In this paper we present applications of the ACGT Master Ontology (MO) which is a new terminology resource for a transnational network providing data exchange in oncology, emphasizing the integration of both clinical and molecular data. The development of a new ontology was necessary due to problems with existing biomedical ontologies in oncology. The ACGT MO is a test case for the application of best practices in ontology development. This paper provides an overview of the application of the ontology within (...) the ACGT project thus far. (shrink)

Ontologies are being ever more commonly used in biomedical informatics and we provide a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonised. We argue that one key foundation for both ontology evaluation and harmonisation is the adoption of a realist paradigm in (...) ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonisation is becoming ever more urgent. We describe one example of such harmonisation within the ACGT project, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research. (shrink)

Telomeres, the ends of chromosomes, shorten with each cell division. To expand their replicative potential, various cell types use the ribonucleoprotein telomerase, which lengthens telomeres by its reverse transcriptase activity. Because of its ability to immortalize cancer cells, telomerase also plays a significant role in tumor growth. However, in recent years, a wide variety of non‐canonical effects of telomerase that are independent of telomere lengthening have been discovered, and even the notion that telomerase is restricted to very few cell (...) types has been questioned. These effects also seem to be important in carcinogenesis and might explain the tumor‐promoting effects of telomerase independently of telomere elongation. Here, the current understanding of the extratelomeric roles of telomerase and their physiological and pathological significance is reviewed. BioEssays 30:728–732, 2008. © 2008 Wiley Periodicals, Inc. (shrink)

Mathias Frisch provides the first sustained philosophical discussion of conceptual problems in classical particle-field theories. Part of the book focuses on the problem of a satisfactory equation of motion for charged particles interacting with electromagnetic fields. As Frisch shows, the standard equation of motion results in a mathematically inconsistent theory, yet there is no fully consistent and conceptually unproblematic alternative theory. Frisch describes in detail how the search for a fundamental equation of motion is partly driven by pragmatic considerations (...) (like simplicity and mathematical tractability) that can override the aim for full consistency. The book also offers a comprehensive review and criticism of both the physical and philosophical literature on the temporal asymmetry exhibited by electromagnetic radiation fields, including Einstein's discussion of the asymmetry and Wheeler and Feynman's influential absorber theory of radiation. Frisch argues that attempts to derive the asymmetry from thermodynamic or cosmological considerations fail and proposes that we should understand the asymmetry as due to a fundamental causal constraint. The book's overarching philosophical thesis is that standard philosophical accounts that strictly identify scientific theories with a mathematical formalism and a mapping function specifying the theory's ontology are inadequate, since they permit neither inconsistent yet genuinely successful theories nor thick causal notions to be part of fundamental physics. (shrink)

I criticize two accounts of the temporal asymmetry of electromagnetic radiation - that of Huw Price, whose account centrally involves a reinterpretation of Wheeler and Feynman's infinite absorber theory, and that of Dieter Zeh. I then offer some reasons for thinking that the purported puzzle of the arrow of radiation does not present a genuine puzzle in need of a solution.

Much has been written on the role of causal notions and causal reasoning in the so-called 'special sciences' and in common sense. But does causal reasoning also play a role in physics? Mathias Frisch argues that, contrary to what influential philosophical arguments purport to show, the answer is yes. Time-asymmetric causal structures are as integral a part of the representational toolkit of physics as a theory's dynamical equations. Frisch develops his argument partly through a critique of anti-causal arguments and (...) partly through a detailed examination of actual examples of causal notions in physics, including causal principles invoked in linear response theory and in representations of radiation phenomena. Offering a new perspective on the nature of scientific theories and causal reasoning, this book will be of interest to professional philosophers, graduate students, and anyone interested in the role of causal thinking in science. (shrink)

This essay makes a plea for the relevance of moral considerations in debates about immigration. It offers a standpoint that demonstrates why one should think of immigration as a moral problem that must be considered in the context of global justice.

This article highlights the continuing relevance of a classic bioethical text, “Bioethics as a Discipline,” published by the Hastings Center’s cofounder Daniel Callahan in 1973. Connecting the text’s programmatic recommendations with later reflections and interventions Callahan wrote about the development of bioethics illuminates how the vision Callahan established and the reality this vision helped create were interrelated—just not in the way Callahan had hoped for. Although this portrait relies on an individual perception of the development of bioethics, it might nevertheless, (...) through its unique linkage of different bioethical temporalities, contribute to a broader reassessment of what bioethics became and why. (shrink)

The associative theory of creativity states that creativity is associated with differences in the structure of semantic memory, whereas the executive theory of creativity emphasises the role of top-down control for creative thought. For a powerful test of these accounts, individual semantic memory structure was modelled with a novel method based on semantic relatedness judgements and different criteria for network filtering were compared. The executive account was supported by a correlation between creative ability and broad retrieval ability. The associative account (...) was independently supported, when network filtering was based on a relatedness threshold, but not when it was based on a fixed edge number or on the analysis of weighted networks. In the former case, creative ability was associated with shorter average path lengths and higher clustering of the network, suggesting that the semantic networks of creative people show higher small-worldness. (shrink)

Though much attention has been paid to different principles of justice, far less has been done reflecting on what the larger concern behind the notion is. In this work, Mathias Risse proposes that the perennial quest for justice is about ensuring that each individual has an appropriate place in what our uniquely human capacities permit us to build, produce, and maintain, and is appropriately respected for the capacity to hold such a place to begin with. Risse begins by investigating (...) the role of political philosophers and exploring how to think about the global context where philosophical inquiry occurs. Next, he offers a quasi-historical narrative about how the notion of distributive justice identifies a genuinely human concern that arises independently of cultural context and has developed into the one we should adopt now. Finally, he investigates the core terms of this view, including stringency, moral value, ground and duties of justice. (shrink)

This book assesses the impact of the work of Chris Brown in the field of International Political Theory. The volume engages with general issues of IPT as well as basic issues such as the use and role of practical reasoning and presents a nuanced understanding about issues regarding the legitimacy of war and violence. It explores questions that pertain to human rights, morality, and ethics, and generally an outlook for devising a ‘better’ world. The project is ideal for audiences with (...) interest in International Relations, Ethics and Morality Studies and International Political Theory. (shrink)

This article comments on Jonathan Wolff’s contribution ‘Paying People to Act in Their Own Interests: Incentives versus Rationalisation in Public Health ’ from an economics perspective. The role of incentives in public health is discussed from both a neoclassical and behavioural economics viewpoint. Jonathan Wolff contributes to this discussion by outlining a new mechanism. He demonstrates that incentives may matter in a different way than has been considered so far. In particular, Wolff shows that we should not view individuals in (...) isolation when we consider the effects of incentives. (shrink)

The grounds of justice -- "Un pouvoir ordinaire": shared membership in a state as a ground of -- Justice -- Internationalism versus statism and globalism: contemporary debates -- What follows from our common humanity? : the institutional stance, human rights, and nonrelationism -- Hugo Grotius revisited : collective ownership of the Earth and global public reason -- "Our sole habitation" : a contemporary approach to collective ownership of the earth -- Toward a contingent derivation of human rights -- Proportionate use (...) : immigration and original ownership of the Earth -- "But the earth abideth for ever" : obligations to future generations -- Climate change and ownership of the atmosphere -- Human rights as membership rights in the global order -- Arguing for human rights : essential pharmaceuticals -- Arguing for human rights : labor rights as human rights -- Justice and trade -- The way we live now -- "Imagine there's no countries" : a reply to John Lennon -- Justice and accountability : the state -- Justice and accountability : the World Trade Organization. (shrink)

Classical dispersion relations are derived from a time-asymmetric constraint. I argue that the standard causal interpretation of this constraint plays a scientifically legitimate role in dispersion theory, and hence provides a counterexample to the causal skepticism advanced by John Norton and others. Norton ([2009]) argues that the causal interpretation of the time-asymmetric constraint is an empty honorific and that the constraint can be motivated by purely non-causal considerations. In this paper I respond to Norton's criticisms and argue that Norton's skepticism (...) derives its force partly by holding causal principles to a standard too high to be met by other scientifically legitimate constraints. (shrink)

Si l’intérêt de Peirce pour l’historien des sciences William Whewell est bien connu, l’influence de ce dernier sur la première formulation du pragmatisme peircien a moins été étudiée. Le présent article s’appuie sur une conférence, consacrée à Whewell et donnée par Peirce en 1869, pour analyser plus en détail ce que Peirce pouvait alors entendre par « éclaircissement des conceptions ». Les repères décisifs sont ici fournis par le triple rapport au kantisme, à l’histoire des sciences et aux controverses scientifiques.

in Dirac's classical theory of the electron—is causally non-local. I distinguish two distinct causal locality principles and argue, using Dirac's theory as my main case study, that neither can be reduced to a non-causal principle of local determinism.

I discuss two case studies from classical electrodynamics challenging the distinction between laws that delineate physically possible words and initial conditions. First, for many reasonable initial conditions there exist no global solutions to the Maxwell‐Lorentz equations for continuous charge distributions. Second, in deriving an equation of motion for a charged point particle one needs to invoke an asymptotic condition that seems to express a physically contingent fact even though it is mathematically necessary for the derivation.

Although championed by the Marquis the Condorcet and many others, majority rule has often been rejected as indeterminate, incoherent, or implausible. Majority rule’s arch competitor is the Borda count, proposed by the Count de Borda, and there has long been a dispute between the two approaches. In several..

Nobody has offered such a comprehensive philosophical approach to trade. Nonetheless, James's approach does not succeed. First, we explore James's constructivist method, which does less work than he suggests. The second topic is James's take on the different ‘grounds’ of justice. We explore the shortcomings of approaches that focus exclusively on trade. Our third topic is why James thinks trade is such a ground. The fourth topic is how James argues for his proposed ‘structural equity.’ This proposal remains under-argued. Our (...) fifth topic is to explore why structural equity would generate several specific principles. Finally, we discuss James's notion of autarky. Autarky sets the benchmark for James's ideas about how to divide gains of trade. We doubt that it can do so. (shrink)

Journal of Political Philosophy, EarlyView.

This paper addresses the question of how (not what) we should think about human rights and religious arguments. Thinking about this relationship is today particularly important, because conflicts over human rights in practice often turn around their theoretical problems. Should religious arguments be used to justify human rights? Or do we want human rights to be free from any partisan endorsement so as to avoid divisive interpretations of universal principles? Underlying these hard questions is the issue of justification in view (...) of a plurality of cultural and religious traditions around the globe. If human rights can be transformed so as to defy the charge of Euro-centrism (of being parochially rooted in only one cultural and religious tradition), they need to creatively draw on, not pit themselves against, this plurality. This paper suggests a framework for such a positive and inclusive engagement with various cultures and religions that goes beyond the mainstream liberal model of “public reason”. (shrink)

Poly(ADP‐ribosyl)ation is a post‐translational modification occurring in the nucleus. The most abundant and best‐characterized enzyme catalyzing this reaction, poly(ADP‐ribose) polymerase 1 (PARP1), participates in fundamental nuclear events. The enzyme functions as molecular “nick sensor”. It binds with high affinity to DNA single‐strand breaks resulting in the initiation of its catalytic activity. Activated PARP1 promotes base excision repair. In addition, PARP1 modifies several transcription factors and thereby precludes their binding to DNA. We propose that a major function of PARP1 includes the (...) silencing of transcription preventing expression of damaged genes. Concomitant stimulation of DNA repair suggests that PARP1 acts as a switch between transcription and DNA repair. Another PARP‐type enzyme, tankyrase, is involved in the regulation of telomere elongation. Tankyrase modifies a telomere‐associated protein and thereby prevents it masking telomeric repeats providing access of telomerase for telomere elongation. Therefore, poly(ADP‐ribosyl)ation reactions may act as molecular switches in DNA metabolism. BioEssays 23:543–548, 2001. © 2001 John Wiley & Sons, Inc. (shrink)

Volume 20, Issue 7, July 2020, Page W17-W19.

In this paper I propose a reasonably sharp formulation of the temporal asymmetry of radiation. I criticize accounts that propose to derive the asymmetry from a low-entropy assumption characterizing the state of the early universe and argue that these accounts fail, since they presuppose the very asymmetry they are intended to derive. r 2006 Elsevier Ltd. All rights reserved.

Priority setting in health care is ubiquitous and health authorities are increasingly recognising the need for priority setting guidelines to ensure efficient, fair, and equitable resource allocation. While cost-effectiveness concerns seem to dominate many policies, the tension between utilitarian and deontological concerns is salient to many, and various severity criteria appear to fill this gap. Severity, then, must be subjected to rigorous ethical and philosophical analysis. Here we first give a brief history of the path to today’s severity criteria in (...) Norway and Sweden. The Scandinavian perspective on severity might be conducive to the international discussion, given its long-standing use as a priority setting criterion, despite having reached rather different conclusions so far. We then argue that severity can be viewed as a multidimensional concept, drawing on accounts of need, urgency, fairness, duty to save lives, and human dignity. Such concerns will often be relative to local mores, and the weighting placed on the various dimensions cannot be expected to be fixed. Thirdly, we present what we think are the most pertinent questions to answer about severity in order to facilitate decision making in the coming years of increased scarcity, and to further the understanding of underlying assumptions and values that go into these decisions. We conclude that severity is poorly understood, and that the topic needs substantial further inquiry; thus we hope this article may set a challenging and important research agenda. (shrink)

This essay defends an account of the duties to the global poor that is informed by the empirical question of what makes countries rich or poor, and that tends to be broadly in agreement with John Rawlss account in The Law of Peoples. I begin by introducing the debate about the sources of growth and explore its implications for duties towards the poor. Next I explore whether (and deny that) there are any further-reaching duties towards the poor. Finally, I ask (...) about the moral foundations for the duties to the poor of the sort that earlier parts argue there are. (shrink)

ALTHOUGH majority rule finds ready acceptance whenever groups make decisions, there are surprisingly few philosophically interesting arguments in support of it.1 Jeremy Waldron’s The Dignity of Legislation contains the most interesting recent defense of majority rule. Waldron combines his own argument from respect with May’s influential characterization of majority rule, tying both to a reinterpretation of a well-known passage from Locke’s Second Treatise (“the body moves into the direction determined by the majority of forces”). Despite its impressive resourcefulness, Waldron’s defense (...) is deficient, and one goal of this essay is to show how. Yet our main concern is not to criticize Waldron, but to demonstrate general deficiencies of arguments for majority rule and to suggest a strategy for a more adequate and more complete defense. Such arguments tend to have one of two weaknesses: Either they assume that collective decisionmaking is done in terms of ranking options and thus neglect both aggregation methods using more information than the relative standing of options in rankings (such as so-called positional methods) and rules that are not aggregation methods at all (such as fair-division procedures); or they also constitute arguments for other decision rules. In the first case, the argument is too narrow, in the second it is too broad. The narrowness problem is bigger than stated so far because arguments for majority rule tend to assume not only that decisions are made by ranking options, but also that only two options are to be ranked. Both problems arise for Waldron’s defense and leave it incomplete. Yet such incompleteness also characterizes the state of the art in arguing for majority rule. So in addition to.. (shrink)

This paper considers the trend towards megaregionalism that became prominent in the trade domain in the last years of the Obama administration. While megaregionalism has fallen by the wayside since Trump’s inauguration, the underlying rationale for such treaties will most likely reassert itself rather soon. So there are structural issues that need to be discussed from a standpoint of global justice. In all likelihood, megaregionalism is detrimental to global justice. TTIP in particular, or anything like it, might derail any possibility (...) for a trade organization to aid the pursuit of justice at the global level, and any possibility that trade will be used to that end. From the standpoint of global justice one must hope that megaregionalism does not replace WTO multilateralism. The global-justice framework used here is the grounds-of-justice approach offered in the author’s 2012 On Global Justice. (shrink)