The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

In a morally fragmented society there is no good reason for ethics committees to assume any particular point of view, yet failure to do so compromises their ability to function in either a case‐review or an educational capacity. A casuist methodology might enable committees to fulfill both roles.

This commentary expands the discussion of Cesario's Missing Forces Flaw by identifying and discussing variables that influence police shooting decisions but are often absent from bias-based research. Additionally, the closing identifies novel recommendations for future contextually related research.

Judicial reasoning in termination of treatment decisions has neglected valid state interests in the preservation of life and the ethical integrity of medicine. Courts must balance these interests against individual liberty, rather than assuming that patient autonomy is absolute.

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)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)

In the philosophy of love, the possibility of loving a non-human animal is rarely acknowledged and often explicitly denied. And yet, loving a non-human animal is very common. Evidently, then, there is something wrong with both “human-focused” accounts (e.g. Niko Kolodny, Troy Jollimore), which assume we can only love human beings, and “person-focused” accounts (e.g. David Velleman, Bennett Helm), which understand the nature of love in terms of its being essentially directed toward those with a capacity for normative self-reflection (...) (i.e. “persons”). Even aside from the experiences of those who love a non-human animal, on which I draw, we already have reason to be worried about these latter, “person-focused,” views, insofar as they deny the possibility of loving the various human beings who do not meet their criteria for “personhood,” including at least some human beings with “severe” or “profound” cognitive disabilities. With this in mind, I argue that what we need is the (broader) notion of a “somebody” as a distinctive kind of love-object. This is the notion of a kind of presence of which we are acutely aware when, for example, we look into another’s eyes and see that there is “somebody home.” With this presence, there is a possibility of “togetherness,” and I suggest that it is precisely in the realm of togetherness that the possibility of love arises; the kind of love we speak of when we speak of loving our friends, family and romantic partners, and also, I argue, our animal companions. (shrink)

Nigel Blake; Church Schools, Religious Education and the Multi-ethnic Community: a reply to David Aspin, Journal of Philosophy of Education, Volume 17, Issue 2.

In lieu of an abstract, here is a brief excerpt of the content:Philosophy of Music Education Review 12.1 (2004) 67-70 [Access article in PDF] Response to Mary J. Reichling, "Intersections: Form, Feeling, and Isomorphism" David Stevenson Vassalboro, Maine Mary J. Reichling's essay regarding the three concepts, form, feeling, and isomorphism, is lucid, well structured, and aptly supported by research of other music education philosophers. She states her purpose in the opening paragraph: "to examine and to elucidate various aspects of (...) these three concepts in her [Susanne Langer's] writing, as they are fundamental to an understanding of her aesthetic theory and to the construction of a philosophy of music and music education."A philosophy of music education must be the focus in all ensuing debate, and must remain of paramount importance. Arguments, especially dialectic arguments, are not won or lost; they merely strip away the outer garments until more and more of the truth is exposed. My thoughts regarding Reichling's essay are offered in this vein.Reichling amply makes the point that music is a dynamic moving form. She asserts that "Langer argues that form is not separable from content," clarifying further by saying that "By content Langer is designating the form's import or meaning." And she offers other examples of dynamic, moving forms, among them, "forms created by movements of clouds or fog through the mist and early light." [End Page 67]At this point, perhaps interjecting the notion of perception is in order. I would suggest that the cloud formations offer no content or meaning outside of the viewer's perceptions or imagination. Music (art), being the nebulous subject that it is, ensconced in subjectivity and steeped in perception, both interpersonal and intrapersonal at the same time, exists to be taken by individuals, each at his or her own level of accomplishment, understanding, and interest. Therefore, does the meaning inhere in the form, as Langer and Reichling assert, or is it assigned by the listener (in the case of music) or by the viewer (in the case of the cloud formation)? "If the doors of perception were cleansed every thing would appear to man as it is: infinite."1 William Blake's observation notwithstanding, the truth is that perception is the only thing that we have with which to view our existence. I believe that there is such a thing as absolute truth, and that reality does exist. However, we mere mortals lack the ability to view the world through anything other than our own perceptions. The knowledge or meaning gained through contemplation of the form is, in all likelihood, quite different for each observer.Likewise, imagination and conceptual ability play a role in interpreting what the senses have perceived. Langer, and by quotation, Reichling, offers the notion of a red dot placed on the rim of a spinning wheel that appears to the viewer as a red circle. "When the spinning stops, the form, the red circle, evaporates. Did it really exist? Does it have ontological status? Is it merely an illusion?" I asked my students to close their eyes and imagine a spinning wheel with a red dot placed on the rim. I asked them, "As the wheel spins, do you see the dot?" The answer was that they saw a red circle. Did they really see a red circle, or even a spinning wheel? Of course not, we were in a music classroom. Yet they were able to conceptualize or imagine the image, and I would suggest that that carries more weight in the realm of art than does actual ontological status.The problem with the experiment of the preceding paragraph is that "Langer argues that form is not separable from content, writing that it is not possible 'to divorce the logical form from its one embodiment or expression.'" In the subsequent paragraph Reichling states, When the music stops, when the ballet is concluded, when the play ends, when the wheel stops spinning, memory may remain but the content (content as meaning-my parenthetical interjection), the feeling, the red circle, the image the dancer created is gone. Is this illogical or has knowledge... (shrink)

Questions could and should be raised about the political profile of English Romanticism both in particular and in general. Wordsworth’s poetry is especially useful to me here because of the way in which, through formal discontinuities, it dramatizes political conflicts. Reacting against these discontinuities, aesthetically minded critics have simply tended to leave out of the canon those poems which have the greatest capacity to help us become aware of a political poetics. In this respect it may well be that Wordsworth (...) is the most stylistically perverse of the Romantic poets. Not the most difficult to read, necessarily—Percy Bysshe Shelley’s breath-suspending songs and William Blake’s determination to produce “variety in every line” with the aim of unfettering poetry surely make more aggressive and obvious demands on the reader.1 But in these cases we can be reasonably sure that the difficulties are part of a conscious and coherent intention to set imagination to work in kindling sparks from ashes. Wordsworth also set out to do this, and we can agree that he did so with some success in some poems. But critics from Samuel Taylor Coleridge onward have rightly questioned the unity of Wordsworth’s canon in this respect. In Biographia Literaria, Coleridge notices the “inconstancy of the style,” an unevenness and a general inability to satisfy the demands of “good poetry” conceived as something possessing an organic form.2 This concern with a wholeness and consistency of artifice is more Coleridge’s than Wordsworth’s, and it seems to me that it is precisely the disjunctions in the poems that embody some of their most original and historically urgent meanings. The blemishes recorded by Coleridge—alternating and dissimilar states of feeling, overminuteness in description, and obsession with “accidental circumstances” , overuse of the dramatic mode, disproportion of thought to event, and so forth—can in fact serve as eloquent signals for discerning the complexities of the poems as they address a historical crisis in consensus embodied exactly in the unstable vehicle of the Wordsworthian speaker.3 3. I have explored the “formal” implications of this crisis in Irony and Authority in Romantic Poetry , and the terms of its historical discourse in Wordsworth and the Figurings of the Real . David Simpson is professor of English at Northwestern University. He is the author of Irony and Authority in Romantic Poetry , Wordsworth and the Figurings of the Real , and Fetishism and Imagination: Dickens, Melville, Conrad and editor of German Aesthetic and Literary Criticism: Kant, Fichte, Schelling, Schopenhauer, Hegel. (shrink)

Alex Zamalin's Black Utopia: The History of an Idea from Black Nationalism to Afrofuturism offers the most thorough scholarly survey of African American utopian literature currently available. The scope of the project is ambitious—the book's chapters proceed chronologically from the genre's utopian beginnings in Martin Delany's Blake; Or, the Huts of America, through the anti-utopian turn of the twentieth century found in texts such as George Schuyler's Black Empire, and concluding with the ambiguous utopias and heterotopias of Octavia Butler (...) and Samuel Delany. Unlike recent scholarship on black speculative fiction (andré m. carrington, Sandra Jackson... (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Philosophy of Music Education Review 12.1 (2004) 67-70 [Access article in PDF] Response to Mary J. Reichling, "Intersections: Form, Feeling, and Isomorphism" David Stevenson Vassalboro, Maine Mary J. Reichling's essay regarding the three concepts, form, feeling, and isomorphism, is lucid, well structured, and aptly supported by research of other music education philosophers. She states her purpose in the opening paragraph: "to examine and to elucidate various aspects of (...) these three concepts in her [Susanne Langer's] writing, as they are fundamental to an understanding of her aesthetic theory and to the construction of a philosophy of music and music education."A philosophy of music education must be the focus in all ensuing debate, and must remain of paramount importance. Arguments, especially dialectic arguments, are not won or lost; they merely strip away the outer garments until more and more of the truth is exposed. My thoughts regarding Reichling's essay are offered in this vein.Reichling amply makes the point that music is a dynamic moving form. She asserts that "Langer argues that form is not separable from content," clarifying further by saying that "By content Langer is designating the form's import or meaning." And she offers other examples of dynamic, moving forms, among them, "forms created by movements of clouds or fog through the mist and early light." [End Page 67]At this point, perhaps interjecting the notion of perception is in order. I would suggest that the cloud formations offer no content or meaning outside of the viewer's perceptions or imagination. Music (art), being the nebulous subject that it is, ensconced in subjectivity and steeped in perception, both interpersonal and intrapersonal at the same time, exists to be taken by individuals, each at his or her own level of accomplishment, understanding, and interest. Therefore, does the meaning inhere in the form, as Langer and Reichling assert, or is it assigned by the listener (in the case of music) or by the viewer (in the case of the cloud formation)? "If the doors of perception were cleansed every thing would appear to man as it is: infinite."1 William Blake's observation notwithstanding, the truth is that perception is the only thing that we have with which to view our existence. I believe that there is such a thing as absolute truth, and that reality does exist. However, we mere mortals lack the ability to view the world through anything other than our own perceptions. The knowledge or meaning gained through contemplation of the form is, in all likelihood, quite different for each observer.Likewise, imagination and conceptual ability play a role in interpreting what the senses have perceived. Langer, and by quotation, Reichling, offers the notion of a red dot placed on the rim of a spinning wheel that appears to the viewer as a red circle. "When the spinning stops, the form, the red circle, evaporates. Did it really exist? Does it have ontological status? Is it merely an illusion?" I asked my students to close their eyes and imagine a spinning wheel with a red dot placed on the rim. I asked them, "As the wheel spins, do you see the dot?" The answer was that they saw a red circle. Did they really see a red circle, or even a spinning wheel? Of course not, we were in a music classroom. Yet they were able to conceptualize or imagine the image, and I would suggest that that carries more weight in the realm of art than does actual ontological status.The problem with the experiment of the preceding paragraph is that "Langer argues that form is not separable from content, writing that it is not possible 'to divorce the logical form from its one embodiment or expression.'" In the subsequent paragraph Reichling states, When the music stops, when the ballet is concluded, when the play ends, when the wheel stops spinning, memory may remain but the content (content as meaning-my parenthetical interjection), the feeling, the red circle, the image the dancer created is gone. Is this illogical or has knowledge... (shrink)

By including aspects of human thought and culture in his system, Hegel invited comparison of his thought with other thinkers and even other genres. David Punter has made such a comparison in Blake, Hegel, and Dialectic. Such a comparative work is extremely difficult to pull off because of the difficulty of explicating the central concepts of two such great and diverse thinkers and then finding a common ground for comparison. Punter is a Blake scholar whose previous publications (...) reflect this interest. For a non-philosopher to tackle the concept of dialectic in Hegel is a difficult task indeed. (shrink)

An analysis of Geoffrey Hill's lyric poem about William Blake illuminates the relations between art, prophecy, and imperial politics across more than two centuries. Hill's poem responds to David V. Erdman's argument that Blake was resolutely, if ineffectually and sometimes secretly, opposed to war. It also establishes Hill's own cryptic but definite resistance to contemporary war and warmongers, while it mourns poetry's public powerlessness to halt the violent competition for material resources. Ignored by the majority, poetry fails (...) to bring about the ethical social change that poets often envision. The layering of perspectives (Hill the poet and scholar writing about Erdman the scholar, who is explicating Blake the poet and artist) allows for a multidimensional interpretation of the role of poets and prophetic poetry. Despite their fury at society's deafness and greed, and frustration at their own incapacities, poets—because if they are great poets, they are prophets, too—continue to speak to their audiences about the problems of this world and about the better worlds that can be imagined. Hill's text obliquely teaches how the small success of a great poem can provide a minor note of consolation as it objects to terror and tyranny. (shrink)

An analysis of Geoffrey Hill's lyric poem about William Blake illuminates the relations between art, prophecy, and imperial politics across more than two centuries. Hill's poem responds to David V. Erdman's argument that Blake was resolutely, if ineffectually and sometimes secretly, opposed to war. It also establishes Hill's own cryptic but definite resistance to contemporary war and warmongers, while it mourns poetry's public powerlessness to halt the violent competition for material resources. Ignored by the majority, poetry fails (...) to bring about the ethical social change that poets often envision. The layering of perspectives (Hill the poet and scholar writing about Erdman the scholar, who is explicating Blake the poet and artist) allows for a multidimensional interpretation of the role of poets and prophetic poetry. Despite their fury at society's deafness and greed, and frustration at their own incapacities, poets—because if they are great poets, they are prophets, too—continue to speak to their audiences about the problems of this world and about the better worlds that can be imagined. Hill's text obliquely teaches how the small success of a great poem can provide a minor note of consolation as it objects to terror and tyranny. (shrink)

In this book, which thoroughly revises and greatly expands his classic work Sameness and Substance, David Wiggins retrieves and refurbishes in the light of twentieth-century logic and logical theory certain conceptions of identity, of substance and of persistence through change that philosophy inherits from its past. In this new version, he vindicates the absoluteness, necessity, determinateness and all or nothing character of identity against rival conceptions. He defends a form of essentialism that he calls individuative essentialism, and then a (...) form of realism that he calls conceptualist realism. In a final chapter he advocates a human being-based conception of the identity and individuation of persons, arguing that any satisfactory account of personal memory must make reference to the life of the rememberer himself. This important book will appeal to a wide range of readers in metaphysics, philosophical logic, and analytic philosophy. (shrink)

Most theists accept an anthropomorphic view of the divine: a God whose cognition and incarnate embodiment closely resembles human cognition and human embodiment. Most theists also accept an Anselmian view of God on which God has the maximal set of ontological (including moral) perfections. This chapter defends the view that Anselmianism entails that the anthropomorphic view of God is false and that some nonhuman animal is divine. Two arguments are given for this position, which we can call zootheism. The first (...) argument, the Power Argument, claims that because nonhuman animals have moral interests, maximal fairness entails a share in power over those interests. This, in turn, entails a direct share of power within the Godhead, which entails that some nonhuman animal is divine. The second argument, the Incarnation Argument, hues closely to Christian arguments for an incarnation: because God loves us, God will share in our suffering and will pursue non-privileged kinds of incarnate embodiments. This naturally motivates incarnating as a nonhuman animal, particularly given the historically privileged status of humans. Moreover, maximal fairness and maximal love entail that God also pre-existed as a nonhuman animal. Thus, God is, and always was, a nonhuman animal. (shrink)

Drawing on work of the past decade, this volume brings together articles from the philosophy, history, and sociology of science, and many other branches of the biological sciences. The volume delves into the latest theoretical controversies as well as burning questions of contemporary social importance. The issues considered include the nature of evolutionary theory, biology and ethics, the challenge from religion, and the social implications of biology today (in particular the Human Genome Project).

Alvin Plantinga theorizes the existence of a sensus divinitatis – a special cognitive faulty or mechanism dedicated to the production and non-inferential justification of theistic belief. Following Chris Tucker, we offer an evidentialist-friendly model of the sensus divinitatis whereon it produces theistic seemings that non-inferentially justify theistic belief. We suggest that the sensus divinitatis produces these seemings by tacitly grasping support relations between the content of ordinary experiences (in conjunction with our background evidence) and propositions about God. Our model offers (...) advantages such as eliminating the need for a sui generis religious faculty, harmonizing the sensus divinitatis with prominent theories in the cognitive science of religion, and providing a superior account of natural revelation. (shrink)

The epistemic value of seemings is increasingly debated. Such debates are hindered, however, by a lack of consensus about the nature of seemings. There are four prominent conceptions in the literature, and the plausibility of principles such as phenomenal conservatism, which assign a prominent epistemic role to seemings, varies greatly from one conception to another. It is therefore crucial that we identify the correct conception of seemings. I argue that seemings are best understood as sui generis mental states with propositional (...) content and a distinct phenomenal character. Rival conceptions are shown to succumb to numerous difficulties. (shrink)

This book addresses concerns about educational and moral standards in a world increasingly characterised by nihilism. On the one hand there is widespread anxiety that standards are falling; on the other, new machinery of accountability and inspection to show that they are not. The authors in this book state that we cannot avoid nihilism if we are simply _laissez-faire_ about values, neither can we reduce them to standards of performance, nor must we return to traditional values. They state that we (...) need to create a new set of values based on a critical assessment of contemporary practice in the light of a number of philosophical texts that address the question of nihilism, including the work of Nietzsche. (shrink)

Creative accounting involves accountants in making accounting policy choices or manipulating transactions in such a way as to convey a preferred and deliberately chosen impression in the accounts. Although it is regarded as unethical by most observers, a defense of creative accounting can be based on the assumption that users of accounts can identify bias in accounting policy choices and make appropriate adjustments. In this paper we take the example of the Barcelona Football Club where the club management made three (...) key accounting policy choices that resulted in the presentation of a favourable position, and a supporters club presented an alternative report choosing three alternative accounting policies that presented an unfavourable position. We presented each of these financial reports to one of two groups of Spanish bank loan officers: we found that the more favourable set of accounts was significantly more likely to attract a positive response to a loan request. This result undermines the validity of defending creative accounting based on the argument that accounts users can identify manipulation. (shrink)

BackgroundAdvances in healthcare artificial intelligence (AI) are occurring rapidly and there is a growing discussion about managing its development. Many AI technologies end up owned and controlled by private entities. The nature of the implementation of AI could mean such corporations, clinics and public bodies will have a greater than typical role in obtaining, utilizing and protecting patient health information. This raises privacy issues relating to implementation and data security. Main bodyThe first set of concerns includes access, use and control (...) of patient data in private hands. Some recent public–private partnerships for implementing AI have resulted in poor protection of privacy. As such, there have been calls for greater systemic oversight of big data health research. Appropriate safeguards must be in place to maintain privacy and patient agency. Private custodians of data can be impacted by competing goals and should be structurally encouraged to ensure data protection and to deter alternative use thereof. Another set of concerns relates to the external risk of privacy breaches through AI-driven methods. The ability to deidentify or anonymize patient health data may be compromised or even nullified in light of new algorithms that have successfully reidentified such data. This could increase the risk to patient data under private custodianship.ConclusionsWe are currently in a familiar situation in which regulation and oversight risk falling behind the technologies they govern. Regulation should emphasize patient agency and consent, and should encourage increasingly sophisticated methods of data anonymization and protection. (shrink)

Lipsey and Lancaster's "general theory of second best" is widely thought to have significant implications for applied theorizing about the institutions and policies that most effectively implement abstract normative principles. It is also widely thought to have little significance for theorizing about which abstract normative principles we ought to implement. Contrary to this conventional wisdom, I show how the second-best theorem can be extended to myriad domains beyond applied normative theorizing, and in particular to more abstract theorizing about the normative (...) principles we should aim to implement. I start by separating the mathematical model used to prove the second-best theorem from its familiar economic interpretation. I then develop an alternative normative-theoretic interpretation of the model, which yields a novel second best theorem for idealistic normative theory. My method for developing this interpretation provides a template for developing additional interpretations that can extend the reach of the second-best theorem beyond normative theoretical domains. I also show how, within any domain, the implications of the second-best theorem are more specific than is typically thought. I conclude with some brief remarks on the value of mathematical models for conceptual exploration. (shrink)

The text of each poem is given in letterpress on the page facing the beautiful color reproductions of the plate. The book is printed on vellum.

The epistemic value of seemings is increasingly debated. Such debates are hindered, however, by a lack of consensus about the nature of seemings. There are four prominent conceptions in the literature, and the plausibility of principles such as phenomenal conservatism, which assign a prominent epistemic role to seemings, varies greatly from one conception to another. It is therefore crucial that we identify the correct conception of seemings. I argue that seemings are best understood as sui generis mental states with propositional (...) content and a distinct phenomenal character. Rival conceptions are shown to succumb to numerous difficulties. (shrink)

Early moderns such as Locke and Descartes thought we could guarantee the justification of our beliefs, even in worlds most hostile to their truth, if only we form those beliefs with sufficient care. That is, they thought it possible for us to be impeccable with respect to justification. This principle has traditionally been used to argue for internalism. By placing all of the normatively relevant conditions in our minds, we ensure reflective access to what those norms require of us and (...) so sustain the possibility of impeccability (unlike externalism). However, recent challenges to transparency leave this reasoning vulnerable. In response, I show how impeccability can be sustained without requiring transparency. The account only works if we define internal states as those directly accessible to our rational belief forming systems. I argue that this sort of causal internalism, while somewhat revisionary, preserves traditional motivations for internalism while avoiding problems faced by other varieties. The result is a renewed argument for internalism that simultaneously moves us away from access internalism and towards a species of mentalism. (shrink)

This chapter contains sections titled: Characteristics and Development of Critical Theory The Educational Relevance of Critical Theory Distinctive Insights and Contributions Differing Receptions of Critical Theory Critical Theory and the Student Movement An “Other” Critical Pedagogy?