In a series of papers over a period of several years Barry Smith andWerner Ceusters have offered a number of cogent criticisms of historical approaches to creating, maintaining, and applying biomedical terminologies and ontologies. And they have urged the adoption of what they refer to as a “realism-based” approach. Indeed, at times they insist that the realism-based approach not only offers clear advantages and a well-founded methodological basis for ontology development and evaluation, but that such a realist perspective is in (...) fact necessary for understanding and using terminologies and ontologies in science. -/- This paper explores a number of questions surrounding such claims, provides a careful characterization of the type of realism recommended by Smith and Ceusters, and evaluates the role that realism plays in the critiques and recommendations that they offer. The conclusion reached is that while Smith’s and Ceusters’ criticisms of prior practice in the treatment of ontologies and terminologies in medical informatics are often both perceptive and well founded, and while at least some of their own proposals demonstrate obvious merit and promise, none of this either follows from or requires the brand of realism that they propose. (shrink)

Philosophers frequently struggle with the relation of metaphysics to the everyday world, with its practical value, and with its relation to empirical science. This paper distinguishes several different models of the relation between philosophical ontology and applied (scientific) ontology that have been advanced in the history of philosopy. Adoption of a strong participation model for the philosophical ontologist in science is urged, and requirements and consequences of the participation model are explored. This approach provides both a principled view and justification (...) of the role of the philosophical ontologist in contemporary empirical science as well as guidelines for integrating philosophers and philosophical contributions into the practice of science. (shrink)

In “Ontological realism: Methodology or misdirection?” I offered a detailed critique of the position referred to as “realism” taken by Barry Smith and Werner Ceusters. This position is claimed to serve as the basis for a “realist methodology” that they seek to impose on the development of scientific ontologies, particularly within the biomedical sciences. Here, in part responding to a reply to those criticisms by Smith and Ceusters, I return the focus to an examination of fundamental incoherencies in this realist (...) approach and propose an alternative that is amenable to much of what Smith and Ceusters hope to accomplish. And I sketch what I believe is needed to advance ontology theory and practice in the sciences. (shrink)

This paper advances a detailed exploration of the complex relationships among terms, concepts, and synonymy in the UMLS Metathesaurus, and proposes the study and understanding of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a context and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to (...) synonymy and its relation to terms and concepts. A model theory for a segment of the Metathesaurus is then constructed, and its adequacy relative to the informal treatment is demonstrated. Finally, it is shown how this approach clarifies and addresses the puzzles educed from the informal discussion, and how the model-theoretic perspective may be employed to evaluate some fundamental criticisms of the Metathesaurus. (shrink)

MedDRA (the Medical Dictionary for Regulatory Activities Terminology) is a controlled vocabulary widely used as a medical coding scheme. However, MedDRA’s characterization of its structural hierarchy exhibits some confusing and paradoxical features. The goal of this paper is to examine these features, determine whether there is a coherent view of the MedDRA hierarchy that emerges, and explore what lessons are to be learned from this for using MedDRA and similar terminologies in a broad medical informatics context that includes relations among (...) multiple disparate terminologies, thesauri, and ontologies. (shrink)

Babylon Knowledge Explorer (BKE) is an integrated suite of tools and information sources developed in GlaxoSmithKline's Analysis, Applications, and Research Technologies Department to support the prototyping and implementation of ontology-driven information systems and ontology-enhanced knowledge applications. In this paper we describe the current state of BKE development and focus on some of its distinctive or novel approaches, highlighting -/- * How BKE makes use of multiple large pre-existing ontologies in support of text and data mining. * The methodology employed for (...) importing an ontology and making it immediately accessible to BKE's tools, interfaces, and API. * A formal description of BKE's ontology-based fact model and how this is employed in implementing information retrieval and data mining capabilities. * A sample application built on BKE that illustrates an ontologyenhanced machine learning tool. (shrink)

For centuries (indeed for millennia) philosophers have complained about pseudo-philosophy being practiced by others claiming to be philosophers — and about people being taken in and suffering in one way or another from the mimicry, exploitation, and fakery of the pseudo-philosophers. But no attempt at a careful, comprehensive, and useful characterization of pseudo-philosophy has emerged. This book is a comprehensive historical, theoretical, and practical treatment of pseudo-philosophy — a concept often encountered in both formal and popular philosophy, but rarely with (...) any degree of seriousness and precision. It presents a theory of pseudo-philosophy through the use of models of the genuine philosopher and pseudo-philosopher, and then applies that theory to specific real-world cases. -/- Available on Amazon in either KIndle or paperback format. More details — as well as the complete Preface, Postscript, and References sections — available on my False Wisdom blog (falsephilosophy on blogspot: see External Links below). (shrink)

In 'Notes on the Theory of Reference' Quine offers a brief argument, based on Tarski's Convention T and semantic definition of truth, that the theory of meaning is 'in a worse state' than is the theory of reference and that the concepts of the theory of meaning are inherently more 'foggy and mysterious' than those of thetheory of reference. A careful reconstruction of Quine's argument, however, is sufficient to show both that he covertly imposes a double standard of clarity on (...) the two theories in question and that in so far as Tarski's contributions clarify or explicate the notion of truth they do likewise for the notion of analyticity. Consequently, the appeal which Quine makes to Tarski's definition of truth cannot be used in the manner he wishes, to draw a clear boundary between the theories of meaning and reference. (shrink)

In 'Notes on the Theory of Reference' Quine offers a brief argument, based on Tarski's Convention T and semantic definition of truth, that the theory of meaning is 'in a worse state' than is the theory of reference and that the concepts of the theory of meaning are inherently more 'foggy and mysterious' than those of thetheory of reference. A careful reconstruction of Quine's argument, however, is sufficient to show both that he covertly imposes a double standard of clarity on (...) the two theories in question and that in so far as Tarski's contributions clarify or explicate the notion of truth they do likewise for the notion of analyticity. Consequently, the appeal which Quine makes to Tarski's definition of truth cannot be used in the manner he wishes, to draw a clear boundary between the theories of meaning and reference. (shrink)

This study compares the neural substrate of moral decision making processes between Korean and American participants. By comparison with Americans, Korean participants showed increased activity in the right putamen associated with socio-intuitive processes and right superior frontal gyrus associated with cognitive control processes under a moral-personal condition, and in the right postcentral sulcus associated with mental calculation in familiar contexts under a moral-impersonal condition. On the other hand, American participants showed a significantly higher degree of activity in the bilateral anterior (...) cingulate cortex (ACC) associated with conflict resolution under the moral-personal condition, and in the right medial frontal gyrus (MFG) associated with simple cognitive branching in non-familiar contexts under the moral-impersonal condition when a more lenient threshold was applied, than Korean participants. These findings support the ideas of the interactions between the cultural background, education, and brain development, proposed in the field of cultural psychology and educational psychology. The study introduces educational implications relevant to moral psychologists and educators. (shrink)

The present study aims to examine the relationship between the cortical midline structures (CMS), which have been regarded to be associated with selfhood, and moral decision making processes at the neural level. Traditional moral psychological studies have suggested the role of moral self as the moderator of moral cognition, so activity of moral self would present at the neural level. The present study examined the interaction between the CMS and other moral-related regions by conducting psycho-physiological interaction analysis of functional images (...) acquired while 16 subjects were solving moral dilemmas. Furthermore, we performed Granger causality analysis to demonstrate the direction of influences between activities in the regions in moral decision-making. We first demonstrate there are significant positive interactions between two central CMS seed regions—i.e., the medial prefrontal cortex (MPFC) and posterior cingulate cortex (PCC)—and brain regions associated with moral functioning including the cerebellum, brainstem, midbrain, dorsolateral prefrontal cortex, orbitofrontal cortex and anterior insula (AI); on the other hand, the posterior insula (PI) showed significant negative interaction with the seed regions. Second, several significant Granger causality was found from CMS to insula regions particularly under the moral-personal condition. Furthermore, significant dominant influence from the AI to PI was reported. Moral psychological implications of these findings are discussed. The present study demonstrated the significant interaction and influence between the CMS and morality-related regions while subject were solving moral dilemmas. Given that, activity in the CMS is significantly involved in human moral functioning. (shrink)

During the set-up phase of an international study of genetic influences on outcomes from sepsis, we aimed to characterise potential differences in ethics approval processes and outcomes in participating European countries. Between 2005 and 2007 of the FP6-funded international Genetics Of Sepsis and Septic Shock project, we asked national coordinators to complete a structured survey of research ethic committee approval structures and processes in their countries, and linked these data to outcomes. Survey findings were reconfirmed or modified in 2017. Eighteen (...) countries participated in the study, recruiting 2257 patients from 160 ICUs. National practices differed widely in terms of composition of RECs, procedures and duration of the ethics approval process. Eight countries used a single centralised process for approval, seven required approval by an ethics committee in each participating hospital, and three required both. Outcomes of the application process differed widely between countries because of differences in national legislation, and differed within countries because of interpretation of the ethics of conducting research in patients lacking capacity. The RECs in four countries had no lay representation. The median time from submission to final decision was 1.5 months; in nine approval was received within 1 month; six took over 6 months, and in one 24 months; had all countries been able to match the most efficient approvals processes, an additional 74 months of country or institution-level recruitment would have been available. In three countries, rejection of the application by some local RECs resulted in loss of centres; and one country rejected the application outright. The potential benefits of the single application portal offered by the European Clinical Trials Regulation will not be realised without harmonisation of research ethics committee practices as well as national legislation. (shrink)

This research examines the association between attitudes on cheating and cognitive moral development. In this research, we use Rest's (1979a) Defining Issues Test, the Attitudes on Honesty Scale (Authors) and Academic Integrity Index (Authors); the last two are adaptations of the DIT. A total of 220 students from three universities participated in the study (66 psychology majors and 154 business majors). The data indicate that 66.4 percent of the students reported that they cheated in high school, college, or both high (...) school and college. Psychology majors scored higher than business majors on both the Defining Issues Test (Rest, 1979a) and the Attitudes on Honesty Scale (AHS, Authors). Using factor analysis, we found significant associations between students' ratings of the importance considerations present in the three cheating scenarios and their estimates of whether cheating would occur (i.e., the Academic Integrity Index). Finally, using logistic regression, we found that the scores on the Attitudes on Honesty Scale and Academic Integrity Index associate with the self-reported cheating behavior of college students. (shrink)

The relationship between the United Kingdom and the United States seems to embody most fully the type of the ‘special relationship’ today. It is a relationship founded ultimately on biological kinship, structured by mutual economic and strategic interests and cemented by a sense of political and ‘spiritual’ affinity. At least the broad contours of such contemporary ‘special relationships’ are sufficiently clear. This is far from being the case with those of the Archaic and Classical Greek world, for two main reasons. (...) First, and more decisively, our sources for the history of that world – literary, epigraphical, archaeological – are normally scrappy, discontinuous and variously slanted. Second, and only in part because of the nature of the evidence, the workings of all ancient Greek interstate relationships, whether ‘special’ or not, are in principle controversial. For in the absence of governments and parties in the modern sense it is frequently impossible to explain confidently a particular foreign policy decision taken by a Greek state. A fortiori it is in principle even more difficult to describe and account for ‘special’ relationships between states that apparently transcended purely immediate, local and narrowly self-interested considerations. (shrink)

Research reported by Posner & Raichle may be usefully applied to the rehabilitation of persons with brain damage. Their findings are related to the “dual premotorsystems hypothesis” that reciprocally interactive medial and lateral brain systems are involved in attention and learning. Recent studies show that “brain healing” occurs through dynamic reorganization involving attentional networks postulated by Posner & Raichle.

After yeast cells commit to the cell cycle in a process called START, genes required for DNA synthesis are expressed in late G1. Periodicity is mediated by a hexameric sequence, known as a MCB element, present in all DNA synthesis gene promoters. A complex that specifically binds MCBs has been identified. One polypeptide in the MCB complex is Swi6, a transcription factor that together with Swi4 also binds G1 cyclin promoters and participates in a positive feedback loop at START. The (...) finding that Swi6 is directly involved in both START and DNA synthesis gene control suggest a model in which Swi6, activated through its participation in START, serves as the central transcription factor in coordinating late G1 gene expression. The mechanism may be conserved in all eukaryotic cells. (shrink)

We describe a simple, flexible exercise that can be implemented in the philosophy of science classroom: students are asked to determine the contents of a closed container without opening it. This exercise has revealed itself as a useful platform from which to examine a wide range of issues in the philosophy of science and may, we suggest, even help us think about improving the public understanding of science.

We agree with many theoretical points presented by Rogers & McClelland (R&M), especially the role of domain-general learning of coherent covariation. Nonetheless, we argue that in failing to be informed by key aspects of development, including the role of labels on categorization and the emergence of constraints on learning, their model fails to capture important features of the ontogeny of knowledge.