis in favor of exhortation.Zakai's best contribution is in his search for the general framework of God's redemption of the "engine" driving history (120ff.; 213ff.). He finds the answer in "seasons" of revival such as the Great Awakening. This is true, but Edwards notes other special events like the Reformation that "promoted the work of redemption" (Works, 9. 272), but are not revivals in the usual sense. For Edwards, special events are of many kinds and are identified by interpretation based on God's Providence. As Miller claimed, interpretation is essential; without it we may have a chronicle of events, but no history. Zakai seems to underestimate this point and the many problems it poses.The book strikes me as one more attempt—George Marsden's recent book, Jonathan Edwards: A Life (New Haven, 2003), is another—to rescue Edwards from "profane" interpreters like Miller who saw that Edwards learned from the Enlightenment even though he challenged many of its ideas. In my view, Edwards can well take care of himself.John E. SmithYale UniversityCopyright © 2004 Journal of the History of Philosophy, Inc.... (shrink)