Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need (...) to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The emphasis on evidence based medicine (EBM) has placed increased focus on finding timely answers to clinical questions in presence of patients. Using a combination of natural language processing for the generation of clinical excerpts and information theoretic distance based clustering, we evaluated multiple approaches for the efficient presentation of context-sensitive EBM excerpts.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Keith Ansell-Pearson, An Introduction to Nietzsche as Political Thinker (Cambridge: Cambridge University Press, 1994) hb: 0-521-41722-8. pb: 0-521-42721-5. Paul Patton, ed., Nietzsche, Feminism and Political Theory (London: Routledge. 1993) 0-4150-8256-0. Lester M. Hunt, Nietzsche and the Origin of Virtue (London: Routledge, 1993) 0-4150-9580-8. David Owen, Maturity and Modernity. Nietzsche, Weber, Foucault and the Ambivalence of Reason (London: Routledge, 1994) 0-4150-5398-6. Peter Lassmann and Ronald Spiers, eds., Weber: Political Writings (Cambridge: Cambridge University Press. 1994) hb: 0-521 -39312-4. pb: 0-521 -39719-7. Friedrich (...) Nietzsche, On the Genealogy of Morality and Other Writings, ed. Keith Ansell-Pearson, tr. Carol Diethe (Cambridge University Press, 1994) hb: 0-521-40459-2. pb: 0-521-40610-2. (shrink)

'Justice' and 'democracy' have alternated as dominant themes in political philosophy over the last fifty years. Since its revival in the middle of the twentieth century, political philosophy has focused on first one and then the other of these two themes. Rarely, however, has it succeeded in holding them in joint focus. This volume brings together leading authors who consider the relationship between democracy and justice in a set of specially written chapters. The intrinsic justness of democracy is challenged, the (...) relationship between justice, democracy and impartiality queried and the relationship between justice, democracy and the common good examined. Further chapters explore the problem of social exclusion and issues surrounding sub-national groups in the context of democracy and justice. Authors include Keith Dowding, Richard Arneson, Norman Schofield, Albert Weale, Robert E. Goodin, Jon Elster, David Miller, Phillip Pettit, Julian LeGrand and Russell Hardin. (shrink)

The existential analysis -- The death of dasein -- The timeliness of dasein -- The derivation of time -- The time of being.

By triangulating these three unique perspectives on culture, she expands prevalent views of cultural criticism and opens up the discussion to new creative solutions that arise from the intersecting interests of poststructuralist, feminist, and religious studies."--BOOK JACKET.

Le problème philosophique du principe, tout particulièrement et exemplairement dans son traitement métaphysique, réside dans la difficulté à conjoindre d’un côté l’unité, l’antériorité, la supériorité, la différence, la transcendance du principe vis-à-vis de ce dont il est principe (sans quoi le principe n’est pas principe), et de l’autre côté la présence ou la relation effective du principe à la multiplicité dont il est principe (sans quoi le principe n’est principe de rien). Cette double di...

López-Escobar, E. G. K. Introduction.--Kueker, D. W. Back-and-forth arguments and infinitary logics.--Green, J. Consistency properties for finite quantifier languages.--Cunningham, E. Chain models.--Gregory, J. On a finiteness condition for infinitary languages.

New Tenth Anniversary edition of this classic text with a new preface by the author, compares myths about meat-eating with myths about manliness, and seeks to ...

We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...) have fostered the growth of modern evidence-based medicine. Although in this paper we focus on ontologies, the methodology can be generalized to other sorts of terminology-based artifacts, including Electronic Patient Records. (shrink)

In this accessible book, Barry Hallen discusses the major ideas, figures, and schools of thought in African philosophy. While drawing out critical issues in the formation of African philosophy, Hallen focuses on the recent scholarship, current issues, and relevant debates that have made African philosophy an important key to understanding the rich and complex cultural heritage of Africa. Hallen builds upon Africa's connections with Western philosophical traditions and explores African contributions to cultural universalism, cultural relativism, phenomenology, hermeneutics, and Marxism. Hallen (...) also examines African challenges to Western conceptions of philosophy by taking on questions such as whether philosophy can exist in cultures that are significantly based in oral traditions and what may or may not constitute philosophical texts. Among the figures whose work is discussed are Ptah-hotep, Zar'a Ya'aqob, Anton Wilhelm Amo, Paulin Hountondji, V. Y. Mudimbe, Oyeronke Oyewumi, Kwame Anthony Appiah, and Kwasi Wiredu. This clearly written, highly readable, and concise work will be essential for students and scholars of African philosophy as well as readers with a wide range of interests in African studies. (shrink)

People frequently gesture when problem-solving, particularly on tasks that require spatial transformation. Gesture often facilitates task performance by interacting with internal mental representations, but how this process works is not well understood. We investigated this question by exploring the case of mental abacus, a technique in which users not only imagine moving beads on an abacus to compute sums, but also produce movements in gestures that accompany the calculations. Because the content of MA is transparent and readily manipulated, the task (...) offers a unique window onto how gestures interface with mental representations. We find that the size and number of MA gestures reflect the length and difficulty of math problems. Also, by selectively interfering with aspects of gesture, we find that participants perform significantly worse on MA under motor interference, but that perceptual feedback is not critical for success on the task. We conclude that premotor processes involved in the planning of gestures are critical to mental representation in MA. (shrink)

Reasoning about ulterior motives was investigated among children ages 6–10 years (total N = 119). In each of two studies, participants were told about children who offered gifts to peers who needed help. Each giver chose to present a gift in either a public setting, which is consistent with having an ulterior motive to enhance one's reputation, or in a private setting, which is not consistent with having an ulterior motive. In each study, the 6- to 7-year olds showed no (...) evidence of understanding that the public givers might have ulterior motives, but the 8- to 10-year olds rated the private givers more favorably. In , the older children were more likely than the younger children to refer to impression management when explaining their judgments of the givers. The younger children who mentioned impression management did so to justify a preference for public givers (e.g., by explaining that public givers are nicer because more of their peers will know that they are nice). Results from suggest that developmental change in children's reasoning about intentions and social outcomes contributes to their understanding of ulterior motives. (shrink)

Deeply rooted structures of racism, ableism, misogyny, ageism, and transphobia hurt great numbers of people, exposing them to intolerance, economic exclusion, and physical harm around the globe. Billions of land animals suffer and die annually in concentrated feeding operations and slaughterhouses. Our planet and all who live here are in perilous straights as the climate changes. In the face of such grievous problems, people who want to find positive ways to respond often grapple with difficult questions about how to make (...) a difference. Effective Altruism has arisen as an attempt to help answer these questions, encouraging people to give as much money as they can in the most effective ways to address human and animal suffering. But the Effective Altruists’ answers support some of the very social structures that cause suffering, undermining its efforts to “do the most good.” The Good It Promises, The Harm It Does is the first book-length critique of Effective Altruism. It brings together a diverse group of activists and scholars to explore Effective Altruism’s failure to meaningfully address forms of human and animal suffering. (shrink)

Pateman challenges the way contemporary society functions by questioning the standard interpretation of an idea that is deeply embedded in American and British political thought: that our rights and freedoms derive from the social contract explicated by Locke, Hobbes, and Rousseau and interpreted in the United States by the Founding Fathers. The author shows how we are told only half the story of the original contract that establishes modern patriarchy. The sexual contract is ignored and thus men's patriarchal right over (...) women is also glossed over. No attention is paid to the problems that arise when women are excluded from the original contract but incorporated into the new contractual order. One of the main targets of the book is those who try to turn contractarian theory to progressive use, and a major thesis of the book is that this is not possible. Thus those feminists who have looked to a more "proper" contract- one between genuinely equal partners, or one entered into without any coercion- are misleading themselves. In the author's words, "In contract theory universal freedom is always a hypothesis, a story, a political fiction. Contract always generates political right in the forms of domination and subordination." Thus the book is also aimed at mainstream political theorists, and socialist and other critics of contract theory. The author offers a sweeping challenge to conventional understandings- of both left and right- of actual contracts in everyday life: the marriage contract, the employment contract, the prostitution contract, and the new surrogate mother contract. By bringing a feminist perspective to bear on the contradictions and paradoxes surrounding women and contract, and the relation between the sexes, she is able to shed new light on fundamental political problems of freedom and subordination. (shrink)

In just a few years, the book became an underground classic. Neither Man Nor Beast takes Adams' thought one step further.

To show that discrimination against the terminally ill is a real and worrisome phenomenon Reed presents four examples1. Here, I focus on the final two: right-to-try and right-to-die laws. I argue that they are not instances of discrimination, because they grant rights. Reed appears to have overlooked that rights differ from obligations in ways that leave his argumentation unsuccessful. According to the most prominent theory of rights, rights function to protect the personal interests of their holders.2 For that reason, strengthening (...) rights implies weakening discrimination. Granting women the right to vote by itself meant that they were being less discriminated against. Rights also fail to meet standardly accepted definitions of discrimination. As Reed explains, for discrimination to occur, it is necessary that a significant disadvantage is imposed on a socially salient group. Policies can impose disadvantages by being obligations. While rights sometimes enable disadvantages, they never impose them. More precisely, rights may entitle their holders to subject themselves to disadvantages. The right to try entitles the terminally ill to subject themselves to harms caused by investigational drugs. The right to die entitles the terminally ill to voluntarily subject themselves to the deprivation of life. Contrast this with a policy that requires the terminally ill to take investigational drugs. Such a policy would be discriminatory. Whether rights can nevertheless …. (shrink)

The Carol J. Adams Reader gathers together Adams's foundational and recent articles in the fields of critical studies, animal studies, media studies, vegan studies, ecofeminism and feminism, as well as relevant interviews and conversations in which Adams identifies key concepts and new developments in her decades-long work. This volume, a companion to The Sexual Politics of Meat (Bloomsbury Revelations), offers insight into a variety of urgent issues for our contemporary world: Why do batterers harm animals? What is the relationship (...) between genocide and attitudes toward other animals? How do activism and theory feed each other? How do race, gender, and species categories interact in strengthening oppressive attitudes? In clear language, Adams identifies the often hidden aspects of cultural presumptions. The essays and conversations found here capture the decades-long energy and vision that continue to shape new ways of thinking about and responding to oppression. (shrink)

Barry Schein proposes combining a second-order treatment of plurals with DonaldDavidson's suggestion that there are positions for reference to events in ordinary predicates inorder to account for several of the more puzzling features of ...

Shows that current elitist theories are based on an inadequate understanding of the early writings of democratic theory and that much sociological evidence has been ignored.

Carol Zaleski's book is the first objective, comprehensive survey of the mass of evidence surrounding near-death experiences: the extraordinary visions and ecstatic feelings reported by people who have survived a close brush with death. Comparing recent near-death narratives with those of a much earlier period she finds both profound similarities and striking contrasts.

Acceptance of Humean Supervenience and thereductive Humean analyses that entail it leadsto a litany of inadequately explained conflictswith our intuitions regarding laws andpossibilities. However, the non-reductiveHumeanism developed here, on which law claimsare understood as normative rather than factstating, can accommodate those intuitions. Rational constraints on such norms provide aset of consistency relations that ground asemantics formulated in terms offactual-normative worlds, solving theFrege-Geach problem of construing unassertedcontexts. This set of factual-normative worldsincludes exactly the intuitive sets ofnomologically possible worlds associated witheach possible (...) set of laws. The extension ofthe semantics to counterfactual and subjunctiveconditionals is sketched. Potential objectionsinvolving subjectivity, mind-dependence, andnon-factuality are discussed. (shrink)

In this essay, I will argue that contemporary ecofeminist discourse, while potentially adequate to deal with the issue of animals, is now inadequate because it fails to give consistent conceptual place to the domination of animals as a significant aspect of the domination of nature. I will examine six answers ecofeminists could give for not including animals explicitly in ecofeminist analyses and show how a persistent patriarchal ideology regarding animals as instruments has kept the experience of animals from being fully (...) incorporated within ecofeminism. (shrink)

In this essay, I will argue that contemporary ecofeminist discourse, while potentially adequate to deal with the issue of animals, is now inadequate because it fails to give consistent conceptual place to the domination of animals as a significant aspect of the domination of nature. I will examine six answers ecofeminists could give for not including animals explicitly in ecofeminist analyses and show how a persistent patriarchal ideology regarding animals as instruments has kept the experience of animals from being fully (...) incorporated within ecofeminism.2. (shrink)

Carole Pateman is one of the leading political theorists writing today. This wide-ranging volume brings together for the first time a selection of her work on democratic theory and feminist criticism of mainstream political theory. The volume includes substantial discussions of problems of democracy, citizenship and the welfare state, including the largely unrecognized difficulties surrounding women's participation. The inclusion of essays from both a mainstream and feminist perspective provides concrete examples of the differences between these two approaches to democracy, to (...) questions of consent and political obligation, and to the relationship between the private and public spheres. This scholarly and highly challenging work will be of interest to students and researchers in political theory, political science, women's studies and sociology. (shrink)

This article considers the implications for film analysis of the presence or absence of a manual crank. More specifically, it looks at the 16 mm Time and Motion Study Projector as used in behavioral research in the 1960s and 1970s. The controversial concept of ‘interactional synchrony’, or the dance-like coordination of people in conversation, emerged from the use of this hand-turned projector. William S. Condon developed the concept along with the technique of microanalysis. Starting with the projector manufactured by Bell (...) & Howell, he made numerous improvements to facilitate observation—‘sweeping’ over segments of very short duration to discover the rhythmic synchrony of all filmed participants. It led him to a theory of ‘process’ in communication, and in the reception of speech in particular. People always ‘danced’ to the tune of their own voice, and their listeners ‘danced’ to the tune of the speaker—at intervals of one-sixth or one-eighth of a second. This also led Condon to an epistemology of discovery derived partly from philosophy but mostly from his machinery. The universe, he said, is a ‘continuum of order’ whose structures are preserved through translations of order: of thought into speech, speech into vibrations, vibrations into neurons, and back into behavior. The only exceptions are people with disabilities, like the autistics Condon studied from the 1970s onward. But the very distinction of normal and pathological was epiphenomenal to his scanning technique; it was rooted in material and formal qualities of film and of the projector whose crank he turned often. (shrink)

Whether we're buying a pair of jeans, ordering a cup of coffee, selecting a long-distance carrier, applying to college, choosing a doctor, or setting up a 401(k), everyday decisions ; both big and small ; have become increasingly complex due to the overwhelming abundance of choice with which we are presented. As Americans, we assume that more choice means better options and greater satisfaction. But beware of excessive choice: choice overload can make you question the decisions you make before you (...) even make them, it can set you up for unrealistically high expectations, and it can make you blame yourself for any and all failures. In the long run, this can lead to decision-making paralysis, anxiety, and perpetual stress. And, in a culture that tells us that there is no excuse for falling short of perfection when your options are limitless, too much choice can lead to clinical depression. In The Paradox of Choice, Barry Schwartz explains at what point choice ; the hallmark of individual freedom and self-determination that we so cherish ; becomes detrimental to our psychological and emotional well-being. In accessible, engaging, and anecdotal prose, Schwartz shows how the dramatic explosion in choice ; from the mundane to the profound challenges of balancing career, family, and individual needs ; has paradoxically become a problem instead of a solution. Schwartz also shows how our obsession with choice encourages us to seek that which makes us feel worse. By synthesizing current research in the social sciences, Schwartz makes the counter intuitive case that eliminating choices can greatly reduce the stress, anxiety, and busyness of our lives. He offers eleven practical steps on how to limit choices to a manageable number, have the discipline to focus on those that are important and ignore the rest, and ultimately derive greater satisfaction from the choices you have to make."--provided by publisher. (shrink)

This paper explores the analytical relevance of Foucault's notion of biopower in the context of regulating and managing non-human lives and populations, specifically those animals that are the focus of livestock breeding based on genetic techniques. The concept of biopower is seen as offering theoretical possibilities precisely because it is concerned with the regulation of life and of populations. The paper approaches the task of testing the 'analytic mettle' of biopower through an analysis of four policy documents concerned with farm (...) animal genetics: the UK's National Scrapie Plan (2003); the UK National Action Plan on Farm Animal Genetic Resources (2006); the Agriculture and Environment Biotechnology Committee's report on Animals and Biotechnology (2002); and the Farm Animal Welfare Council's report on the Welfare Implications of Animal Breeding and Breeding Technologies in Commercial Agriculture (2004). Of interest is whether and how the four policy case studies articulate a form of biopower in relation to human-livestock animal relations in the context of genetic approaches to livestock breeding, and how biopower is variably expressed in relation to the different policy issues addressed. In concluding, the paper considers the overall applicability and relevance of biopower in the context of regulating animal lives within livestock breeding, highlighting both possibilities and limitations, and offers suggestions for taking forward research on livestock populations from a neo-Foucaultian perspective. (shrink)

All the cards seem to be stacked against belief in immortality. Nonetheless, the resources of particular religious traditions may avail where generic philosophical solutions fall short. With attention to the boredom and narcissism critiques, intimations of deathlessness in Śāntideva's radical altruism, and recent Christian debates on the soul and the intermediate state, I propose two criteria for a coherent religion-specific belief in immortality: (1) the belief is supported by a fully realized religious tradition, (2) the belief satisfies the demand for (...) self-transcendence as well as for self-preservation. Where self-transcendence and self-preservation are kept in balance, and where the whole idea rests upon the lattice-work of a fully realized religious tradition, immortality is a fitting object of belief. Moreover, such belief is compatible with considerable speculative freedom concerning matter and spirit, body and soul, and personal identity over time. (shrink)