(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

By using instrumentation initially designed for counting white blood cells, sperm counts have been utilized by clinicians since 1929, particularly to evaluate cases of suspected infertility. Although this basic biological parameter might be assumed to be stable over time, several studies over the past 20 years have suggested a decline in sperm count or density. The most controversial of these analyses was published in 1992. A flood of criticism followed this analysis of 61 studies that found a 50% decline in (...) sperm density between 1938 and 1990. Critics suggested that historical methods (of counting sperm or conducting studies) were variable and unreliable, differing from modern methods both qualitatively and quantitatively. To address this issue we analyzed these studies for trends in counting methods or their variability. We found neither. Alternative analyses produced some differences in trend estimates, but statistical factors alone could not account for the total decline in sperm density. We reviewed study populations to identify trends in population characteristics, such as abstinence time, that might explain the decline. However, controlling analytically for such factors only increased the rate of decline. We conclude that historical data on sperm density, despite large random error, are surprisingly reliable. Nonetheless, understanding causes of temporal and geographic differences in sperm density must await contemporary data. BioEssays 21:614–621, 1999. © 1999 John Wiley & Sons, Inc. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Journal of Aesthetic Education 38.2 (2004) 120-124 [Access article in PDF] Pictures & Tears. a History of People Who Have Cried in Front of Paintings, by James Elkins. London: Routledge, 2001, xiii + 272pp., $26. In "Tears, Idle Tears" from The Princess, Alfred, Lord Tennyson wonders at the tears forming in his eyes as he gazes out across the fields one fall day. The idyllic countryside, far from (...) providing solace, triggers within him a debilitating sadness, an all-encompassing melancholia, manifested by the tears originating from a deep despair; the autumn fields remind Tennyson's narrative persona of all the days that have passed by him.If Tennyson's eyes had fallen not on autumn fields but on a painting of them then the opening lines to "Tears, Idle Tears" might have served as the perfect epigraphic frame to James Elkins's important study of the tears we do and do not shed when looking at art.One of several recent books by the increasingly influential professor at Chicago's School of the Art Institute, Pictures & Tears probes that aspect of our consciousness that has the capacity [End Page 120] to move us to tears when looking at paintings.Shedding tears in front of paintings? Within contemporary culture it seems rather unlikely for someone to respond to a painting by fighting off, or giving in, to tears. Reactions to paintings in previous periods and societies were wholly different from ours, Elkins argues. Paintings not only incited the passions but were blamed for the onset of numerous, serious medical conditions. Though rare today, cases continue to be reported. The Italian psychiatrist Graziella Magherini even coined a term for it in 1989, "Stendhal syndrome," referring to the novelist whose viewing of art in Florence was accompanied by the onset of a form of nervous exhaustion.While the subtitle of Elkins's book suggests a history of crying in front of pictures, leading us to the nearly tearless present, and thus, presumably, to answers about why we no longer cry in front of paintings, A History of People Who Have Cried in Front of Paintings is somewhat misleading. In the truest sense Pictures & Tears is neither a history of crying in front of pictures nor individual histories of those who have. The book does not follow a linear historical narrative of the tears that pictures have evoked over the centuries. Rather, Elkins's chapters constitute a tableau, the accumulation of fragments, with alternating chapters exploring, first, a particular work of art and the tears it has evoked and, second, ruminations on why that might be the case.At the heart of Elkins's argument is a concern over why we no longer seem willing, or indeed able, to have emotional responses to paintings. Besides the occasional grand response to works of art, particularly those vested withsignificant religious meaning, few admit to intimate connections with paintings. Elkins wants to know why.To answer these questions, Elkins turned to colleagues as well as to people he had never met. His research for the book included letters to fellow scholars and peers, and open calls in newspapers and journals, requesting stories from anyone moved to tears on encountering a painting. He received more than four hundred responses, many of which are included in a substantial appendix. The responses themselves make for an intriguing read and from them Elkins builds a two-pronged argument: we now live in an age that is marked by "stoic intellectualism" (p. 163), yet we still have the capacity to feel an intimate connection to paintings. Art in recent years has demanded greater intellectual engagement, lessintimate involvement. There may be exhibitions that fuel fear, distrust, anger, or rage but these are alienating to the works themselves, although these feelings can certainly be as intense as the more intimate connection that Elkins equates with falling in love.What is it about viewing paintings, as opposed to film or theater, he asks, which prevents full emotional expression? Is it the accoutrements used to view gallery paintings — the exhibition catalogs... (shrink)

PURPOSE—A substantial fraction of the observations made by clinicians and entered into patient records are expressed by means of negation or by using terms which contain negative qualifiers (as in “absence of pulse” or “surgical procedure not performed”). This seems at first sight to present problems for ontologies, terminologies and data repositories that adhere to a realist view and thus reject any reference to putative non-existing entities. Basic Formal Ontology (BFO) and Referent Tracking (RT) are examples of such paradigms. The (...) purpose of the research here described was to test a proposal to capture negative findings in electronic health record systems based on BFO and RT. METHODS—We analysed a series of negative findings encountered in 748 sentences taken from 41 patient charts. We classified the phenomena described in terms of the various top-level categories and relations defined in BFO, taking into account the role of negation in the corresponding descriptions. We also studied terms from SNOMED-CT containing one or other form of negation. We then explored ways to represent the described phenomena by means of the types of representational units available to realist ontologies such as BFO. RESULTS—We introduced a new family of ‘lacks’ relations into the OBO Relation Ontology. The relation lacks_part, for example, defined in terms of the positive relation part_of, holds between a particular p and a universal U when p has no instance of U as part. Since p and U both exist, assertions involving ‘lacks_part’ and its cognates meet the requirements of positivity. CONCLUSION—By expanding the OBO Relation Ontology, we were able to accommodate nearly all occurrences of negative findings in the sample studied. (shrink)

Educating the Virtues David Carr Routledge, 1991. Pp. 304. ISBN 0?415?05746?9. £35. The Philosophical Theology of St Thomas Aquinas By Leo J. Elders E. J. Brill, 1990. Pp. 332. ISBN 0?04?09156?4. $74.36. The State and Justice: An Essay in Political Theory By Milton Fisk Cambridge University Press, 1990. Pp. x + 391. ISBN 0?521?38966?6. £10.95 pbk. Perspectives on Language and Thought: Interrelations in Development Edited by S. A. Gelman and J. P. Byrnes Cambridge University Press, 1992. Pp. xii + 524. (...) ISBN 0?521?37497?9. £50. Aristotle's First Principles By T. H. Irwin Oxford University Press, 1989. Pp. xviii + 702. ISBN 0?198?24717?6. £17.50 Pbk. Truth and Eros: Foucault, Lacan, and the Question of Ethics By John Rajchman Routledge, 1991. Pp. 155. ISBN 0?415?90380?7. £10.99. Logical Forms By Mark Sainsbury Blackwell, 1991. Pp. 408. ISBN 0?631?17777?9. £11.95. Form and Transformation. A Study in the Philosophy of Plotinus By Frederic M. Schroeder McGill?Queen's University Press, 1992. Pp. xiv + 136. ISBN 0?7735?1016?8. £34.95. Did The Greeks Believe Their Myths? An Essay on the Constitutive Imagination By Paul Veyne, translated by Paula Wissing The University of Chicago Press, 1988. Pp. 161. ISBN 0?226?85434?5. £8.75 Pbk. What is Philosophy? By Dietrich von Hildebrand Routledge, 1991. Pp. lvii + 242. ISBN 0?415?02584?2. £12.99. (shrink)

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

It is often alleged that an agent is morally responsible in a liability sense for a transgression just in case s/he deserves a negative interpersonal response for that transgression, blaming responses such as resentment and indignation being paradigms. Aside from a few exceptions, guilt is cited in recent discussions of moral responsibility, if at all, as merely an effect of being blamed, or as a reliable indicator of moral responsibility, but not itself an explanation of moral responsibility. In this paper, (...) I argue that an agent is morally responsible in a liability sense for a transgression just in case s/he deserves to feel moral guilt for that transgression. I argue that this alternative view offers all that the predominant blame-focused view offers, while also solving some puzzling features of moral responsibility. Specifically, it offers a compelling way to reconcile conflicting intuitions about the suberogatory, and allows those who do not understand what Darwall calls ‘second-personal’ reasons to be morally responsible for their immoral acts. (shrink)

When should we make use of the criminal law? Suppose that a responsible legislature seeks to enact a morally justifiable range of criminal prohibitions. What criteria should it apply when deciding whether to proscribe conduct? Crimes, Harms, and Wrongs is a philosophical analysis of the nature, significance, and ethical limits of criminalisation. The authors explore the scope and moral boundaries of harm-based prohibitions, proscriptions of offensive behaviour, and 'paternalistic' prohibitions aimed at preventing self-harm. Their aim is to develop guiding principles (...) for these various grounds of state prohibition, including an analysis of the constraints and mediating factors that weigh for and against criminalisation. Both authors have written extensively in the field. In Crimes, Harms, and Wrongs they have reworked a number of well-known essays and added several important new essays to produce an integrated, accessible, philosophically-sophisticated account that will be of great interest to legal academics, philosophers, and advanced students alike"--Provided by publisher. (shrink)

Aristotle's definition of the soul should be interpreted as: 'the soul is the entelechy of a natural body that serves as its instrument'.

The book opens with a description of the smooth transition from Newtonian to Einsteinian behaviour from electrons as their energy is progressively increased, ...

The criminal law presently distinguishes between actions and omissions, and only rarely proscribes failures to avert consequences that it would be an offense to bring about. Why? In recent years it has been persuasively argued by both Glover and Bennett that, celeris paribus, omissions to prevent a harm are just as culpable as are actions which bring that harm about. On the other hand, and acknowledging that hitherto “lawyers have not been very successful in finding a rationale for it,” Tony (...) Honoré has sought to defend the law's differential treatment. He proposes a “distinct-duties theory” that in addition to the general duties we owe to everyone, we also owe distinct duties to a more limited collection of people and associations, specified by features of our relationship with them. Where a distinct duty holds, breach by omission may well be no better than breach by positive action. But absent a distinct duty, omissions, per Honoré, are less culpable. They are mere failures to intervene and improve or rectify things, whereas actions are positive interventions which make things worse. And, thus, the law has good reason to differentiate between them. (shrink)

In 1956, a few writings of Wittgenstein that he didn't publish in his lifetime were revealed to the public. These writings were gathered in the book Remarks on the Foundations of Mathematics (1956). There, we can see that Wittgenstein had some discontentment with the way philosophers, logicians, and mathematicians were thinking about paradoxes, and he even registered a few polemic reasons to not accept Gödel’s incompleteness theorems.

A Companion to Analytic Philosophy is a comprehensive guide to many significant analytic philosophers and concepts of the last hundred years. Provides a comprehensive guide to many of the most significant analytic philosophers of the last one hundred years. Offers clear and extensive analysis of profound concepts such as truth, goodness, knowledge, and beauty. Written by some of the most distinguished philosophers alive, some of whom have entries in the book devoted to them.

A Companion to Analytic Philosophy is a comprehensive guide to many significant analytic philosophers and concepts of the last hundred years. Provides a comprehensive guide to many of the most significant analytic philosophers of the last one hundred years. Offers clear and extensive analysis of profound concepts such as truth, goodness, knowledge, and beauty. Written by some of the most distinguished philosophers alive, some of whom have entries in the book devoted to them.

It has often been charged that the doctrine of papal infallibility is either false or incoherent. These charges stem, I believe, from a misunderstanding of the logical character of infallible papal utterances, a misunderstanding shared alike by friends and foes of the doctrine. In this paper, I shall argue that the doctrine is both coherent and correct. I devote section I to uncovering some of the sources of this misunderstanding and thereby defending what might be called my negative thesis, namely, (...) that infallible papal utterances are not statements. In section II, I continue defending my negative thesis, not now as an end in itself, but rather as a means of advancing my positive thesis that infallible papal utterances are declarations and have the same logic as other declarations. The latter thesis requires a discussion of the difference between statements and declarations. Section III contains a formal speech act analysis of successful and non-defective statements and declarations with some additional explanatory notes. In section IV, I speak rather generally about the task of philosophical theology in the light of the results and procedures of sections I–III. (shrink)

Thomas Hobbes is recognized as one of the fathers of modern philosophy and political theory. In his own time he was as famous for his work in physics, geometry, and religion. He associated with some of the greatest writers, scientists, and politicians of his age. Martinich has written a complete and accessible biography of Hobbes. The book takes full account of the historical and cultural context in which Hobbes lived, drawing on both published and unpublished sources. It will be a (...) great resource for philosophers, political theorists and historians of ideas. The clear, crisp prose style will also ensure that the book appeals to general readers with an interest in the history of philosophy, the rise of modern science and the English Civil War. (shrink)

In animal husbandry in The Netherlands, as in a wide variety of other societal areas, we see an increased awareness of the fact that progress cannot be attained anymore by simply repeating the way we modernized this sector in the decades before, due to the multiplicity of the problems to be dealt with. The theory of reflexive modernization articulates this macro-social phenomenon, and at the same time serves as a prescriptive master-narrative. In this paper, I analyse the relationship between Feenberg's (...) instrumentalization theory and reflexive design; that is, the approach of doing reflexive modernization. Feenberg's analytical distinction between primary and secondary instrumentalization is useful in highlighting the way social and political values are inscribed into technological arrangements, but is not meant as a method. Reflexive design, on the other hand, is meant to be a reflective and deliberative method that aims to articulate, assess and reintegrate hitherto unquestioned values and presuppositions into new designs of production systems. Reflexive design thus may be seen as a conscious strategy of making explicit the separate stages of instrumentalization in advance, instead of criticizing the implicit embedding of dominant values in technological artefacts once they have been realized. The approach is illustrated with a case from animal husbandry. (shrink)