According to the PubMed resource from the U.S. National Library of Medicine, over 750,000 scientific articles have been published in the ~5000 biomedical journals worldwide in the year 2007 alone. The vast majority of these publications include results from hypothesis-driven experimentation in overlapping biomedical research domains. Unfortunately, the sheer volume of information being generated by the biomedical research enterprise has made it virtually impossible for investigators to stay aware of the latest findings in their domain of interest, let alone to (...) be able to assimilate and mine data from related investigations for purposes of meta-analysis. While computers have the potential for assisting investigators in the extraction, management and analysis of these data, information contained in the traditional journal publication is still largely unstructured, free-text descriptions of study design, experimental application and results interpretation, making it difficult for computers to gain access to the content of what is being conveyed without significant manual intervention. In order to circumvent these roadblocks and make the most of the output from the biomedical research enterprise, a variety of related standards in knowledge representation are being developed, proposed and adopted in the biomedical community. In this chapter, we will explore the current status of efforts to develop minimum information standards for the representation of a biomedical experiment, ontologies composed of shared vocabularies assembled into subsumption hierarchical structures, and extensible relational data models that link the information components together in a machine-readable and human-useable framework for data mining purposes. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

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.

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)

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)

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)

It is plausible that there are epistemic reasons bearing on a distinctively epistemic standard of correctness for belief. It is also plausible that there are a range of practical reasons bearing on what to believe. These theses are often thought to be in tension with each other. Most significantly for our purposes, it is obscure how epistemic reasons and practical reasons might interact in the explanation of what one ought to believe. We draw an analogy with a similar distinction between (...) types of reasons for actions in the context of activities. The analogy motivates a two-level account of the structure of normativity that explains the interaction of correctness-based and other reasons. This account relies upon a distinction between normative reasons and authoritatively normative reasons. Only the latter play the reasons role in explaining what state one ought to be in. All and only practical reasons are authoritative reasons. Hence, in one important sense, all reasons for belief are practical reasons. But this account also preserves the autonomy and importance of epistemic reasons. Given the importance of having true beliefs about the world, our epistemic standard typically plays a key role in many cases in explaining what we ought to believe. In addition to reconciling (versions of) evidentialism and pragmatism, this two-level account has implications for a range of important debates in normative theory, including the interaction of right and wrong reasons for actions and other attitudes, the significance of reasons in understanding normativity and authoritative normativity, the distinction between ‘formal’ and ‘substantive’ normativity, and whether there is a unified source of authoritative normativity. (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 ...

A dogma of contemporary ethical theory maintains that the nature of normative support for affective attitudes is the very same as the nature of normative support for actions. The prevailing view is that normative reasons provide the support across the board. I argue that the nature of normative support for affective attitudes is importantly different from the nature of normative support for actions. Actions are indeed supported by reasons. Reasons are gradable and contributory. The support relations for affective attitudes are (...) neither. So-called reasons of the right kind for affective attitudes are facts that make those very attitudes fitting. Unlike reasons, fit-making facts for affective attitudes do not conflict with each other or combine in the explanation of further normative facts. More fit-making facts just make a more complex set of reactions fitting. This result undermines various analyses and unity theses in the philosophy of normativity. (shrink)

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)

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 develops the Value-Based Theory of Reasons in some detail. The central part of the paper introduces a number of theoretically puzzling features of normative reasons. These include weight, transmission, overlap, and the promiscuity of reasons. It is argued that the Value-Based Theory of Reasons elegantly accounts for these features. This paper is programmatic. Its goal is to put the promising but surprisingly overlooked Value-Based Theory of Reasons on the table in discussions of normative reasons, and to draw attention (...) to a number of areas for fruitful further research. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (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)

Distinguished scholar Barry Stroud presents a sustained and intricate philosophical argument based upon the question of whether physical objects are 'actually' coloured, or whether they merely appear to be so. He demonstrates how this specific question is inextricably linked to some of the most fundamental issues in metaphysics. He also questions the very nature and constitution of these specific metaphysical issues. This long-awaited model of subtle, elegant, and rigorous philosophical writing ahould have a wide readership among philosophers working in (...) all areas of philosophy. (shrink)

Originally published in 1984, this volume documents Bertrand Russelle(tm)s travels in America covering the period 1945-1970. It is presented in two halves with the first a biographical account of Russelle(tm)s involvement with the United States, with special reference to the seven visits he made there during this time period. Throughout this section the most representative of Russelle(tm)s journalistic writings are highlighted and these are presented as full texts in the second half of the book. This collection is assembled to provide (...) an understanding of Russelle(tm)s deep and many-sided involvement with the United States during his life. A documented account, it is supplemented with important letters, photographs and newspaper articles. (shrink)

The appeal of materialism lies precisely in this, in its claim to be natural metaphysics within the bounds of science. That a doctrine which promises to gratify our ambition (to know the noumenal) and our caution (not to be unscientific) should have great appeal is hardly something to be wondered at. (Putnam (1983), p.210) Materialism says that all facts, in particular all mental facts, obtain in virtue of the spatio- temporal distribution, and properties, of matter. It was, as Putnam says, (...) “metaphysics within the bounds of science”, but only so long as science was thought to say that the world is made out of matter.1 In this century physicists have learned that there is more in the world than matter and, in any case, matter isn’t quite what it seemed to be. For this reason many philosophers who think that metaphysics should be informed by science advocate physicalism in place of materialism. Physicalism claims that all facts obtain in virtue of the distribution of the fundamental entities and properties –whatever they turn out to be- of completed fundamental physics. Later I will discuss a more precise formulation. But not all contemporary philosophers embrace physicalism. Some- and though a minority not a small or un-influential one- think that physicalism is rather the metaphysics for an unjustified scientism; i.e. it is scientistic metaphysics. Those among them that think that physicalism can be clearly formulated think that it characterizes a. (shrink)

Faced with the paradox of undermining futures, Humeans have resigned themselves to accounts of chance that severely conflict with our intuitions. However, such resignation is premature: The problem is Humean supervenience (HS), not Humeanism. This paper develops a projectivist Humeanism on which chance claims are understood as normative, rather than fact stating. Rationality constraints on the cotenability of norms and factual claims ground a factual-normative worlds semantics that, in addition to solving the Frege-Geach problem, delivers the intuitive set of possibilia (...) for each chance law. Hence, the account does not entail HS, and the paradox does not arise. A confirmation theory is developed, and the 'principal principle' is justified. (shrink)

Henri Bergson (1859-1941) was once the most famous philosopher in the world, but his reputation waned in the latter half of the 20th century. Barry Allen here makes the case for Bergson as a great philosopher, one whose thought has much to contribute to contemporary philosophical questions. Living in Time presents chapters on each of Bergson's four major works, explaining his theories of time, perception, memory, and panpsychic consciousness, his innovative concept of virtual existence, his objection to Darwin, his (...) controversy with Einstein, his philosophy of creative evolution, and his social philosophy of closed and open society. In particular Allen focusses on Bergson's powerful ideas on time. Classical arguments for determinism fallaciously apply spatial concepts to consciousness; once we take time seriously, which means acknowledging its reality as duration and its difference from space, Bergson showed that the arguments for determinism become insupportable. Bergson's ideas on time and evolution offer a comparison with Nietzsche, which Allen develops, exposing both philosophical concurrence and systematic difference. The book's conclusion discusses the question of Bergson and naturalism and summarizes the ontology of the virtual that emerges as a core part of Bergson's thought. (shrink)

We argue that a particular approach to satisfying the broad predictive ambitions of the sciences demands law confirmation. On this approach we confirm non-nomic generalizations by confirming there are no actually realized ways of causing disconfirming cases. This gives causal generalizations a crucial role in prediction. We then show how rational judgements of relevant causal similarity can be used to confirm that causal generalizations themselves have no actual disconfirmers, providing a distinctive and clearly viable methodology for inductively confirming them. Finally, (...) we argue that for agents in our epistemic position using this methodology to confirm causal generalizations of adequate breadth will commonly demand law confirmation. We make a prima facie assessment of the methodology’s fit with scientific practice and briefly consider the prospects for an associated analysis of laws. (shrink)

We use normative reasons in a bewildering variety of different ways. And yet, as many recent theorists have shown, one can discern systematic distinctions underlying this complexity. This paper is a contribution to this project of constructive normative metaphysics. We aim to bring a black sheep back into the flock: the balancing model of weighing reasons. This model is threatened by a variety of cases in which distinct reasons overlap, in the sense that they do not contribute separate weight for (...) or against an option. Our response is to distinguish between derivative reasons and load-bearing reasons, only the latter of which contribute non-overlapping weight to an option. This distinction is close at hand for analyses of reasons in terms of the promotion of significant outcomes. But we also develop an account of this distinction for fundamentalist theories of normative reasons. (shrink)

A novel motivation for a Humean projectivist construal of our concept of scientific law is provided. The analysis is partially developed and used to explain intuitions that are problematic for a Humean reductionist construal of lawhood. A possible non-Humean rejoinder is discussed and rejected. In an appendix, further intuitions that are problematic for Humean reductionists are explained projectively.

A collection of newly commissioned papers on themes from David Albert's Time and Chance (HUP, 2000), with replies by Albert. Introduction [Barry Loewer, Brad Weslake, and Eric Winsberg] I. Overview of Time and Chance 1. The Mentaculus: A Probability Map of the Universe [Barry Loewer] II. Philosophical Foundations 2. The Metaphysical Foundations of Statistical Mechanics: On the Status of PROB and PH [Eric Winsberg] 3. The Logic of the Past Hypothesis [David Wallace] 4. In What Sense Is the (...) Early Universe Fine-Tuned? [Sean M. Carroll] 5. The Meta-Reversibility Objection [Christopher J. G. Meacham] 6. Typicality versus Humean Probabilities as the Foundation of Statistical Mechanics [Dustin Lazarovici] 7. The Past Hypothesis and the Nature of Physical Laws [Eddy Keming Chen] 8. On the Albertian Demon [Tim Maudlin] III. Underwriting the Asymmetries of Knowledge and Intervention 9. Reading the Past in the Present [Nick Huggett] 10. Causes, Randomness, and the Past Hypothesis [Mathias Frisch] 11. Time, Flies, and Why We Can’t Control the Past [Alison Fernandes] 12. The Concept of Intervention in Time and Chance [Sidney Felder] Conclusion [David Albert]. (shrink)

Responsibility for Human Rights provides an original theoretical analysis of which global actors are responsible for human rights, and why. It does this through an evaluation of the different reasons according to which such responsibilities might be assigned: legalism, universalism, capacity and publicness. The book marshals various arguments that speak in favour of and against assigning 'responsibility for human rights' to any state or non-state actor. At the same time, it remains grounded in an incisive interpretation of the world we (...) actually live in today, including: the relationship between sovereignty and human rights, recent events in 'business and human rights' practice, and key empirical examples of human rights violations by companies. David Karp argues that relevantly public actors have specific human rights responsibility. However, states can be less public, and non-state actors can be more public, than might seem apparent at first glance. (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)

Colors are of philosophical interest for two kinds of reason. One is that colors comprise such a large and important portion of our social, personal and epistemological lives and so a philosophical account of our concepts of color is highly desirable. The second reason is that trying to fit colors into accounts of metaphysics, epistemology and science leads to philosophical problems that are intriguing and hard to resolve. Not surprisingly, these two kinds of reasons are related. The fact that colors (...) are so significant in their own right, makes more pressing the philosophical problems of fitting them into more general metaphysical and epistemological frameworks. (shrink)