Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway (http://pir.georgetown.edu/pro). (shrink)
The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)
1. Among the most striking features of the political arrangements on this planet is its division into sovereign states.1 To be sure, in recent times, globalization has woven together the fates of communities and individuals in distant parts of the world in complex ways. It is partly for this reason that now hardly anyone champions a notion of sovereignty that would entirely discount a state’s liability the effects that its actions would have on foreign nationals. Still, state sovereignty persists as (...) a political fact. The number of states has increased enormously due to upheavals of the 20th century, and there is nothing in principle morally wrong with the existence of states - or so we will assume.2 What must be explored, then, are the limits of normatively plausible sovereignty. How bad does a government have to be for outsiders to be allowed to interfere? What responsibilities does a country incur because of its contribution to global warming? What obligations arise through trading? In this paper, we explore another pertinent question: to what extent is a country allowed to influence who lives on its territory by regulating immigration? The angle from which we approach this question continues to be neglected even now that questions of global justice are receiving much attention. Immigration amounts to a change in political relationships as immigrants alter their standing within one community and acquire a status elsewhere. Yet it also amounts to an alteration in physical relationship, since they acquire a relationship to a territory, making a life for themselves with the resources offered by a part of the earth.3 We base our exploration of.. (shrink)
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Little work has been done to explore the moral foundations of the state’s right to territory.1 In modern times, the state has mostly been assumed to be a territorial unit, and no need was perceived to reflect on precisely what justifies its territorial jurisdiction. The state’s territoriality is related to another topic that has remained under-theorized: immigration. There is, moreover, an obvious relationship between these topics: the more powerful a state’s rights over its territory, the more powerful the right to (...) constrain access to that territory might become – or so, at any rate, we might suppose. Rights to territory and rights to immigration are usefully theorized together.2 Our starting point is a Lockean analysis of the moral foundations of territoriality offered by Simmons (2001). This is a natural starting point not only because Simmons is one of the very few contemporary writers who have taken up philosophical questions about territoriality in the first place, but also because Locke’s thought, as Simmons makes clear, actually allows for the development of a sophisticated account of territoriality. This makes Locke stand out simply because generally modern political.. (shrink)
Among psychologists and vision scientists,binocular rivalry has enjoyed sustainedinterest for decades dating back to the 19thcentury. In recent years, however, rivalry''saudience has expanded to includeneuroscientists who envision rivalry as a tool for exploring the neural concomitants ofconscious visual awareness and perceptualorganization. For rivalry''s potential to berealized, workers using this tool need toknow details of this fascinating phenomenon,and providing those details is the purpose ofthis article. After placing rivalry in ahistorical context, I summarize major findingsconcerning the spatial characteristics and thetemporal dynamics (...) of rivalry, discuss two majortheoretical accounts of rivalry ( eye vs stimulus rivalry) and speculate on possibleneural concomitants of binocular rivalry. (shrink)
Rawls's Law of Peoples has not gathered a great deal of public support. The reason for this, I suggest, is that it ignores the differences between the international and domestic realms as regards the methodology of reciprocal agreement. In the domestic realm, reciprocity produces both stability and respect for individual moral agency. In the international realm, we must choose between these two values — seeking stable relations between states, or respect for individual moral agency. Rawls's Law of Peoples ignores the (...) stark nature of this choice by insisting that the only legitimate extension of liberal toleration abroad is the toleration of different forms of political organization. It is this attempt to overcome liberalism's tragic dilemma which, I suggest, has made Rawls's international theory less attractive than his domestic theory. I also suggest that this difficulty is at the base of the further difficulties identified by Henry Shue and Martha Nussbaum in their accompanying essays. Key Words: Rawls • international • toleration • reciprocity • state • Nussbaum • Shue. (shrink)
Two decades of research on euthanasia in the Netherlands have resulted into clear insights in the frequency and characteristics of euthanasia and other medical end-of-life decisions in the Netherlands. These empirical studies have contributed to the quality of the public debate, and to the regulating and public control of euthanasia and physician-assisted suicide. No slippery slope seems to have occurred. Physicians seem to adhere to the criteria for due care in the large majority of cases. Further, it has been shown (...) that the majority of physicians think that the euthanasia Act has improved their legal certainty and contributes to the carefulness of life-terminating acts. In 2005, eighty percent of the euthanasia cases were reported to the review committees. Thus, the transparency envisaged by the Act still does not extend to all cases. Unreported cases almost all involve the use of opioids, and are not considered to be euthanasia by physicians. More education and debate is needed to disentangle in these situations which acts should be regarded as euthanasia and which should not. Medical end-of-life decision-making is a crucial part of end-of-life care. It should therefore be given continuous attention in health care policy and medical training. Systematic periodic research is crucial for enhancing our understanding of end-of-life care in modern medicine, in which the pursuit of a good quality of dying is nowadays widely recognized as an important goal, in addition to the traditional goals such as curing diseases and prolonging life. (shrink)
Anticipating Mikhail Bakhtin’s appreciation for the unfinalizability of Fedor Dostoevskij’s universe, prominent Protestant theologian Karl Barth celebrates the Russian novelist’s presentation of “the impenetrable ambiguity of human life” characteristic of both the ending of Dostoevsky’s novels and Paul’s Epistle to the Romans. Barth’s unique reading of The Brothers Karamazov not only demonstrates the barrenness of the “theocratic dream” but also complements Bakhtin’s discussion of polyphony with an explicitly theological dimension by focusing on the dialogue between Creator and the created. Dostoevsky’s (...) prophetic voice provides Barth with a poetic expression of the divine command that highlights the ethical dimension inherent in every theological choice. (shrink)
This essay attempts to identify the ethical principles appropriate to a second-order political agent—an agent, that is, whose primary responsibility lies not in the implementation of state power, but in the response to and evaluation of that state power. The specific agent I examine is the human rights non-governmental organization, and the specific context is that of humanitarian military intervention. I argue that the specific role of the human rights NGO gives rise to ethical permissions not available to government agents. (...) In particular, such NGOs may have permissions to ignore the motivation of government agents, and support even substantially unjust interventions, where such interventions would have substantial benefit for the defense and preservation of basic human rights. a Footnotesa Previous versions of this paper were presented at Brown University, the Edmond J. Safra Center for Ethics at Harvard University, and the Carr Center for Human Rights Policy at Harvard University. I am grateful to all participants for their questions and comments. Thanks in particular go to the editors of this volume, whose help with this paper has been especially valuable. Responsibility for errors, of course, remains my own. (shrink)
The International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH) was formed over 20 years ago with a goal of harmonizing research regulations among the European Union, United States, and Japan. Harmonization was intended to speed approval of pharmaceuticals, avoid unnecessary repetition of studies, and ensure protection of research participants. This paper examines United States, European Union, and ICH pediatric research regulations in five domains: parental permission, assent/dissent, payment, risk/benefit and inclusion of disabled children/wards (...) of state. The purpose is to examine similarities and differences among the regulations to help investigators, policy makers and the public to understand what each regulatory framework can learn from the others. Additionally, the paper suggests philosophical differences in how these entities view pediatric research which may serve as barriers to harmonization in the future. (shrink)
This article sets forward a new concept of reflection, to be contrasted with more usual reading of the concept for which we use the term `reflectivity'. The contrast is related to a distinction between normalizing education and counter-education. We claim that within the framework of normalizing education there is no room for reflection, but only for reflectivity. In contrast to reflectivity, reflection manifests a struggle of the subject against the effects of power which govern the constitution of her conceptual apparatus, (...) her knowledge, her consciousness and her limitations and possibilities for successful functioning. Reflectivity re-presents the hegemonic realm of self-evidence and the productive violence of social and cultural order. Reflection, by contrast, aims to challenge the supposedly self-evident and the present order of things. Reflection aims at transcendence and represents a moral commitment in respect of the otherness of the Other, which power relations in every realm of self-evidence oblige us to neglect, to destroy or consume. Transcendence is a concrete utopia, and so is the subject in her nonrepressive communication with the Other: they are part and parcel of our present possibilities, sometimes in microscopic arenas, struggled for, and from time to time even realized. (shrink)
This paper extends the dialogue of educational philosophy to the experience of beginners entering the teaching profession. Rather than impose the ideas of any specific philosopher or theorist, or indeed official standard, the exploration presented here owes its origins to phenomenology and the use of grounded theory. Working from a narrative data base and focussing on the knowing of name in the first instance, the authors develop their emergent ideas on self and identity in relation to children taught, through connection (...) to a wider literature that includes reference to Giddens, Illeris, Deleuze and Heidegger, for example. The paper is thus also an exercise in suggesting that research on practice by academics working in professional education, who are non-philosophers, can lead to constructive and relevant engagement with philosophy in developing theory from and about about practice, even though the approach, in the initial stages, may well be serendipitous and eclectic in nature. (shrink)
This paper extends the dialogue of educational philosophy to the experience of beginners entering the teaching profession. Rather than impose the ideas of any specific philosopher or theorist, or indeed official standard, the exploration presented here owes its origins to phenomenology and the use of grounded theory. Working from a narrative data base and focussing on the knowing of name in the first instance, the authors develop their emergent ideas on self and identity in relation to children taught, through connection (...) to a wider literature that includes reference to Giddens, Illeris, Deleuze and Heidegger, for example. The paper is thus also an exercise in suggesting that research on practice by academics working in professional education, who are non-philosophers, can lead to constructive and relevant engagement with philosophy in developing theory from and about about practice, even though the approach, in the initial stages, may well be serendipitous and eclectic in nature. (shrink)
This historical compendium investigates scientific methods conceived between the Renaissance and the nineteenth century. Beginning with attacks on Scholasticism and the rist of the New Science, the authors explain the roles of both major andminor figures in describing scientific methods. Although the chapters are interrelated and contain explicit comparisons, each chapter is a complete study in itself. The authors' emphasis on writing for the non-specialist and their liberal use of primary sources make this an outstanding textbook.
Connecting people across the digital divide is as much a social effort as a technological one. We are developing a community-centred approach to learn how interaction techniques can compensate for poor communication across the digital divide. We have incorporated the lessons learned regarding social intelligence design in an abstraction and in a device called the SoftBridge. The SoftBridge allows communication to flow from endpoints through adapters, getting converted if necessary, and out to destination endpoints. Field trials are underway with two (...) communities in South Africa: disadvantaged Deaf users and an isolated rural community. Initial lessons learned show that we have to design user interfaces that allow users to understand and cope with delay. We also learned that social concerns are often more important than the technical issues in designing such systems. (shrink)
