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)

The paper proposes a formal account of Aristotle's trichotomy of verbs, in terms of properties of their continuous tensings, into S(state)-verbs, K(kinesis)-verbs, and E-(energeia)-verbs. Within a Fregean tense framework in which predicates are relativized to times, an account of the continuous tenses is presented and a preliminary account of the trichotomy devised, which permits an illuminating analogy to be drawn between the temporal properties of E- and K-verbs and the spatial properties of stuffs and substances. This analogy is drawn upon (...) in constructing a sophisticated version of the preliminary theory accommodating more of the linguistic data. (shrink)

This paper develops an account of the metaphysics of fundamental laws I call “the Package Deal Account ” that is a descendent of Lewis’ BSA but differs from it in a number of significant ways. It also rejects some elements of the metaphysics in which Lewis develops his BSA. First, Lewis proposed a metaphysical thesis about fundamental properties he calls “Humean Supervenience” according to which all fundamental properties are instantiated by points or point sized individuals and the only fundamental relations (...) are geometrical spatial and temporal relations between these. While the BSA does not require HS Lewis seems to hope that it is true. In contrast, the PDA is not committed to HS or even to the fundamental arena in which fundamental properties are instantiated possessing geometrical structure and thus is able to accommodate relations and structures found in contemporary physics that apparently conflict with HS. Second, although Lewis’ BSA doesn’t require HS his Humeanism does require that fundamental properties are categorical. In contrast, the PDA allows for the possibility that fundamental properties are individuated in terms of laws and so are not categorical. Third, the PDA expands and develops the criteria for what counts in favor of a candidate system with more attention to the criteria employed by physicists in evaluating proposed theories. Fourth and most importantly, unlike Lewis’ BSA, the PDA does not presuppose metaphysically primitive elite properties/quantities that Lewis calls “perfectly natural” properties/quantities or presuppose a metaphysically preferred language whose terms denote such properties/quantities. It replaces Lewis’ account with an account on which natural properties are not metaphysically prior to the laws but are elements of a package that includes a fundamental arena that plays the role of space-time as well as fundamental laws and properties. By doing so it responds to some epistemological and metaphysical issues that have been raised regarding natural properties and their role in the BSA. In sum, the PDA goes further in explicating the notion of laws in terms of the aims and practices of science especially fundamental physics rather than in terms of prior metaphysics. I begin by reviewing Lewis’ account of perfectly natural properties and his Humean BSA of laws. (shrink)

(2000). CASSIRER, SCHLICK AND ‘STRUCTURAL’ REALISM: THE PHILOSOPHY OF THE EXACT SCIENCES IN THE BACKGROUND TO EARLY LOGICAL EMPIRICISM. British Journal for the History of Philosophy: Vol. 8, No. 1, pp. 71-106.

abstract This article defends luck egalitarianism as an interpretation of the egalitarian ideal against two major criticisms levelled against it by Elizabeth Anderson — that it is trapped in the distributive paradigm, and that it treats the victims of bad option luck too harshly to be considered an egalitarian theory. Against the first criticism, I argue that luck egalitarianism will condemn non‐material inequalities and injustices if an appropriate conception of well‐being is adopted. I demonstrate this by showing how the approach (...) is sensitive to the five faces of oppression developed by Iris Young. Although the second criticism is more troubling, it does not defeat luck egalitarianism, either. I will show that few of the inequalities that arise in the real world result from option luck. Further, if cases do occur, rather than abandoning the theory, the best response is to combine luck egalitarianism with another egalitarian principle that will ensure that the basic needs of all citizens are satisfied. The paper concludes by defending the appeal of the distinction between option luck and brute luck, in light of the preceding discussion. (shrink)

When can or should citizenship be granted to prospective members of states? When can or should states withdraw citizenship from their existing members? In recent decades, political philosophers have paid considerable attention to the first question, but have generally neglected the second. There are of course good practical reasons for prioritizing the question of when citizenship should be granted—many individuals have a strong interest in acquiring citizenship in particular political communities, while many fewer are at risk of denationalization. Still, loss (...) of membership in a political community is a practice with a long history that continues to take place today. -/- Concerns about national security have recently led several liberal democratic states to pass, strengthen or consider legislation that would empower their governments to denationalize certain persons.] At the international level, formal norms governing denationalization are vague and generally toothless, and there are no international legal norms that restrict denationalization to citizens who hold another citizenship or wish to take up citizenship elsewhere (Worster, 2009). So it is important to determine whether there are conditions under which denationalization can be morally justified and, if so, what those conditions are. We shall argue that while denationalization is ordinarily impermissible, there is a class of crime committed by citizens that may render it not only permissible, but a fitting response on the part of the state. (shrink)

The first book to focus on the intersection of Western philosophy and the Asian martial arts, _Striking Beauty_ comparatively studies the historical and philosophical traditions of martial arts practice and their ethical value in the modern world. Expanding Western philosophy's global outlook, the book forces a theoretical reckoning with the concerns of Chinese philosophy and the aesthetic and technical dimensions of martial arts practice. _Striking Beauty_ explains the relationship between Asian martial arts and the Chinese philosophical traditions of Confucianism, Buddhism, (...) and Daoism, in addition to Sunzi's _Art of War_. It connects martial arts practice to the Western concepts of mind-body dualism and materialism, sports aesthetics, and the ethics of violence. The work ameliorates Western philosophy's hostility toward the body, emphasizing the pleasure of watching and engaging in martial arts, along with their beauty and the ethical problem of their violence. (shrink)

International policies often make the conferral of aid, debt relief, or additional trading opportunities to a country depend upon its having successfully implemented specific policies, achieved certain social or economic outcomes, or demonstrated a commitment to conducting itself in specified ways. Such policies are conditionality arrangements. My aim in this article is to explore whether conditionality arrangements that would make the conferral of debt relief depend on whether the debtor country achieves a certain status with respect to the human right (...) fulfilment of its population can be justified. I argue that many objections that are typically advanced against conditionality arrangements are unconvincing, and that the possible benefits of human rights conditionality are sufficient to warrant serious intellectual and practical exploration. Whether or not particular arrangements are justified cannot be determined in advance of such exploration. (shrink)

In this article I respond to the eight critical essays in this issue that evaluate the claims in my book with Gerhard Øverland, Responding to Global Poverty: Harm, Responsibility, and Agency.

The collapse of Communism in the regimes in Eastern Europe and the former Soviet Union has brought forth a plethora of alternative political and economic models for the reorganization of those societies. The vacuum that has been left could be regarded as an ideal laboratory for the testing of competing theories, and the temptations to experiment with the more benign forms of constructivist rationalism are likely to prove irresistible. If liberal capitalism is to be successfully created, it will clearly not (...) have the same biography as it has had in the Western European and Anglo-American countries, where its emergence was the result of slow evolution: often its appearance and survival were due to a quite fortuitous combination of circumstances. In those countries it was not the result of any deliberate democratic choice but the outcome of a happy confluence of traditional rules and customary practices, and the participants in them had little idea of the form of the system that they were creating. Indeed, ideological sanctification was almost an afterthought, and democratic approval was belated and in most cases not enthusiastic. Britain was a liberal capitalist society, and possessed the necessary body of private law, some time before the franchise was significantly democratized . It is, of course, recent theoretical and empirical research which has revealed that the political choice mechanisms that developed haphazardly after the success of the market are a potential threat to it. (shrink)

The present paper examines the arguments and data presented by Nisbett and Wilson relevant to their thesis that subjects do not have access to their own cognitive processes. It is concluded that their review of previous research is selective and incomplete and that the data they present in behalf of their thesis does not withstand a demand characteristics analysis. Furthermore, their use of observer-subject similarity as evidence of subjects' inability to access cognitive processes makes tests of their hypothesis confounded and, (...) at the same time, reveals limitations in the application of the pre-inquiry quasi-control to research on social behavior. Problems with postexperiment questionnaires, such as the demand characteristics of the inquiry procedure are also considered. Although there are difficulties in assessing subjects' cognitive processes, many of these may be overcome through the application of novel techniques and research conducted on more traditional methods. In contrast to the view that subjects have limited access to cognitive processes and that their verbal reports are not valid, it is concluded that subjects' verbalizations are a rich source of psychological data which must be pursued if we are to tap their cognitive processes and are to gain an adequate understanding of human behavior. (shrink)

This paper advances two arguments about environmental problems. First, it interrogates the strength and limitations of empiricist accounts of problems and issues offered by actor-network theory. Drawing on the work of C.S. Peirce, it considers how emerging environmental problems often lead to abductive inferences about the existence of hidden causes that may or may not have caused the problem to emerge. The analysis of environmental problems should be empiricist in so far as it is sceptical of the claims of those (...) who know in advance what the problem is, but it should also be alert to processes and things that are not readily traceable or perceived. Secondly, the paper’s contention is that environmental problems almost invariably involve an encounter between unlike or disparate materials or processes. In such circumstances, the challenge is to develop a form of inquiry that is alert to both the specificity of such encounters and to the specificity of the political situations in which they come to matter. (shrink)

There is no cure or vaccine for HIV/AIDS. The only life-prolonging treatment available is antiretroviral (ARV) therapy. WHO estimates, however, that less than 5 percent of those who require treatment in developing countries currently enjoy access to these medicines. In Africa fewer than 50,000 people–less than 2 percent of the people in need–currently receive ARV therapy. These facts have elicited strongly divergent reactions, and views about the appropriate response to this crisis have varied widely.The intensity of the debate concerning access (...) to life-prolonging medicines for the treatment of HIV/AIDS, and the heated rhetoric with which they are often conducted, suggest that these disagreements may be rooted in deeper disagreements of value. It is not obvious, however, what disagreements of value are at stake in this debate. By analyzing the statements of scholars, public officials, activist organizations, and private sector representatives, each of whom may endorse very different policy recommendations on access to HIV/AIDS drugs, we have identified and created a typology of the different sources of disagreement in the debate. We conclude that the central disagreements concerning access to medicines arise from competing understandings of how responsibilities for bringing remedy to hardships should be allocated to different agents and institutions. A central lesson that emerges from our analysis is that thinking about “health equity” must extend beyond the explanation and justification of goals, values, and ideals, and engage more honestly with the difficult question of how responsibilities for bringing remedy to health crises should be allocated in complex social contexts. (shrink)

It seems plausible to extend to the field of Disability Studies a certain nominalist point of view which is evident in Foucault’s work. What I have in mind is an “implantation of impairments” thesis, modelled after what Foucault calls the “implantation of perversions.” After sketching some features of this Foucauldian argument, I discuss the ideas of knowledge and power that it presupposes, then outline a critical perspective on Foucault’s nominalism.

Kripke's Wittgenstein on Rules and Private Language has enlivened recent discussion of Wittgenstein's later philosophy. Yet it is quite possible to disengage his interpretive thesis from its supporting argumentation. Doing so leaves one with an intriguing sceptical argument which Kripke first powerfully advances, then tries to halt. But contrary to the impression his argument may leave, Kripke's solution and the position it concedes to the Sceptic are deeply allied. Here I shall demonstrate their common assumption, and on that basis argue (...) that Kripke's solution begs the Sceptic's question. Furthermore, I believe we can live with the Sceptic. The sceptical argument can be turned into a reasonable contribution to a kind of nominalism in the philosophy of meaning and truth. (shrink)

There is the world of ideas and the world of practice; the French are often for sup pressing the one and the English the other; but neither is to be suppressed. -Matthew Arnold The Function of Criticism at the Present Time From its inception, bioethics has confronted the need to reconcile theory and practice. At first the confrontation was purely intellectual, as writers on ethical theory (within phi losophy, theology, or other humanistic disciplines) turned their attention to topics from the (...) world of medical practice. Recently the confrontation has grown more intense. The ap pointment of clinical ethicists in hospitals and other health care settings is an accelerating trend in North America. Concomitantly, those institutions involved in training peo ple in clinical ethics have added organized exposure to the world of practice, in the form of placement requirements, to the normal academic course load. In common with other dis ciplines, bioethics has begun to see clinical training as a con dition of didactic theory and apprenticeship. (shrink)

EVERY speaker of a language knows a bewildering variety of linguistic facts, and will come to know many more. It is knowledge that connects sound and meaning. Questions about the nature of this knowledge cannot be separated from fundamental questions about the nature of language. The conception of language we should adopt depends on the part it plays in explaining our knowledge of language. This chapter explores options in accounting for language, and our knowledge of language, and defends the view (...) that individuals’ languages are constituted by the standing knowledge they carry from one speech situation to another. (shrink)

Kant empahtically denied that living forms unfold according to a mechanical law. Yet if living nature were not law-like, natural science would be futile. The justification for a concept of purposiveness is to ensure “the lawfulness of the contingent” against the last exception. It was not until we learned to think about contingency without effacing it that natural history crossed the threshold of a science, Darwin leading the way. While his theory of evolution proposes mechanical explanations for a wide range (...) of natural historical phenomena, the explanations do not overcome but actually presuppose life’s ultimate contingency. (shrink)

Are there matters we should exclude from inquiry? Personal privacy apart, it seems difficult to justify. By what higher, better knowledge than the results of inquiry itself could one know what inquiry ought not know? Is such knowledge a metaphysical intuition whose authority cannot be questioned? Isn't that a fairy-tale? But what about ethics? What about ethical limitations on knowledge? Can they not concern more than simply what to do with knowledge we have, concerning instead the very dynamic of knowledge, (...) the direction of inquiry itself? Might not the best ethics of knowledge teach that certain directions of inquiry are forbidden, like a trespass against personal privacy? (shrink)

This chapter contains sections titled: References.

Scholars have detected hostility to technology in Daoist thought. But is this a problem with any machine or only some applications of some machines by some people? I show that the problem is not with machines per se but with the people who introduce them, or more exactly with their knowledge. It is not knowledge as such that causes the disorder Laozi and Zhuangzi associate with machines; it is confused, disordered knowledge—superficial, inadequate, unsubtle, and artless. In other words the problem (...) is not with machines but with the ethics of engineering and the government of technology. The Daoist argument does not devalue machines or knowledge of them; instead, it sets a new goal, defining an alternative ideal—alternative to techniques held hostage to despotic ideas about efficiency and profit. (shrink)

This study investigated several issues with 1498 managers nationwide regarding, for example, how ethical they felt their organizations were and whether their personal principles must be compromised for the organization's sake. In addition their decision criteria for two scenarios involving ethical implications were articulated.

From Leibniz and Georg Ernst Stahl to Albrecht von Haller, Germans of the eighteenth century calved off an experimental physiology from medicine and made this research a centerpiece of their new model university, first under Haller at Göttingen, then under von Humboldt at Berlin. Haller made Göttingen the most important center for the advancement of Enlightenment science in Germany, but that is not where Johann Herder went looking for new ideas in psychology, turning instead to France, avidly studying Condillac and (...) Diderot, and meeting the latter in Paris in 1769. Herder wanted to use French psychology in his theory of how the history of art recapitulates the development of the senses. To work out his ideas he found it necessary to ignore Kant's careful distinction between life and matter. Kant made life an inexplicable boundary for mechanical explanation, though with Herder it became the key concept for interpreting nature. That all the forces in the physical world are held to express one organizing, integrating vital principle is what excited Goethe about Herder's work and provoked the Naturphilosophie that Schelling invented at this time in close collaboration with Goethe. (shrink)

Screening for prostate cancer with the prostate-specific antigen blood test is controversial, as evidence to date has not demonstrated such screening does more good than harm. While the potential benefit of PSA screening on reducing prostate cancer mortality has not been documented in randomized trials, many risks of PSA screening have been well documented. These risks include a substantially higher risk of a prostate cancer diagnosis over a screenee’s lifetime, false-positive and false-negative test results, possible complications from biopsies done in (...) response to suspicious test results, and substantial risks of side effects from subsequent prostate cancer treatments. Nevertheless, PSA screening is widespread in the United States, and many physicians in a national survey reported supporting routine PSA screening as well as getting PSA tests themselves, despite the lack of evidence. (shrink)

My primary focus in this paper is on an objection to Humean account of laws and specifically to David Lewis’ “best systems analysis” (BSA). The objection is that the laws according to the BSA (which I call L-laws) fail to account for the ability of laws to explain. In contrast governing laws (which I will call G-laws) are alleged to account for the role of laws in scientific explanations by virtue of their governing role. If governing is required for laws (...) to be explanatory then Humean accounts like Lewis’ are dead in the water since explanation is central to the role of laws in the sciences. However, I will argue that there are effective rebuttals to arguments that Humean laws don’t explain and that actually it is governing accounts that have difficulty with explanation. (shrink)

There is more to truthfulness than truthful speech. There is a truthfulness of questions and doubts, a truthfulness that imposes reserve, a truthfulness that remonstrates and provokes without counterassertion. These are a pragmatic philosopher’s kind of truthfulness on the other side of a metaphysical Truth of objects. Rorty’s metaphilosophical criticism does not attack an argument directly. Instead, it questions the reason for taking the argument seriously. For Rorty, the problems are always the problem. For instance, in his many interventions on (...) the topic of philosophical ideas about truth, it is not the value of truth he debunks. It is the value of epistemological discourse about “the truth.” He is not cavalier about truth or its value, though he is about epistemology, rationalism, and sometimes about philosophy itself. (shrink)

A critical study of Ian Hacking, _Rewriting the Soul_ (1995). Special attention is paid to his idea of the indeterminacy of the past; the truth-value of claims concerning alleged recovered memories; the concept of human kinds and their supposed difference from natural kinds; and Hacking’s Foucault-inspired conception of knowledge.

Robert Nozick's adherence to Locke's puzzling doctrine about punishment can seem strange. Why does Nozick follow Locke in claiming that individuals in a state of nature have a right to punish any wrongdoer?Here reflection on this question proceeds by stages to a conclusion that Nozick as well as any other state-of-nature theorist of similar stripe should find disturbing. For, as we shall see, what Nozick describes as the general right of a minimal state to punish cannot arise within a state (...) of nature from the more plausible right of individuals to punish only those who harm them. (shrink)

The World Wide Web Consortium (W3C) has sanctioned languages for ontology formulation, of which the most important is the Web Ontology Language (OWL). These have spawned in their turn powerful open-source software for developing and reasoning with ontologies and for querying data stores aligned to ontologies. Unfortunately, the resultant popularity of semantic technology has itself led to a situation where ontologies are now being created in heterogeneous, uncoordinated ways, thereby leading to a new problem of semantic stovepipes, and thus to (...) a new failure of data integration and reuse. The best practices here described counteract this tendency by providing a set of principles and rules to lead to the development of ontologies in a consistent, non-redundant fashion. (shrink)

In this article I respond to the eight critical essays in this issue that evaluate the claims in my book with Gerhard Øverland, Responding to Global Poverty: Harm, Responsibility, and Agency.