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) 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.

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)

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.

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 ...

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

The world as we experience it is full of colour. This book defends the radical thesis that no physical object has any of the colours we experience it as having. The author provides a unified account of colour that shows why we experience the illusion and why the illusion is not to be dispelled but welcomed. He develops a pluralist framework of colour-concepts in which other, more sophisticated concepts of colour are introduced to supplement the simple concept that is presupposed (...) in our ordinary colour experience. The discussion draws on philosophical and scientific literature, both historical and modern, but it is not technical, and will appeal to a broad range of philosophers, cognitive scientists and historians of science. (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)

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

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)

The idea that research should become more interdisciplinary has become commonplace. According to influential commentators, the unprecedented complexity of problems such as climate change or the social implications of biomedicine demand interdisciplinary efforts integrating both the social and natural sciences. In this context, the question of whether a given knowledge practice is too disciplinary, or interdisciplinary, or not disciplinary enough has become an issue for governments, research policy makers and funding agencies. Interdisciplinarity, in short, has emerged as a key political (...) preoccupation; yet the term tends to obscure as much as illuminate the diverse practices gathered under its rubric. This volume offers a new approach to theorising interdisciplinarity, showing how the boundaries between the social and natural sciences are being reconfigured. It examines the current preoccupation with interdisciplinarity, notably the ascendance of a particular discourse in which it is associated with a transformation in the relations between science, technology and society. Contributors address attempts to promote collaboration between, on the one hand, the natural sciences and engineering and, on the other, the social sciences, arts and humanities. From ethnography in the IT industry to science and technology studies, environmental science to medical humanities, cybernetics to art-science, the collection interrogates how interdisciplinarity has come to be seen as a solution not only to enhancing relations between science and society, but the pursuit of accountability and the need to foster innovation. Interdisciplinarity is essential reading for scholars, students and policy makers across the social sciences, arts and humanities, including anthropology, geography, sociology, science and technology studies and cultural studies, as well as all those engaged in interdisciplinary research. It will have particular relevance for those concerned with the knowledge economy, science policy, environmental politics, applied anthropology, ELSI research, medical humanities, and art-science. (shrink)

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)

We have now reached the point at which cloud computing and other types of advanced infrastructure are bringing about a situation in which knowledge objects can be delivered in an efficient manner to hose who need to consume them. And just as highways were the infrastructure necessary for a manufacturing economy, serving as the arteries along which raw materials and manufactured goods coming in from all directions could flow, so we believe that ontologies will in the future provide an important (...) pillar in the infrastructure that is necessary for the accurate and safe delivery of all varieties of knowledge. (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)

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)

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)

This is the first comprehensive view of the work of scholars in several different disciplines contributing to the development of the psychology of science. This new field of inquiry is a systematic elaboration and application of psychological concepts and methods to clarify the nature of the scientific enterprise. While the psychology of science overlaps the philosophy, history, and sociology of science in important ways, its predominant focus is on individuals and small groups, rather than broad social institutions and concepts. The (...) introduction surveys the field and traces its evolution in a historical context. Several contributors address epistemological issues raised by the psychology of science. Subsequent chapters discuss developments in the cognitive psychology of science, scientific theory, and the influence of social relationships on scientists' work. The conclusion proposes an agenda for further progress in this new approach to understanding science. (shrink)

‘Eruv’ is a Hebrew word meaning literally ‘mixture’ or ‘mingling’. An eruv is an urban region demarcated within a larger urban region by means of a boundary made up of telephone wires or similar markers. Through the creation of the eruv, the smaller region is turned symbolically (halachically = according to Jewish law) into a private domain. So long as they remain within the boundaries of the eruv, Orthodox Jews may engage in activities that would otherwise be prohibited on the (...) Sabbath, such as pushing prams or wheelchairs, or carrying walking sticks. There are eruvim in many towns and university campuses throughout the world. There are five eruvim in Chicago, five in Brooklyn, twenty three in Queens and Long Island, and at least three in Manhattan. The US Supreme Court is (like most other major US Federal Government buildings) located within the eruv of Washington DC. In many cases, not all of those living within or near the area of an actual or proposed eruv will themselves be Orthodox Jews, and this has sometimes led to protests against eruv creation. It is such protests which triggered the writing of this essay. (shrink)

Introduction to Xenophon's work and overview of his philosophy. _Greece and Rome_ New Surveys in the Classics Vol 48.

Did Freud present a scientific hypothesis about the unconscious, as he always maintained and as many of his disciples keep repeating? This question has long prompted debates concerning the legitimacy and usefulness of psychoanalysis, and it is of utmost importance to Lacanian analysts, whose main project has been to stress Freud's scientific grounding. Here Jacques Bouveresse, a noted authority on Ludwig Wittgenstein, contributes to the debate by turning to this Austrian-born philosopher and contemporary of Freud for a candid assessment of (...) the early issues surrounding psychoanalysis. Wittgenstein, who himself had delivered a devastating critique of traditional philosophy, sympathetically pondered Freud's claim to have produced a scientific theory in proposing a new model of the human psyche. What Wittgenstein recognized--and what Bouveresse so eloquently stresses for today's reader--is that psychoanalysis does not aim to produce a change limited to the intellect but rather seeks to provoke an authentic change of human attitudes. The beauty behind the theory of the unconscious for Wittgenstein is that it breaks away from scientific, causal explanations to offer new forms of thinking and speaking, or rather, a new mythology. Offering a critical view of all the texts in which Wittgenstein mentions Freud, Bouveresse immerses us in the intellectual climate of Vienna in the early part of the twentieth century. Although we come to see why Wittgenstein did not view psychoanalysis as a science proper, we are nonetheless made to feel the philosopher's sense of wonder and respect for the cultural task Freud took on as he found new ways meaningfully to discuss human concerns. Intertwined in this story of Wittgenstein's grappling with the theory of the unconscious is the story of how he came to question the authority of science and of philosophy itself. While aiming primarily at the clarification of Wittgenstein's opinion of Freud, Bouveresse's book can be read as a challenge to the French psychoanalytic school of Lacan and as a provocative commentary on cultural authority. (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)

The subject of personal identity is one of the most central and most contested and exciting in philosophy. Ever since Locke, psychological and bodily criteria have vied with one another in conflicting accounts of personal identity. Carol Rovane argues that, as things stand, the debate is unresolvable since both sides hold coherent positions that our common sense, she maintains, is conflicted; so any resolution to the debate is bound to be revisionary. She boldly offers such a revisionary theory of (...) personal identity by first inquiring into the nature of persons. Rovane begins with a premise about the distinctive ethical nature of persons to which all substantive ethical doctrines, ranging from Kantian to egoist, can subscribe. From this starting point, she derives two startling metaphysical possibilities: there could be group persons composed of many human beings and muliple persons within a single human being. Her conclusions supports Locke's distinction between persons and human beings, but on altogether new grounds. These grounds lie in her radically normative analysis of the condition of personal identity, as the condition in which a certain normative commitment arises, namely, the commitment to achieve overall rational unity within a rational point of view. It is by virtue of this normative commitment that individual agents can engage one another specifically as persons, and possess the distinctive ethical status of persons. Carol Rovan is Associate Professor of Philosophy at Yale University. Originally published in 1997. The Princeton Legacy Library uses the latest print-on-demand technology to again make available previously out-of-print books from the distinguished backlist of Princeton University Press. These editions preserve the original texts of these important books while presenting them in durable paperback and hardcover editions. The goal of the Princeton Legacy Library is to vastly increase access to the rich scholarly heritage found in the thousands of books published by Princeton University Press since its founding in 1905. (shrink)

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.

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 ...

In behavioral ethics today, there is debate as to which theory of moral development is the best for understanding ethical decision making, thereby facilitating ethical behavior. This debate between behavioral ethicists has been profoundly influenced by the field of moral psychology. Unfortunately, in the course of this marriage between moral psychology and business ethics and subsequent internal debate, a simple but critical understanding of human being in the field of management has been obscured; i.e., that morality is not a secondary (...) phenomenon arising out of something else. Therefore, in this paper, we will argue that there is a need in behavioral ethics to shift our understanding away from the influence of contemporary moral psychology and back to management theorist Ghoshal’s :75–91, 2005) view of what it means to be human in which the moral is fundamental. To assist in this labor, we will build on the philosophical work of Emmanuel Levinas who sees ethics, regardless of the setting, as a metaphysical concern. What this means is that Levinas sees the essential moral character of human life and the reality of human agency as ontologically fundamental, or constitutive of human nature itself. In other words, the ethical is the “first cause” in regard to understanding the nature and action of the individual, including within organizations. Thus, morality in any sphere of human endeavor, including in business, is not merely epiphenomenal to some more fundamental reality. (shrink)

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.

There is no broadly accepted definition of ‘life.’ Suggested definitions face problems, often in the form of robust counter-examples. Here we use insights from philosophical investigations into language to argue that defining ‘life’ currently poses a dilemma analogous to that faced by those hoping to define ‘water’ before the existence of molecular theory. In the absence of an analogous theory of the nature of living systems, interminable controversy over the definition of life is inescapable.

History has left a territory composed of two municipalitics, whose shape is unique, belonging partly to the Netherlands and partly to Belgium. Earlier both parts belonged to the former Duchy of Brabant, a tenitory that is now split up into the Dutch province of Noord-Brabant (including Baarle-Nassau) and thc Belgian provinces of Antwerp (which includes Baarle-Hertog), Vlaams Brabant, Brussels, and Brabant-Wallon. People are quite comfortable with this situation, even though it raises many complicated and difficult problems that even the most (...) brilliant jurists are puzzled. Baarle-Hertog is called on older Belgian maps Barle-Duc (Hertog = Duke, fr: duc) and must not be confused with the prefectoral town of Bar-le-Duc, Meuse, France. (shrink)