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)

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)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (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)

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)

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)

Many artists and music labels rely on partnerships with brands to pay for the production costs of their music videos. In exchange, the brands are featured in those videos. To enhance the transparency of these embedded forms of advertising, sponsorship disclosures are required. However, it remains unknown what the content of these disclosures in music videos should be to enhance sponsor transparency for adolescents. We examined how disclosure type affected adolescents’ conceptual and attitudinal persuasion knowledge. In addition, effects on responses (...) toward the brand, music video, and artist were examined. An experiment showed that none of the tested disclosures enhanced adolescents’ conceptual persuasion knowledge. However, disclosures explaining that the embedded brand helped pay for the production cost of the video led to lower attitudinal persuasion knowledge and, consequently, to more positive attitudes toward the brand, video, and artist, and to increased intentions to purchase the brand. (shrink)

Young single women's and men's cognitive scripts for the event “a first date” were examined to determine their content and to test for hypothesized differences in behavioral expectations. Participants were asked to list 20 expected actions involved in a first date for a woman and for a man. High agreement among participants was found for the content and sequence of actions that hypothetically would occur on a first date. The respondents listed a total of 19 different actions for women, and (...) 27 for men. The scripts for women and men differed significantly. The scripts for women emphasized the private sphere ; the scripts for men focused on control of the public domain. Gender roles were more prevalent in experienced daters' scripts. The results indicate that young adults' interpersonal scripts for dating maintain the traditional gender-power ratio. (shrink)

Would you want to be operated on by a surgeon trained at a medical school that did not evaluate its students? Would you want to fly in a plane designed by people convinced that the laws of physics are socially constructed? Would you want to be tried by a legal system indifferent to the distinction between fact and fiction? These questions may seem absurd, but these are theories being seriously advanced by radical multiculturalists that force us to ask them. These (...) scholars assert that such concepts as truth and merit are inextricably racist and sexist, that reason and objectivity are merely sophisticated masks for ideological bias, and that reality itself is nothing more than a socially constructed mechanism for preserving the power of the ruling elite. In Beyond All Reason, liberal legal scholars Daniel A. Farber and Suzanna Sherry mount the first systematic critique of radical multiculturalism as a form of legal scholarship. Beginning with an incisive overview of the origins and basic tenets of radical multiculturalism, the authors critically examine the work of Derrick Bell, Catherine MacKinnon, Patricia Williams, and Richard Delgado, and explore the alarming implications of their theories. Farber and Sherry push these theories to their logical conclusions and show that radical multiculturalism is destructive of the very goals it wishes to affirm. If, for example, the concept of advancement based on merit is fraudulent, as the multiculturalists claim, the disproportionate success of Jews and Asians in our culture becomes difficult to explain without opening the door to age-old anti-Semitic and racist stereotypes. If historical and scientific truths are entirely relative social constructs, then Holocaust denial becomes merely a matter of perspective, and Creationism has as much "validity" as evolution. The authors go on to show that rather than promoting more dialogue, the radical multiculturalist preferences for legal storytelling and identity politics over reasoned argument produces an insular set of positions that resist open debate. Indeed, radical multiculturalists cannot critically examine each others' ideas without incurring vehement accusations of racism and sexism, much less engage in fruitful discussion with a mainstream that does not share their assumptions. Here again, Farber and Sherry show that the end result of such thinking is not freedom but a kind of totalitarianism where dissent cannot be tolerated and only the naked will to power remains to settle differences. Sharply written and brilliantly argued, this book is itself a model of the kind of clarity, civility, and dispassionate critical thinking which the authors seek to preserve from the attacks of the radical multiculturalists. With far-reaching implications for such issues as government control of hate speech and pornography, affirmative action, legal reform, and the fate of all minorities, Beyond All Reason is a provocative contribution to one of the most important controversies of our time. (shrink)

Blue collar women in declining industries tend to suffer permanent job loss as a result of dislocation, and women living in rural areas may be particularly vulnerable to extended unemployment. Relatively little is known about their experiences, in part because existing conceptual models do not adequately represent women's perspectives. In this study it is proposed that an ethic of care, as conceptualized by Carol Gilligan, shapes women's interpretations of the meaning of job dislocation. Gilligan's constructs are applied to a study (...) of middle aged women who were dislocated when an apparel manufacturing plant in their rural Southern community closed unexpectedly. The focus is on three moral dilemmas and the opportunities for growth that occurred as a result of the crisis, as women reconstructed the meaning of the experience. The potential contributions of the ethic of care perspective to other studies of job loss is discussed. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

This theory accords to volitions the status of basic mental actions, maintaining that these are spontaneous exercises of the will--a "two-way" power which ...

There is accumulating evidence that disgust plays an important role in prejudice toward individuals with obesity, but that research is primarily based on self-reported emotions. In four studies, we examined whether participants displayed a physiological marker of disgust in response to images of obese individuals, and whether these responses corresponded with their self-reported disgust to those images. All four studies showed the predicted self-reported disgust response toward images of obese individuals. Study 1 further showed that participants exhibited more levator activity (...) to images of obese individuals than to neutral images. However, Studies 2–4 failed to provide any evidence that the targets’ body size affected levator responses. These findings suggest that disgust may operate at multiple levels, and that the disgust response to images of obese individuals may be more of a cognitive-conceptual one than a physiological one. (shrink)

Durkheim écrit ce livre avec un but double : d'abord il voulait expliquer ce qui crée une société, ce qui la tient ensemble ; ensuite il voulait éclaircir l'influence qu'a la société sur la pensée logique. Pour Durkheim, la religion est la clé utilisée pour déverrouiller ces deux problématiques.Dans ce livre, Durkheim argumente que les représentations religieuses sont en fait des représentations collectives : l'essence du religieux ne peut être que le sacré. Il est une caractéristique qui se trouve universellement (...) dans toutes les religions. Le sacré, être collectif et impersonnel, représente ainsi la société elle-même. Ensuite il argumente que la société a un impact majeur dans la genèse de la pensée logique. C'est la société qui fournit à l'individu les catégories (le temps, l'espace, le nombre etc.) et les concepts nécessaires pour la pensée logique. (shrink)

There is a long tradition in philosophy and literary theory defending the view that engagement with literature promotes readers’ empathy. Until the last century, few of the empirical claims adduced in that tradition were investigated experimentally. Recent work in psychology and neuropsychology has now shed new light on the interplay of empathy and literature. This article surveys the experimental findings, addressing three central questions: What is it to read empathically? Does reading make us more empathic? What characteristics of literature, if (...) any, affect readers’ empathy? While experimental studies have delivered no conclusive answers to these questions, it has exposed their psychological complexity and constructed a more nuanced picture of the diverse ways in which literature interacts with our empathic capacities. (shrink)

With special emphasis on Foucault's many recently published lecture series this book provides an updated, comprehensive presentation of his most important diagnoses, his many ground-breaking analytical concepts as well as a systematic account of his unique conception of philosophy.

When we perceive an object, we perceive the object from a perspective. As a consequence of the perspectival nature of perception, when we perceive, say, a circular coin from different angles, there is a respect in which the coin looks circular throughout, but also a respect in which the coin's appearance changes. More generally, perception of shape and size properties has both a constant aspect—an aspect that remains stable across changes in perspective—and a perspectival aspect—an aspect that changes depending on (...) one's perspective on the object. How should we account for the perspectival aspect of spatial perception? We present a framework within which to discuss the perspectival aspect of perception and put forward three desiderata that any account of the perspectival aspect of perception should satisfy. We discuss views on which the perspectival aspect of perception is analyzed in terms of constitutively mind-dependent appearance properties as well as views on which the perspectival aspect of perception is analyzed in terms of representations of mind-independent perspectival properties. (shrink)

First published in 1818, The World as Will and Representation contains Schopenhauer's entire philosophy, ranging through epistemology, metaphysics, philosophy of mind and action, aesthetics and philosophy of art, to ethics, the meaning of life and the philosophy of religion, in an attempt to account for the world in all its significant aspects. It gives a unique and influential account of what is and is not of value in existence, the striving and pain of the human condition and the possibility of (...) deliverance from it. This new translation of the first volume of what later became a two-volume work reflects the eloquence and power of Schopenhauer's prose and renders philosophical terms accurately and consistently. It offers an introduction, glossary of names and bibliography, and succinct editorial notes, including notes on the revisions of the text which Schopenhauer made in 1844 and 1859. (shrink)

We argue that the trend toward providing users with feasible and actionable explanations of AI decisions—known as recourse explanations—comes with ethical downsides. Specifically, we argue that recourse explanations face several conceptual pitfalls and can lead to problematic explanation hacking, which undermines their ethical status. As an alternative, we advocate that explanations of AI decisions should aim at understanding.

In his Treatise, Hume confronted the tensions between his project of uncovering the causal operations of the human mind and the extreme skeptical tendencies of his system. Louis Loeb argues that Hume overreaches, and he advances a controversial interpretation of Hume's epistemological framework that shows how Hume could have avoided the more destructive positions in his work.

Hume's claim that a state is a belief is often intertwined—though without his remarking on this fact—with epistemic approval of the state. This requires explanation. Beliefs, in Hume's view, are steady dispositions (not lively ideas), nature's provision for a steady influence on the will and action. Hume's epistemic distinctions call attention to circumstances in which the presence of conflicting beliefs undermine a belief's influence and thereby its natural function. On one version of this interpretation, to say that a belief is (...) justified, ceteris paribus, is to say that for all that has been shown the belief would be steady in its influence under suitable reflection. On a second version, it is to say that prima facie justification is an intrinsic property of the state, in virtue of its steadiness. These versions generate different understandings of the relationship between Parts iii and iv of Book I of the Treatise. (shrink)

A dialogue between a foreign philosopher and a powerful statesman outline Plato's reflections on the family, the status of women, property rights, and criminal law.

The Anthropocene is heralded as a new epoch distinguishing itself from all foregoing eons in the history of the Earth. It is characterized by the overarching importance of the human species in a number of respects, but also by the recognition of human dependence and precariousness. A critical human turn affecting the human condition is still in the process of arriving in the wake of an initial Copernican Revolution and Kant's ensuing second Copernican Counter-revolution. Within this landscape, issues concerning the (...) human - its finitude, responsiveness, responsibility, maturity, auto-affection and relationship to itself - appear rephrased and re-accentuated as decisive probing questions. In this book Sverre Raffnsøe explores how the change has ramifications for the kinds of knowledge that can be acquired concerning human beings and for the human sciences as a study of human existential beings in the world. (shrink)

Criticism on Bhagavadgītā, Hindu sacred work.

This article critically reflects on the research portfolio by the ecological economist Clive Spash who has helped pinpoint specific and systemic blindspots in a political-economic system that prioritises myopic development trajectories divorced from ecological reality. Drawing on his published work and collaborations it seeks to make sense of the slow, or absent, progress in averting global warming and ecological destruction. Three strands of key concern and influence are identified and discussed with reference to their orientation and explicit expression regarding Ontology, (...) Epistemology and Axiology. Some complementary points about indeterminacy and holism are presented to further strengthen the arguments for a transition towards a social-ecological economic system that puts values and principles back into focus. While Clive Spash's work has made a strong case within the economic community and appealing to ecology professionals, the value-myopia or value-vacuum has to be tackled across all disciplines, politics and society for a meaningful and urgently required transformation in decision making. Hence, the article finishes with some suggestions for the (higher) education system, and highlights the importance of simplicity and sufficiency, as well as strong sustainability-driven citizen and community action as necessary catalysts of change in this social-ecological transformation. (shrink)