Physicists regularly invoke universal laws, such as those of motion and electromagnetism, to explain events. Biological and medical scientists have no such laws. How then do they acquire a reliable body of knowledge about biological organisms and human disease? One way is by repeatedly returning to, manipulating, observing, interpreting, and reinterpreting certain subjects—such as flies, mice, worms, or microbes—or, as they are known in biology, “model systems.” Across the natural and social sciences, other disciplinary fields have developed canonical examples that (...) have played a role comparable to that of biology’s model systems, serving not only as points of reference and illustrations of general principles or values but also as sites of continued investigation and reinterpretation. The essays in this collection assess the scope and function of model objects in domains as diverse as biology, geology, and history, attending to differences between fields as well as to epistemological commonalities. Contributors examine the role of the fruit fly Drosophila and nematode worms in biology, troops of baboons in primatology, box and digital simulations of the movement of the earth’s crust in geology, and meteorological models in climatology. They analyze the intensive study of the prisoner’s dilemma in game theory, ritual in anthropology, the individual case in psychoanalytic research, and Athenian democracy in political theory. The contributors illuminate the processes through which particular organisms, cases, materials, or narratives become foundational to their fields, and they examine how these foundational exemplars—from the fruit fly to Freud’s Dora—shape the knowledge produced within their disciplines. Contributors Rachel A. Ankeny Angela N. H. Creager Amy Dahan Dalmedico John Forrester Clifford Geertz Carlo Ginzburg E. Jane Albert Hubbard Elizabeth Lunbeck Mary S. Morgan Josiah Ober Naomi Oreskes Susan Sperling Marcel Weber M. Norton Wise. (shrink)

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

In their paper, “Conversational Artificial Intelligence in Psychotherapy: A New Therapeutic Tool or Agent?” Sedlakova and Trachsel (2023) claim that therapeutic insights and therapeutic changes are...

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

Rapid advancements in artificial intelligence and machine learning (AI/ML) in healthcare raise pressing questions about how much users should trust AI/ML systems, particularly for high stakes clinical decision-making. Ensuring that user trust is properly calibrated to a tool’s computational capacities and limitations has both practical and ethical implications, given that overtrust or undertrust can influence over-reliance or under-reliance on algorithmic tools, with significant implications for patient safety and health outcomes. It is, thus, important to better understand how variability in trust (...) criteria across stakeholders, settings, tools and use cases may influence approaches to using AI/ML tools in real settings. As part of a 5-year, multi-institutional Agency for Health Care Research and Quality-funded study, we identify trust criteria for a survival prediction algorithm intended to support clinical decision-making for left ventricular assist device therapy, using semistructured interviews (n=40) with patients and physicians, analysed via thematic analysis. Findings suggest that physicians and patients share similar empirical considerations for trust, which were primarilyepistemicin nature, focused on accuracy and validity of AI/ML estimates. Trust evaluations considered the nature, integrity and relevance of training data rather than the computational nature of algorithms themselves, suggesting a need to distinguish ‘source’ from ‘functional’ explainability. To a lesser extent, trust criteria were also relational (endorsement from others) and sometimes based on personal beliefs and experience. We discuss implications for promoting appropriate and responsible trust calibration for clinical decision-making use AI/ML. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

In “Revive and Refuse: Capacity, Autonomy, and Refusal of Care After Opioid Overdose”, Marshall, Derse, Weiner, and Joseph contend that patients who may appear to satisfy the standard criteria for...

We report specific heat and μSR measurements on Th and/or B substituted UBe13. The specific heat data show that either Th or B substitution reduces the Kondo temperature TK and increases the entropy at the superconducting transition by almost 20%, indicating an enhanced density of states. However, whereas μSR shows clear evidence for magnetic correlations for Th substitutions, no magnetism is observed for B substitutions. The enhanced specific heat jump in the B-substituted material is associated with a change in the (...) superconducting properties as TK is reduced. (shrink)

BackgroundIn the Canadian Alliance for Healthy Hearts and Minds (CAHHM) cohort, participants underwent magnetic resonance imaging (MRI) of the brain, heart, and abdomen, that generated incidental findings (IFs). The approach to managing these unexpected results remain a complex issue. Our objectives were to describe the CAHHM policy for the management of IFs, to understand the impact of disclosing IFs to healthy research participants, and to reflect on the ethical obligations of researchers in future MRI studies.MethodsBetween 2013 and 2019, 8252 participants (...) (mean age 58 ± 9 years, 54% women) were recruited with a follow-up questionnaire administered to 909 participants (40% response rate) at 1-year. The CAHHM policy followed a restricted approach, whereby routine feedback on IFs was not provided. Only IFs of severe structural abnormalities were reported.ResultsSevere structural abnormalities occurred in 8.3% (95% confidence interval 7.7–8.9%) of participants, with the highest proportions found in the brain (4.2%) and abdomen (3.1%). The majority of participants (97%) informed of an IF reported no change in quality of life, with 3% of participants reporting that the knowledge of an IF negatively impacted their quality of life. Furthermore, 50% reported increased stress in learning about an IF, and in 95%, the discovery of an IF did not adversely impact his/her life insurance policy. Most participants (90%) would enrol in the study again and perceived the MRI scan to be beneficial, regardless of whether they were informed of IFs. While the implications of a restricted approach to IF management was perceived to be mostly positive, a degree of diagnostic misconception was present amongst participants, indicating the importance of a more thorough consent process to support participant autonomy.ConclusionThe management of IFs from research MRI scans remain a challenging issue, as participants may experience stress and a reduced quality of life when IFs are disclosed. The restricted approach to IF management in CAHHM demonstrated a fair fulfillment of the overarching ethical principles of respect for autonomy, concern for wellbeing, and justice. The approach outlined in the CAHHM policy may serve as a framework for future research studies.Clinical trial registrationhttps://clinicaltrials.gov/ct2/show/nct02220582. (shrink)

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. (shrink)

We report the identification of a recurrent, 520-kb 16p12.1 microdeletion associated with childhood developmental delay. The microdeletion was detected in 20 of 11,873 cases compared with 2 of 8,540 controls and replicated in a second series of 22 of 9,254 cases compared with 6 of 6,299 controls. Most deletions were inherited, with carrier parents likely to manifest neuropsychiatric phenotypes compared to non-carrier parents. Probands were more likely to carry an additional large copy-number variant when compared to matched controls. The clinical (...) features of individuals with two mutations were distinct from and/or more severe than those of individuals carrying only the co-occurring mutation. Our data support a two-hit model in which the 16p12.1 microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large deletions or duplications. Analysis of other microdeletions with variable expressivity indicates that this two-hit model might be more generally applicable to neuropsychiatric disease. © 2010 Nature America, Inc. All rights reserved. (shrink)

Previous research has yielded inconsistent findings concerning the relationship between envy and schadenfreude. Three studies examined whether the distinction between benign and malicious envy can resolve this inconsistency. We found that malicious envy is related to schadenfreude, while benign envy is not. This result held both in the Netherlands where benign and malicious envy are indicated by separate words (Study 1: Sample A, N = 139; Sample B, N = 150), and in the USA where a single word is used (...) to denote both types (Study 2, N = 180; Study 3, N = 349). Moreover, the effect of malicious envy on schadenfreude was independent of other antecedents of schadenfreude (such as feelings of inferiority, disliking the target person, anger, and perceived deservedness). These findings improve our understanding of the antecedents of schadenfreude and help reconcile seemingly contradictory findings on the relationship between envy and schadenfreude. (shrink)

MEDIEVAL LOGICS LAMBERT MARIE DE RIJK (ed.), Die mittelalterlichen Traktate De mod0 opponendiet respondendi, Einleitung und Ausgabe der einschlagigen Texte. (Beitrage zur Geschichte der Philosophie und Theologie des Mittelalters, Neue Folge Band 17.) Miinster: Aschendorff, 1980. 379 pp. No price stated. THE SEVENTEENTH CENTURY MARTA FATTORI, Lessico del Novum Organum di Francesco Bacone. Rome: Edizioni dell'Ateneo 1980. Two volumes, il + 543, 520 pp. Lire 65.000. VIVIAN SALMON, The study of language in 17th century England. (Amsterdam Studies in the Theory (...) and History of Linguistic Science, Series 111: Studies in theHistory of Linguistics, Volume 17.) Amsterdam: John Benjamins B.V., 1979.x + 218 pp. Dfl. 65. Theoria cum Praxi. Zum Verhaltnis von Theorie und Praxis im 17. und 18. Jahrhundert. (Akten des 111. Internationalen Leibnizkongress, Hannover, 12. bis 17.November 1977, Band 111: Logik, Erkenntnistheorie, Wissenschaftstheorie, Metaphysik, Theologie.) Wiesbaden: Franz Steiner Verlag, 1980. vii + 269 pp. DM 48. CLASSICAL AND NON-CLASSICAL LOGICS MICHAEL CLARK, The place of syllogistic in logical theory. Nottingham: University of Nottingham Press, 1980. ix + 151 pp. £3.00. A.F. PARKER-RHODES, The theory of indistinguishables. Dordrecht, Boston and London: D. Reidel Publishing Company, 1981. xvii + 216 pp. Dfl.90.00/$39.50. NICHOLAS RESCHER and ROBERT BRANDOM, The logic of inconsistency. Oxford:Basil Blackwell, 1980. x + 174 pp. f 11.50. MISCELLANEOUS J. ZELENY, The logic of Marx. Translated from the German by T. Carver. Oxford: Basil Blackwell, 1980. xcii + 247 pp. £12.50. FELIX KAUFMANN, The infinite in mathematics. Edited by Brian McGuinness. Introduction by E. Nagel. Translation from the German by Paul Foulkes. Dordrecht: Reidel, 1978. xvii + 235 pp. Dfl 85/$39.50 (cloth); Dfl 45/$19.95 (paper). PAMELA MCCORDUCK, Machines who think. San Francisco: W.H. Freeman and Company, 1979. xiv + 275 pp. $14.95. J. MITTELSTRASS (ed.), Enzyklopadie Philosophie und Wissenschaftstheorie Bd. 1 : A-G. Mannheim, Wien, Ziirich: Bibliographisches Institut, 1980. 835 pp. DM 128. (shrink)

Book Information Strong Hermeneutics: Contingency and Moral Identity. By Nicholas H. Smith. Routledge. London. 1997. Pp. x + 197. Paperback, £14.99.

Qualitative and quantitative methods were used to investigate how shopping behaviors and environment influence dietary intake and weight status among homeless Minnesotans living in food deserts. Seven focus groups (n = 53) and a quantitative survey (n = 255), using the social cognitive theory as the theoretical framework, were conducted at two homeless shelters (S1 and S2) in the Twin Cities area. Heights, weights, and 24-h dietary recalls were also collected. Food stores within a five-block radius of the shelters were (...) evaluated for the price and availability of foods and compared to the Thrifty Food Plan’s market basket prices (MBP). Results showed that almost 80% of the sample was overweight or obese, with women consuming less than the recommended level for the fruits, vegetables, and milk food groups and excess for the fats/oils/sweets food group. Focus groups and participant surveys indicated that the shelter infrastructure and surrounding community influenced the types of foods available, food store access, and the foods purchased and consumed. Participants relied on food assistance programs, including food stamps, to supplement their food supply; however, some felt the high food prices at neighboring stores limited food choice and that food stamps did not adequately cover food costs. Results from the food store survey found the majority of food prices exceeded Midwest or national MBP. To promote healthier dietary intake and weight status, community-based interventions and city planners should aim to increase access to food through improved food availability and food access within the shelter environment and surrounding community. (shrink)

This note is prompted by a re-reading of the late Professor J. L. Austin's British Academy Lecture of 1956 “Ifs and Cans” and Professor P. H. Nowell-Smith's rejoinder to it. Austin states his topic at the beginning, and though he re-formulates it more precisely later on, it will suffice for my purposes to quote the opening short paragraph. He asks: “Are cans constitutionally iffy? Whenever, that is, we say that we can do something, or could do something, or could (...) have done something, is there an if in the offing—suppressed, it may be, but due nevertheless to appear when we set out our sentence in full or when we give an explanation of its meaning?”. Towards the end of his lecture he states his conclusion concerning the issue, viz. determinism, which is usually prominent at least implicitly in our discussion of such questions, in the following terms: “Determinism, whatever it may be, may yet be the case, but at least it appears not consistent with what we ordinarily say and presumably think.”. (shrink)

In recent years the writings of Ludwig Wittgenstein have received much attention from philosophers in general and especially from philosophers interested in religion; and there is no doubt that Wittgenstein's legacy of thought is both highly suggestive and highly problematical. It seems likely, however, that the vogue which Wittgenstein now enjoys owes not a little to his peculiar place in the development of modern philosophy and, in particular, of that empiricist tradition in philosophy which stems from what has been called (...) the revolution in philosophy in the early decades of the present century. (shrink)

In his book on Karl Barth Professor T. F. Torrance spoke at one point of ‘the great watershed of modern theology’. ‘There are,’ he wrote, 1 ‘two basic issues here. On the one hand, it is the very substance of the Christian faith that is at stake, and on the other hand, it is the fundamental nature of scientific method, in its critical and methodological renunciation of prior understanding, that is at stake. This is the great watershed of modern theology: (...) either we take the one way or the other – there is no third alter native… one must go either in the direction taken by Barth or in the direction taken by Bultmann.’. (shrink)

Experimental philosophers have gathered impressive evidence for the surprising conclusion that philosophers' intuitions are out of step with those of the folk. As a result, many argue that philosophers' intuitions are unreliable. Focusing on the Knobe Effect, a leading finding of experimental philosophy, we defend traditional philosophy against this conclusion. Our key premise relies on experiments we conducted which indicate that judgments of the folk elicited under higher quality cognitive or epistemic conditions are more likely to resemble those of the (...) philosopher. We end by showing how our experimental findings can help us better understand the Knobe Effect. (shrink)

Educational theory; knowledge; sufism, an analytical treatise.