The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...) and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have (...) the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas. (shrink)

The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. (...) It is further distinguished from other maps in that it represents not some specific portion of spatial reality (say: Leeds in 1996), but rather the generalized or idealized spatial reality associated with a generalized or idealized human being at some generalized or idealized instant of time. It will be our concern in what follows to outline the approach to ontology that is represented by the FMA and to argue that it can serve as the basis for a new type of anatomical information science. We also draw some implications for our understanding of spatial reasoning and spatial ontologies in general. (shrink)

Surgical devices are often marketed before there is good evidence of their safety and effectiveness. Our paper discusses the ethical issues associated with the early marketing and use of new surgical devices from the perspectives of the six groups most concerned. Health Canada, which is responsible for licensing new surgical devices, should amend their requirements to include rigorous clinical trials that provide data on effectiveness and safety for each new product before it is marketed. Industry should comply with all Health (...) Canada requirements to obtain licenses for new products. Until Health Canada requires effectiveness and safety data, industry should cooperate with physicians in appropriate studies before releasing new products and should make balanced presentations of all the available evidence. Surgeons should, before using a new surgical device, assess the evidence on its effectiveness and safety and ensure they are properly trained and competent in using the device. Surgeons should provide their patients with an evaluation of the available evidence and inform them about possible complications and the surgeon's level of experience with the new device. Patients, who should be given an honest evaluation of the available evidence, possible complications, and the surgeon's experience, should be encouraged to evaluate the evidence and information to their own satisfaction to ensure that fully informed consent is given. Health institutions, responsible for regulating practice within their walls, should review new devices for safety, effectiveness, and economic impacts, before allowing their use. They should also limit the use of new surgical devices to surgeons trained and competent in the new technology. Professional societies should provide guidance on the early adoption of new surgical devices and technologies. We urge all those involved in the development, licensing, and use of new surgical devices to aim for higher ethical standards to protect the health and safety of patients requiring surgery. The lowest acceptable ethical standard would require device manufacturers to provide surgeons with accurate and timely information on the efficacy and safety of their products, allowing surgeons and patients to evaluate the evidence (and the significance of information not yet available) before surgery. (shrink)

The translational research community, in general, and the Clinical and Translational Science Awards (CTSA) community, in particular, share the vision of repurposing EHRs for research that will improve the quality of clinical practice. Many members of these communities are also aware that electronic health records (EHRs) suffer limitations of data becoming poorly structured, biased, and unusable out of original context. This creates obstacles to the continuity of care, utility, quality improvement, and translational research. Analogous limitations to sharing objective data in (...) other areas of the natural sciences have been successfully overcome by developing and using common ontologies. This White Paper presents the authors’ rationale for the use of ontologies with computable semantics for the improvement of clinical data quality and EHR usability formulated for researchers with a stake in clinical and translational science and who are advocates for the use of information technology in medicine but at the same time are concerned by current major shortfalls. This White Paper outlines pitfalls, opportunities, and solutions and recommends increased investment in research and development of ontologies with computable semantics for a new generation of EHRs. (shrink)

Dr. Elisabeth Kübler-Ross is credited as one of the first clinicians to formalize recommendations for working with patients with advanced medical illnesses. In her seminal book, On Death and Dying,...

Dewey was a pragmatist, and pragmatism is an empiricism. I think Dewey would insist that his empirical orientation in the theory of knowledge is not independent of his democratic orientation in social philosophy. My contribution to the discussions of this volume pursues three questions. One is how Dewey saw the connection between empiricism and democracy. Another is whether there is a comparable empiricism in Chinese tradition. A third is whether ideas of knowledge and ideas of government are really as close (...) as Dewey, American Pragmatism, and indeed Western philosophy as a tradition tend to assume they are. (shrink)

I begin by contrasting three approaches one can take to the distinction between the essential and accidental properties: an ontological, a deflationary, and a mind‐dependent approach. I then go on to apply that distinction to the necessary a posteriori, and defend the deflationist view. Finally I apply the distinction to modal truth in general and argue that the deflationist position lets us avoid an otherwise pressing problem for the actualist: the problem of accounting for the source of modal truth.

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)

Barry Allen explores the concept of knowledge in Chinese thought over two millennia and compares the different philosophical imperatives that have driven Chinese and Western thought. Challenging the hyperspecialized epistemology of modern Western philosophy, he urges his readers toward an ethical appreciation of why knowledge is worth pursuing.

Recent work takes both philosophical and scientific progress to consist in acquiring factive epistemic states such as knowledge. However, much of this work leaves unclear what entity is the subject of these epistemic states. Furthermore, by focusing only on states like knowledge, we overlook progress in intermediate cases between ignorance and knowledge—for example, many now celebrated theories were initially so controversial that they were not known. -/- This paper develops an improved framework for thinking about intellectual progress. Firstly, I argue (...) that we should think of progress relative to the epistemic position of an intellectual community rather than individual inquirers. Secondly, I show how focusing on the extended process of inquiry (rather than the mere presence or absence of states like knowledge) provides a better evaluation of different types of progress. This includes progress through formulating worthwhile questions, acquiring new evidence, and increasing credence on the right answers to these questions. I close by considering the ramifications for philosophical progress, suggesting that my account supports rejecting the most negative views while allowing us to articulate different varieties of optimism and pessimism. (shrink)

The study of traditional cultures is supposedly the business of the social sciences. Philosophy too has methodologies and viewpoints that can make positive contributions to their study.

We argue that a modified version of Mill’s method of agreement can strongly confirm causal generalizations. This mode of causal inference implicates the explanatory virtues of mechanism, analogy, consilience, and simplicity, and we identify it as a species of Inference to the Best Explanation (IBE). Since rational causal inference provides normative guidance, IBE is not a heuristic for Bayesian rationality. We give it an objective Bayesian formalization, one that has no need of principles of indifference and yields responses to the (...) Voltaire objection, van Fraassen’s Bad Lot objection, and John Norton’s recent objection to IBE. (shrink)

Andrews explores spiritual practices that were the vital source from which everything else about Transcendentalism-texts, ideas, and social action-flowed. These practices are eminently available to spiritual seekers today, both those who are connected to conventional forms of religiosity and those who are allergic to 'religion.

This essay introduces a running symposium on the work of Richard Rorty and its legacy fifteen years after his passing. The arc of Rorty's thought defines a trajectory through American pragmatism, tracing a variation unimagined until he expressed it. His work raised Anglophone philosophers’ interest in American pragmatism as never before and also focused the interest of the whole world on American pragmatism as never before, even though the result was to define a pragmatism saturated with nominalism and suppressing the (...) most original qualities of the sources that he celebrated. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Reviewed by:Broken Bodies and Healing Communities: The Challenge of HIV and AIDS in the South African ContextEmily Reimer-BarryBroken Bodies and Healing Communities: The Challenge of HIV and AIDS in the South African Context Edited by Neville Richardson Pietermaritzburg, South Africa: Cluster Publications, 2009. 209 pp. $12.00.The township of Mpophomeni, like many communities in South Africa, has been tragically devastated by HIV/AIDS. Christian churches in the region have responded to (...) this ongoing crisis in a variety of ways. In this collection of essays, edited by Neville Richardson, a team of international scholars from various subfields has combined ethnography and qualitative research with theology, with the goal of understanding how Christian churches have responded to the needs of the people of Mpophomeni. This book is the result of a two-year collaborative research project. The title of the book alerts the reader to two major themes of the unfolding narrative: the reality of brokenness, suffering, and sin (individual, interpersonal, social, and ecclesial) and the goal of healing (again, individual, interpersonal, social, and ecclesial). The ten chapters, individually authored, are divided thematically into three sections: Part 1, “Healing and Community: Perspectives from Zulu Culture and Religion”; Part 2, “Caring, Healing and Faith Communities”; and Part 3, “Caring and Community: Training in a Hospital Setting.” As perhaps expected, the authors’ conclusions remain ambivalent. James R. Cochrane explains: “Religion per se is not innocent of breaking bodies, which should always stand as a warning to us. But religion per se is also the source of healing; indeed, in some ways it is all about healing or wholeness, in relation to the sacred” (115). Churches in Mpophomeni have been “protective spaces” (11), “bridging communities” (91), and “broken bodies” that remember and re-member “the broken body of Jesus” (145–51). But communities are also in flux (101) and are sources of discourse that stigmatizes and shames (172).The book presents clearly argued and compelling essays that work independently and could be read or adopted for class as individual essays. The authors approach some of the same difficult questions from different vantage points, methodological foundations, and subdisciplines. For example, in the first two chapters Sidsel Roalkvam and Jone Salomonsen describe the many social problems in Mpophomeni, including poverty, unemployment, gender inequalities, sexual violence, drug and alcohol addiction, and criminal violence. But their [End Page 225] ethnographic research uncovers some of the rituals of healing that help the community to cope, including the practice of communal “strong prayer” (11–15), and uMemulo rite of passage for girls (23–37).However, I wish there were more coherent conversation between the authors of each individual essay. While Richardson explains that the research was collaborative “not only in terms of interaction between the researchers and the community but also among the researchers themselves” (ix), this collaboration between the researchers is not obvious to the reader in the final format of the book. Perhaps another book format would have more fruitfully conveyed this collaborative stance (for example, the inclusion of responses to each chapter or the addition of a roundtable discussion chapter or coauthored chapters).The ethnographic data presented in the third section is particularly rich and challenging for theology, but the authors could have spent more time unpacking, contextualizing, and analyzing the included quotations from patient–chaplain conversations. If, for example, the story of a thirty-three-year-old HIV+ man who allegedly raped a fifteen-year-old girl to give her “a good lesson for her life” so that she will not dress provocatively is “very characteristic of the material” in the study (203–5), much more needs to be said to explain how pastoral care interventions can address the stated “gender inequalities and the drastically different roles of men and women resulting in the vulnerable position of women” (206).The book is a must-read for scholars working on HIV/AIDS and Christian ethics. It could also provide supplemental readings for an undergraduate or graduate course in this area. [End Page 226]Emily Reimer-BarryUniversity of San DiegoCopyright © 2012 Society of Christian Ethics... (shrink)

The project from which this special issue emerges began in 2019 in a workshop at Rhodes University in the Eastern Cape, entitled, iMpuma-Koloni Bearings: An Other Cape? The call to this workshop brought together a group of scholars from various universities and locations in southern Africa who had a commitment to critical history, to reconsidering the implications of the discipline in the colonial and apartheid project, and to addressing a continued reluctance of the discipline to engage with the critique of (...) history. (shrink)

"Pace" michael devitt and other recent writers, this paper argues that realism essentially involves commitment to a substantial theory of truth. it also tries to chart the ways whereby the commitment arises.

This collection of essays evolved from a colloquium held at the University of British Columbia in 1995 to honour the eminent political scientist and aphorist W.J. Stankiewicz. A theorist and consultant on political decisions, Stankiewicz has been noted for his ability to bring the classical concepts of political science into the decision-making rooms of everyday political action. Among the distinguished Canadian and American contributors are Alan Cairns, Jean Bethke Elshtain, George Feaver, Barry Cooper, Anthony Parel, Arpad Kadarkay and Ian (...) Ross. The contributors have not only explored and extended the central ideas of Stankiew146;s political situations. The volume concludes with two of Professor Stankiewicz's hitherto unpublished essays (on natural law and ecology, and truth in politics). (shrink)

This unique study considers the influences of Stoic critics on the evolution of Thomas More's thought. The author argues that More's engaement with Erasmus's work radicalized his understanding of Christianity and shaped the writing of Utopia.

The principle of non-maleficence, primum non nocere, has deep roots in the history of moral philosophy, being endorsed by John Stuart Mill, W. D. Ross, H. L. A. Hart, Karl Popper and Bernard Gert. And yet, this principle is virtually absent from current debates on social justice. This article suggests that non-maleficence is more than a moral principle; it is also a principle of social justice. Part I looks at the origins of non-maleficence as a principle of ethics, and (...) medical ethics in particular. Part II introduces the idea of non-maleficence as a principle of social justice. Parts III and IV define the principle of justice as non-maleficence in terms of its scope and coherence, while Part V argues that the motivation of not doing harm makes this principle an alternative to two well-established paradigms in the literature on social justice: justice as mutual advantage (David Gauthier) and justice as impartiality (Brian Barry). (shrink)

Our aim in this paper is to bring to light two sources of tension for Christian theists who endorse the principle of unrestricted composition, that necessarily, for any objects, the xs, there exists an object, y, such that the xs compose y. In Value, we argue that a composite object made of wholly valuable parts is at least as valuable as its most valuable part, and so the mereological sum of God and a wholly valuable part would be at least (...) as valuable as God; but Christian theism arguably demands that no concrete object other than God can be as valuable as God. And in Creation, we argue that the conjunction of theism and unrestricted composition, together with the claim that every concrete entity that is numerically distinct from God is created by God, implies that God is created by God. We conclude by examining the prospects of restricting the thesis of unrestricted composition to the domain of material or spatiotemporal objects as a way to sidestep the above arguments against the conjunction of Christian theism and unrestricted composition. (shrink)

Simple random sampling resolutions of the raven paradox relevantly diverge from scientific practice. We develop a stratified random sampling model, yielding a better fit and apparently rehabilitating simple random sampling as a legitimate idealization. However, neither accommodates a second concern, the objection from potential bias. We develop a third model that crucially invokes causal considerations, yielding a novel resolution that handles both concerns. This approach resembles Inference to the Best Explanation (IBE) and relates the generalization’s confirmation to confirmation of an (...) associated law. We give it an objective Bayesian formalization and discuss the compatibility of Bayesianism and IBE. (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)

We start by noting that the set-theoretic and semantic paradoxes are framed in terms of a definition or series of definitions. In the process of deriving paradoxes, these definitions are logically represented by a logical equivalence. We will firstly examine the role and usage of definitions in the derivation of paradoxes, both set-theoretic and semantic. We will see that this examination is important in determining how the paradoxes were created in the first place and indeed how they are to be (...) solved in a uniform way. There are three features that are special about these definitions used in the derivation of most of the above paradoxes. The first is the use of self-reference between the definiens and the definiendum, the second is the generality of the definiendum, and the third is the under-determination and over-determination of concepts that usually occur as a result of these definitions. We will examine the impact of these three features on the logical representation of definitions and show how this representation then leads to a uniform paradox solution using an appropriate logic that is both paraconsistent and paracomplete. However, it is the paracompleteness, exhibited through the rejection of the Law of Excluded Middle, together with the rejection of contraction principles, that enables the solution of the paradoxes to go through. We characterize definitions as involving syntactic identity and/or meaning identity. We point out that some paradoxes do not have explicit self-reference or circularity and some may not utilize the generality of the definiendum, but the general characterizations of definitions that we give will still apply. We also look beyond all this to paradoxes that rely on illicit definitions between objects that are essentially different to start with. (shrink)

Frank Cabrera argues that informational explanatory virtues—specifically, mechanism, precision, and explanatory scope—cannot be confirmational virtues, since hypotheses that possess them must have a lower probability than less virtuous, entailed hypotheses. We argue against Cabrera’s characterization of confirmational virtue and for an alternative on which the informational virtues clearly are confirmational virtues. Our illustration of their confirmational virtuousness appeals to aspects of causal inference, suggesting that causal inference has a role for the explanatory virtues. We briefly explore this possibility, delineating a (...) path from Mill’s method of agreement to Inference to the Best Explanation (IBE). (shrink)