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)

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 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) 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)

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; 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)

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)

Almost every country today contains adherents of different religions and different secular conceptions of the good life. Is there any alternative to a power struggle among them, leading most probably to either civil war or repression? The argument of this book is that justice as impartiality offers a solution. According to the theory of justice as impartiality, principles of justice are those principles that provide a reasonable basis for the unforced assent of those subject to them. The object of this (...) book is to set the theory out, explain its rationale, and respond to a variety of criticism that have been made of it. As the second volume of his work-in-progress, A Treatise on Social Justice, this work lies at the heart of a thriving academic debate which the author has played a key role in shaping. (shrink)

Meaning, Understanding, and Practice is a selection of the most notable essays of leading contemporary philosopher Barry Stroud on a set of topics central to analytic philosophy. In this collection, Stroud offers penetrating studies of meaning, understanding, necessity, and the intentionality of thought. Throughout he asks how much can be expected from a philosophical account of one's understanding of the meaning of something, and questions whether such an account can succeed without implying that the person understands many other things as (...) well. Most of the essays work with ideas derived from Wittgenstein, and five of the essays focus specifically on Wittgenstein's philosophy. Stroud's helpful introduction draws out the recurring themes he pursues and explains how his ideas and aims have developed over the years. (shrink)

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

How to formulate the doctrine of relativism -- Evaluating the doctrine of relativism.

In this book, Carol Gould offers a fundamental reconsideration of the theory of democracy, arguing that democratic decision-making should apply not only to politics but also to economic and social life. Professor Gould redefines traditional concepts of freedom and social equality, and proposes a principle of Equal Positive Freedom in which individual freedom and social co-operation are seen to be compatible. Reformulating basic conceptions of property, authority, economic justice and human rights, the author suggests a number of ways in (...) which these principles could be realised in social institutions. She also discusses such issues as democratic control of technology, the nature of democratic personality, and the question of democracy in international relations. (shrink)

In this book, Carol Gould offers a fundamental reconsideration of the theory of democracy, arguing that democratic decision-making should apply not only to politics but also to economic and social life. Professor Gould redefines traditional concepts of freedom and social equality, and proposes a principle of Equal Positive Freedom in which individual freedom and social co-operation are seen to be compatible. Reformulating basic conceptions of property, authority, economic justice and human rights, the author suggests a number of ways in (...) which these principles could be realised in social institutions. She also discusses such issues as democratic control of technology, the nature of democratic personality, and the question of democracy in international relations. (shrink)

The essays in this volume explore the full range of Husserl's work and reveal just how systematic his philosophy is. There are treatments of his most important contributions to phenomenology, intentionality and the philosophy of mind, epistemology, the philosophy of language, ontology, and mathematics. An underlying theme of the volume is a resistance to the idea, current in much intellectual history, of a radical break between 'modern' and 'postmodern' philosophy, with Husserl as the last of the great Cartesians. Husserl is (...) seen in this volume as a philosopher constantly revising his system in order to be able to integrate philosophy with ideas emanating from science and culture. The so-called rift between analytic and 'continental' philosophy emerges as an artificial construct. (shrink)

Can there be a theory-free experience? And what would be the object of such an experience. Drawing on ideas set out by Husserl in the “Crisis” and in the second book of his “Ideas”, the paper presents answers to these questions in such a way as to provide a systematic survey of the content and ontology of common sense. In the second part of the paper Husserl’s ideas on the relationship between the common-sense world (what he called the ‘life-world’) and (...) the world of physical theory are subjected to a critical evaluation. The relation of Husserl’s ideas to current work in folk psychology and naive physics and to the direct realism of J. J. Gibson are also treated. (shrink)

This volume brings together exciting and provocative new feminist readings of famous classic and contemporary texts from Plato to Habermas.

Barry Dainton presents a fascinating new account of the self, the key to which is experiential or phenomenal continuity. Provided our mental life continues we can easily imagine ourselves surviving the most dramatic physical alterations, or even moving from one body to another. It was this fact that led John Locke to conclude that a credible account of our persistence conditions - an account which reflects how we actually conceive of ourselves - should be framed in terms of mental rather (...) than material continuity. But mental continuity comes in different forms. Most of Locke's contemporary followers agree that our continued existence is secured by psychological continuity, which they take to be made up of memories, beliefs, intentions, personality traits, and the like. Dainton argues that that a better and more believable account can be framed in terms of the sort of continuity we find in our streams of consciousness from moment to moment. Why? Simply because provided this continuity is not lost - provided our streams of consciousness flow on - we can easily imagine ourselves surviving the most dramatic psychological alterations. Phenomenal continuity seems to provide a more reliable guide to our persistence than any form of continuity. The Phenomenal Self is a full-scale defence and elaboration of this premise. The first task is arriving at an adequate understanding of phenomenal unity and continuity. This achieved, Dainton turns to the most pressing problem facing any experience-based approach: losses of consciousness. How can we survive them? He shows how the problem can be solved in a satisfactory manner by construing ourselves as systems of experiential capacities. He then moves on to explore a range of further issues. How simple can a self be? How are we related to our bodies? Is our persistence an all-or-nothing affair? Do our minds consist of parts which could enjoy an independent existence? Is it metaphysically intelligible to construe ourselves as systems of capacities? The book concludes with a novel treatment of fission and fusion. (shrink)

This book is an indispensable resource for anyone interested in the roots, current debates and future development of social theory. It draws together a team of international scholars, and presents an authoritative and panoramic critical survey of the field. The first section, examines the classical tradition. Included here are critical discussions of Comte, Spencer, Marx, Durkheim, Weber, Simmel, Mead, Freud, Mannheim and classical feminist thought, demonstrating not only the critical significance of classical writings, but also their continuing relevance. The second (...) section moves on to examine the terrain of contemporary social theory. The contributors discuss the significance and strengths and weaknesses of structural functionalism, recent Marxian theory, critical theory, symbolic interactionism, phenomenology, exchange theory, contemporary feminism, ethnomethodology, rational choice theory, figurational sociology, the thought of Foucault, multicuturalism and postmodernism. The final section looks at the key debates in current social theory. Questions relating to the body, sexuality, globalism, nationalism, socialism, knowledge, norms, ethics, positivism, post-structuralism, consumption, metatheorizing and cultural studies are fully discussed. The dilemmas and promise of contemporary social theory are revealed with pinpoint accuracy. (shrink)

This book is available either individually, or as part of the specially-priced Arguments of the Philosphers Collection.

Essai montaignien, maximes et fragments, confessions, exercice spirituel, journal, mémoires ou autobiographies, autant de genres abordés dans ce volume. Certains relèvent d'une tradition de la méditation et de l'exercice spirituel, alors que d'autres sont plus inventifs. Les interprétations proposées ici invitent à réssusciter ce mouvement qui animait l'écriture avant qu'il ne se fige.

Describes what the author sees as a suppression of the feminine in Western culture, technology, and philosophy and opens a feminist postmodern space from which fresh differences may emerge. This title explores underdeveloped themes in American and Canadian feminism. It offers a deconstruction of the phallocentric dichotomies of nature and culture.

`In the grand tradition of classical social theory, Barry Smart challenges us to face up to the ambivalences of the contemporary moment and to take responsibility for our individual and social existence' - Douglas Kellner, University of California, Los Angeles ` a brilliant excursus through modern social theory, Smart’s book should be read and re-read for its careful analysis of the dilemmas of morality in postmodernism' - Bryan S. Turner, Deakin University Through a critical discussion of the 'ambivalent fruits' of (...) social analysis, exemplified in particular by the work of Foucault, Derrida, Lyotard, Baudrillard, Vattimo, Beck, Bourdieu, Goffman, Giddens, Levinas and Bauman, this book submits that an important responsibility of social enquiry today is to engage critically with the moral difficulties and ethical dilemmas which have arisen in relation to modernity. Facing Modernity offers a wide-ranging analysis of the ways in which issues of reflexivity, ethics and moral responsibility inform social and political thought. This is illustrated with the examples of risk society, modern forms of subjectivity and the problematic relationship between care of the self and a concern for others, the fashioning of the body, the idea and the practice of justice, and the communitarian call to regulate the pursuit of self interest and rediscover 'community'. A comprehensive overview of the ambiguities and moral dilemmas of modernity, this book will be essential reading for students of sociology, social theory and cultural studies. (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)

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)

Assuming that liberalism, liberal democracy, and the free market are here to stay, this book asks how sustainability can be interpreted in ways that respect liberal democratic values and institutions. Among the problems addressed are the compatibility of liberal procederalism with substantive "green" ideals, the existence and potential of eco-friendly principles and ideas in clasical liberal political theory, the role of rights and duties and of democracy and deliberation, and the "greening" potential of modern environmentally-focused practices in liberal democracies.