A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

As moral injury is a still-emerging concept within the area of military mental health, prevalence estimates for moral injury and its precursor, potentially morally injurious events (PMIEs), remain unknown for many of the world’s militaries. The present study sought to estimate the prevalence of PMIEs in the Canadian Armed Forces (CAF), using data collected from CAF personnel deployed to Afghanistan, via logistic regressions controlling for relevant sociodemographic, military, and deployment characteristics. Analyses revealed that over 65% of CAF members reported exposure (...) to at least one event that would be considered a PMIE. The most commonly PMIEs individuals reported included seeing ill or injured women and children they were unable to help (48.4%), being unable to distinguish between combatants and non-combatants (43.6%), and finding themselves in a threatening situation where they were unable to respond due to the rules of engagement under which they were required to operate (35.4%). These findings provide support for both the presence of exposure to PMIEs in CAF members and the need for formal longitudinal data collection regarding PMIE exposure and moral injury development. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

Research and engineering in the quantum domain involve long chains of activity involving theory development, hypothesis formation, experimentation, device prototyping, device testing, and many more. At each stage multiple paths become possible, and of the paths pursued, the majority will lead nowhere. Our quantum metascience approach provides a strategy which enables all stakeholders to gain an overview of those developments along these tracks, that are relevant to their specific concerns. It provides a controlled vocabulary, built out of terms that are (...) designed to be maximally comprehensible to all groups of stakeholders and across all the sub-fields of the quantum domain. (shrink)

The Infectious Disease Ontology (IDO) is a suite of interoperable ontology modules that aims to provide coverage of all aspects of the infectious disease domain, including biomedical research, clinical care, and public health. IDO Core is designed to be a disease and pathogen neutral ontology, covering just those types of entities and relations that are relevant to infectious diseases generally. IDO Core is then extended by a collection of ontology modules focusing on specific diseases and pathogens. In this paper we (...) present applications of IDO Core within various areas of infectious disease research, together with an overview of all IDO extension ontologies and the methodology on the basis of which they are built. We also survey recent developments involving IDO, including the creation of IDO Virus; the Coronaviruses Infectious Disease Ontology (CIDO); and an extension of CIDO focused on COVID-19 (IDO-CovID-19).We also discuss how these ontologies might assist in information-driven efforts to deal with the ongoing COVID-19 pandemic, to accelerate data discovery in the early stages of future pandemics, and to promote reproducibility of infectious disease research. (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)

Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical defi nitions thereby also supporting reasoning over the tagged data. Aim: This (...) paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. (shrink)

After severe brain injury, one of the key challenges for medical doctors is to determine the patient’s prognosis. Who will do well? Who will not do well? Physicians need to know this, and families need to do this too, to address choices regarding the continuation of life supporting therapies. However, current prognostication methods are insufficient to provide a reliable prognosis. -/- Functional Magnetic Resonance Imaging (MRI) holds considerable promise for improving the accuracy of prognosis in acute brain injury patients. Nonetheless, (...) research on functional MRI in the intensive care unit context is ethically challenging. These studies raise several ethical issues that have not been addressed so far. In this article, Prof. Charles Weijer and his co-workers provide a framework for researchers and ethics committees to design and review these studies in an ethically sound way. (shrink)

In the last two decades we have witnessed considerable efforts directed towards making electronic healthcare records comparable and interoperable through advances in record architectures and (bio)medical terminologies and coding systems. Deep semantic issues in general, and ontology in particular, have received some interest from the research communities. However, with the exception of work on so-called ‘controlled vocabularies’, ontology has thus far played little role in work on standardization. The prime focus has been rather the rapid population of terminologies at the (...) level of fine detail. In this paper, we argue that more efforts are needed on the side of both research and standardization to ensure that the coding systems used in electronic healthcare records enjoy a semantics that is coherent with the semantics of the record. We propose realist ontology as a method to bring about this coherence by means of a robust system of top-level ontological categories. (shrink)

This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...) bearer. A definition of ‘protective resistance’ is proposed for use in the Infectious Disease Ontology (IDO) and we show how this definition can be used to characterize the antibiotic resistance in Methicillin-Resistant Staphylococcus aureus (MRSA). The ontological relations between entities in our MRSA case study are used alongside a series of logical inference rules to illustrate logical reasoning about resistance. A description logic representation of blocking dispositions is also provided. We demonstrate that our characterization of resistance is sufficiently general to cover two other cases of resistance in the infectious disease domain involving HIV and malaria. (shrink)

Ontology has been proposed as a solution to the 'Tower of Babel' problem that threatens the semantic interoperability of information systems constructed independently for the same domain. In information systems research and applications, ontologies are often implemented by formalizing the meanings of words from natural languages. However, words in different natural languages sometimes subdivide the same domain of reality in terms of different conceptual categories. If the words and their associated concepts in two natural languages, or even in two terminological (...) traditions within the same language, do not have common referents in the real world, an ontology based on word meanings will inherit the 'Tower of Babel' problem from the languages involved, rather than solve it. In this paper we present evidence from a preliminary comparison of landscape terms in English with those in the Yindjibarndi language of northwestern Australia demonstrating that this problem is not just hypothetical. Some possible solutions are suggested. (shrink)

When people want to identify the causes of an event, assign credit or blame, or learn from their mistakes, they often reflect on how things could have gone differently. In this kind of reasoning, one considers a counterfactual world in which some events are different from their real-world counterparts and considers what else would have changed. Researchers have recently proposed several probabilistic models that aim to capture how people do (or should) reason about counterfactuals. We present a new model and (...) show that it accounts better for human inferences than several alternative models. Our model builds on the work of Pearl (2000), and extends his approach in a way that accommodates backtracking inferences and that acknowledges the difference between counterfactual interventions and counterfactual observations. We present six new experiments and analyze data from four experiments carried out by Rips (2010), and the results suggest that the new model provides an accurate account of both mean human judgments and the judgments of individuals. (shrink)

The Center for Disease Control and Prevention’s Active Bacterial Core Surveillance (CDC ABCs) Program is a collaborative effort betweeen the CDC, state health departments, laboratories, and universities to track invasive bacterial pathogens of particular importance to public health [1]. The year-end surveillance reports produced by this program help to shape public policy and coordinate responses to emerging infectious diseases over time. The ABCs case report form (CRF) data represents an excellent opportunity for data reuse beyond the original surveillance purposes.

The COVID-19 pandemic prompted immense work on the investigation of the SARS-CoV-2 virus. Rapid, accurate, and consistent interpretation of generated data is thereby of fundamental concern. Ontologies––structured, controlled, vocabularies––are designed to support consistency of interpretation, and thereby to prevent the development of data silos. This paper describes how ontologies are serving this purpose in the COVID-19 research domain, by following principles of the Open Biological and Biomedical Ontology (OBO) Foundry and by reusing existing ontologies such as the Infectious Disease Ontology (...) (IDO) Core, which provides terminological content common to investigations of all infectious diseases. We report here on the development of an IDO extension, the Virus Infectious Disease Ontology (VIDO), a reference ontology covering viral infectious diseases. We motivate term and definition choices, showcase reuse of terms from existing OBO ontologies, illustrate how ontological decisions were motivated by relevant life science research, and connect VIDO to the Coronavirus Infectious Disease Ontology (CIDO). We next use terms from these ontologies to annotate selections from life science research on SARS-CoV-2, highlighting how ontologies employing a common upper-level vocabulary may be seamlessly interwoven. Finally, we outline future work, including bacteria and fungus infectious disease reference ontologies currently under development, then cite uses of VIDO and CIDO in host-pathogen data analytics, electronic health record annotation, and ontology conflict-resolution projects. (shrink)

With the rising poverty in the Philippines, Filipino farm workers in Agusan del Sur faced distinctive challenges in their homes and working environment. This study aimed to discuss Filipino farm workers’ lived experiences, challenges, and coping mechanisms. Filipino farm workers shared their experiences that tapped into their psychological aspects. Mainly, the problem was stress, worry, and frustration centered on poverty and educational attainment. Some farm workers were likely unaware of the main problem that prolonged their hardships. Still, most have managed (...) to fortify their mental health. This report indicates that most Filipino farm workers in Agusan del Sur have a healthy psychological well-being. However, this statement does not change the intensity of their struggle to survive. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

One way to detect, monitor and prevent adverse events with the help of Information Technology is by using ontologies capable of representing three levels of reality: what is the case, what is believed about reality, and what is represented. We report on how Basic Formal Ontology and Referent Tracking exhibit this capability and how they are used to develop an adverse event ontology and related data annotation scheme for the European ReMINE project.

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (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)

There is a narrow thread in the vast literature on Kafka which pertains to Kafka’s knowledge of philosophy, and more precisely to Kafka’s use in his fictional writings of some of the main ideas of Franz Brentano. Kafka attended courses in philosophy at the Charles University given by Brentano’s students Anton Marty and Christian von Ehrenfels, and was for several years a member of a discussion-group organized by orthodox adherents of the Brentanian philosophy in Prague. The present essay summarizes (...) what is known about Kafka’s relations to the Brentanist movement. It draws on Brentanian ideas on the evidence of inner perception, on oblique consciousness, on active introspection, on correct and incorrect judgment, and on consciousness as a species of inner tribunal, in order to throw light on central features of Kafka’s writings, including stylistic features. Special attention is directed towards Die Verwandlung and Der Prozess, and a reading of the latter is offered according to which the trial of Joseph K. occurs entirely within the mind of K. himself. The revisions in the 1997 version of the paper relate especially to the treatment of Kafka and Brentano in Arnold Heidsieck’s book The Intellectual Contexts of Kafka’s Fiction: Philosophy, Law, Religion, of 1994. (shrink)

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (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.

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Many of the items that humans consume are produced in ways that involve serious harms to persons. Familiar examples include the harms involved in the extraction and trade of conflict minerals (e.g. coltan, diamonds), the acquisition and import of non- fair trade produce (e.g. coffee, chocolate, bananas, rice), and the manufacture of goods in sweatshops (e.g. clothing, sporting equipment). In addition, consumption of certain goods (significantly fossil fuels and the products of the agricultural industry) involves harm to the environment, to (...) future persons, and to current persons in low-lying and developing countries, by way of their impacts on climate change. When it comes to such large-scale harms, it's easy for the individual to feel helpless. Even if she sincerely wishes things were otherwise, she may wonder what she could possibly do to make them so. In this paper I briefly explore several promising avenues for generating duties in individuals to consume ethically, and develop one in particular: that an individual ought to signal her commitments to others, as a first step in collectivizing to act against unjust global labour practices. (shrink)

The goal of the Department of Defense Net-Centric Data Strategy is to improve data sharing throughout the DoD. Data sharing is a critical element of interoperability in the emerging system-of-systems. Achieving interoperability requires the elimination of two types of data heterogeneity: differences of syntax and differences of semantics. This paper builds a path toward semantic uniformity through application of a disciplined approach to ontology. An ontology is a consensus framework representing the types of entities within a given domain and the (...) relations between them. The construction of an ontology begins when a Community of Interest (COI) identifies its authoritative data sources (ADS), which are usually manifest in relevant doctrinal publications, glossaries, data dictionaries, and logical data models. The identified terms are then defined in relation to a common logical framework that has been designed to ensure interoperability with other ontologies created on the basis of the same strategy. As will be described, the Command and Control (C2) Ontology will include representations of a substantial number of entities within the Command and Control (C2) domain. If domain ontologies (e.g. Strike and Counterinsurgency) semantically align with the C2 Ontology, then a substantial barrier to systems interoperability is thereby crossed. (shrink)

A critique of dubious contrasts between "science" and "religion" drawn on the basis of cognitive-evolutionary accounts of human psychology, e.g.,. the claim that religious concepts are “likely” and “natural” for the human mind whereas scientific thinking is “rare” and “unnatural.” Initially made by biologist Lewis Wolpert in *The Unnatural Nature of Science* (1993) and anthropologist Pascal Boyer in *Religion Explained: The Evolutionary Origins of Religious Thought* (2001), they are developed at length by philosopher R. N. McCauley in a*Why Religion is (...) Natural and Science is Not* (2011). These contrasts involve tendentiously narrow or broad definitions of the terms “science” and “religion” and the obliteration of the complex historical and intellectual relations between the ideas and practices currently identified by those terms. (shrink)

In this response to comments on my article, “The Chimera of Relativism,” in the same issue of *Common Knowledge* , by cognitive neuroscientist Andreas Roepstorff, classicist G. E. R. Lloyd, and anthropologist Martin Holbraad, I illustrate and reinforce Lloyd's cautions regarding the hazards of intercultural—here, Chinese-Western—comparisons in studies of culture and cognition. Examination of a foundational study in East-West cultural/cognitive differences cited by Roepstorff indicates extensive conceptual and methodological problems in that tradition of research. Although Holbraad champions a more radical (...) relativism than that offered in my work, the moves he urges have either been present in my work from the beginning or are both dubiously radical and otherwise undesirable. (shrink)

I have two aims in this paper. In §§2-4 I contend that Moore has two arguments (not one) for the view that that ‘good’ denotes a non-natural property not to be identified with the naturalistic properties of science and common sense (or, for that matter, the more exotic properties posited by metaphysicians and theologians). The first argument, the Barren Tautology Argument (or the BTA), is derived, via Sidgwick, from a long tradition of anti-naturalist polemic. But the second argument, the Open (...) Question Argument proper (or the OQA), seems to have been Moore’s own invention and was probably devised to deal with naturalistic theories, such as Russell’s, which are immune to the Barren Tautology Argument. The OQA is valid and not (as Frankena (1939) has alleged) question-begging. Moreover, if its premises were true, it would have disposed of the desire-to-desire theory. But as I explain in §5, from 1970 onwards, two key premises of the OQA were successively called into question, the one because philosophers came to believe in synthetic identities between properties and the other because it led to the Paradox of Analysis. By 1989 a philosopher like Lewis could put forward precisely the kind of theory that Moore professed to have refuted with a clean intellectual conscience. However, in §§6-8 I shall argue that all is not lost for the OQA. I first press an objection to the desire-to-desire theory derived from Kripke’s famous epistemic argument. On reflection this argument looks uncannily like the OQA. But the premise on which it relies is weaker than the one that betrayed Moore by leading to the Paradox of Analysis. This suggests three conclusions: 1) that the desire-to-desire theory is false; 2) that the OQA can be revived, albeit in a modified form; and 3) that the revived OQA poses a serious threat to what might be called semantic naturalism. (shrink)

There are two motivations commonly ascribed to historical actors for taking up statistics: to reduce complicated data to a mean value (e.g., Quetelet), and to take account of diversity (e.g., Galton). Different motivations will, it is assumed, lead to different methodological decisions in the practice of the statistical sciences. Karl Pearson and W. F. R. Weldon are generally seen as following directly in Galton’s footsteps. I argue for two related theses in light of this standard interpretation, based on a reading (...) of several sources in which Weldon, independently of Pearson, reflects on his own motivations. First, while Pearson does approach statistics from this "Galtonian" perspective, he is, consistent with his positivist philosophy of science, utilizing statistics to simplify the highly variable data of biology. Weldon, on the other hand, is brought to statistics by a rich empiricism and a desire to preserve the diversity of biological data. Secondly, we have here a counterexample to the claim that divergence in motivation will lead to a corresponding separation in methodology. Pearson and Weldon, despite embracing biometry for different reasons, settled on precisely the same set of statistical tools for the investigation of evolution. (shrink)

Newton’s impact on Enlightenment natural philosophy has been studied at great length, in its experimental, methodological and ideological ramifications. One aspect that has received fairly little attention is the role Newtonian “analogies” played in the formulation of new conceptual schemes in physiology, medicine, and life science as a whole. So-called ‘medical Newtonians’ like Pitcairne and Keill have been studied; but they were engaged in a more literal project of directly transposing, or seeking to transpose, Newtonian laws into quantitative models of (...) the body. I am interested here in something different: neither the metaphysical reading of Newton, nor direct empirical transpositions, but rather, a more heuristic, empiricist construction of Newtonian analogies. Figures such as Haller, Barthez, and Blumenbach constructed analogies between the method of celestial mechanics and the method of physiology. In celestial mechanics, they held, an unknown entity such as gravity is posited and used to mathematically link sets of determinate physical phenomena (e.g., the phases of the moon and tides). This process allows one to remain agnostic about the ontological status of the unknown entity, as long as the two linked sets of phenomena are represented adequately. Haller et. al. held that the Newtonian physician and physiologist can similarly posit an unknown called ‘life’ and use it to link various other phenomena, from digestion to sensation and the functioning of the glands. These phenomena consequently appear as interconnected, goal-oriented processes which do not exist either in an inanimate mechanism or in a corpse. In keeping with the empiricist roots of the analogy, however, no ontological claims are made about the nature of this vital principle, and no attempts are made to directly causally connect such a principle and observable phenomena. The role of the “Newtonian analogy” thus brings together diverse schools of thought, and cuts across a surprising variety of programs, models and practices in natural philosophy. (shrink)

Taking my cue from Michael Smith, I try to extract a decent argument for non-cognitivism from the text of the Treatise. I argue that the premises are false and that the whole thing rests on a petitio principi. I then re-jig the argument so as to support that conclusion that Hume actually believed (namely that an action is virtuous if it would excite the approbation of a suitably qualified spectator). This argument too rests on false premises and a begged (...) question. Thus the Motivation Argument fails BOTH as an argument for noncognitivism AND as an argument for what Hume actually believed, that moral distinctions are not derived from reason and that moral properties are akin to secondary qualities. So far as the Motivation Argument is concerned, both cognitivists and rationalists can rest easy. Themes: 1) Hume’s Slavery of Reason thesis is only defensible if passions are not only desires but sometimes dispositions to acquire desires (DTADs). 2) A desire for our good on the whole, which Humeans need to posit to fend off apparent counterexamples to the Slavery of Reason Thesis, does not sit well with the Humean theory of how novel desires arise (an objection due originally to Reid). 3) Hume is wrong to suppose that ‘abstract or demonstrative reasoning never influences any of our actions, but only as it directs our judgment concerning causes and effects’ as the examples of Russell and Hobbes convincingly demonstrate. This ironic as both Russell and Hobbes subscribed to the Slavery of Reason Thesis. 4) I critique Michael Smith’s critique of motivational externalism. (shrink)

We describe a prototype ontology-driven information system (ODIS) that exploits what we call Portion of Reality (POR) representations. The system takes both sensor data and natural language text as inputs and composes on this basis logically structured POR assertions. The goal of our prototype is to represent both natural language and sensor data within a single framework that is able to support both axiomatic reasoning and computation. In addition, the framework should be capable of discovering and representing new kinds of (...) situations and thematic roles, (e.g., roles such as agent, patient and instrument), based on new compositions of existing representations. We applied our prototype in an intelligence analysis use case to test the hypothesis that a framework of this sort can produce usefully structured information from combined natural language and sensor data inputs. We further tested our hypothesis by adding an enhanced US Air Force ontology framework to our ODIS in order to (1) process a collection of sensor data, intel reports, and mission plans; (2) build composite POR representations from these data; and (3) machine analyze the fused results to infer mission threats. (shrink)

Until very recently the received wisdom on Russell’s moral philosophy was that it is uninspired and derivative, from Moore in its first phase and from Hume and the emotivists in its second. In my view this is a consensus of error. In the latter part of this essay I contend: 1) that Russell’s ‘work in moral philosophy’ had at least three, and (depending how you look at it) up to six ‘main phases’; 2) that in some of those phases, it (...) was not derivative, but on the contrary, highly original; 3) that Russell was a pioneer of two of the chief forms of ethical anti-realism that have dominated debate in this century, emotivism and the error theory (so that if the theory of Human Society was derived from emotivism, it was derived from a family of theories that Russell himself helped to create); 4) that the revolt against Hegelianism, which led to the birth of Analytic Philosophy, had an ethical dimension to it; and 5) that Russell played an important part in the debates that led up to Moore’s Principia Ethica, so that the view form which his own opinions were derived is one that he helped to develop. -/- I also argue that Russell himself pioneered a rather puritanical conception of philosophy which tended to extrude his own writings on politics and practical ethics as not really philosophical. Since this conception has been largely abandoned, it is time to let them back into the fold. I argue that this views of practical affairs are often backed by interesting philosophical arguments, illustrating this thesis with a reconstruction and critique of Russell’s Hobbesian argument for world government. (shrink)

Hume is widely regarded as the grandfather of emotivism and indeed of non-cognitivism in general. For the chief argument for emotivism - the Argument from Motivation - is derived from him. In my opinion Hume was not an emotivist or proto-emotivist but a moral realist in the modern ‘response-dependent’ style. But my interest in this paper is not the historical Hume but the Hume of legend since the legendary Hume is one of the most influential philosophers of the present age. (...) According to Michael Smith ‘the Moral Problem’ – the central issue in meta-ethics - is that the premises of Hume’s argument appear to be true though the non-cognitivist conclusion appears to be false. Since the argument seems to be valid, something has got to give. Smith struggles to solve the problem by holding on to something like the premises of the argument whilst trying to fend off the conclusion. In my view this is a wasted effort. Hume was not arguing for non-cognitivsm in the first place, and the arguments for non-cognitivism that can be extracted from his writings are no good. Either the premises are false or the inferences are invalid. And this is despite the fact that Hume was substantially right about reason and the passions. Thus ‘the Moral Problem’ is not a problem, and the legendary Hume does not deserve his influence. -/- An important theme in this paper is the concept of a DTAD or a dispositions to acquire desires. These play an important role in motivation but unlike desires (with which they are sometimes confused ) they are NOT propositional attitudes. (shrink)

The essay is critically examines the conceptual problems with the influential modularity model of mind. We shall see that one of the essential characters of modules, namely informational encapsulation, is not only inessential, it ties a knot at a crucial place blocking the solution to the problem of understanding the formation of concepts from percepts (nodes of procedural knowledge). Subsequently I propose that concept formation takes place by modulation of modules leading to cross-representations, which were otherwise prevented by encapsulation. It (...) must be noted that the argument is not against modular architecture, but a variety of an architecture that prevents interaction among modules. This is followed by a brief argument demonstrating that module without modularization, i.e. without developmental history, is impossible. Finally the emerging picture of cognitive development is drawn in the form of the layers in the fabric of mind, with a brief statement of the possible implications. (shrink)

How should we think of the preferences of citizens? Whereas self-optimal policy is relatively straightforward to produce, socially optimal policy often requires a more detailed examination. In this paper, we identify an issue that has received far too little attention in welfarist modelling of public policy, which we name the "hidden assumptions" problem. Hidden assumptions can be deceptive because they are not expressed explicitly and the social planner (e.g. a policy maker, a regulator, a legislator) may not give them the (...) critical attention they need. We argue that ethical expertise has a direct role to play in public discourse because it is hard to adopt a position on major issues like public health policy or healthcare prioritisation without making contentious assumptions about population ethics. We then postulate that ethicists are best situated to critically evaluate these hidden assumptions, and can therefore play a vital role in public policy debates. (shrink)

Mehlman and Li offer a framework for approaching the bioethical issues raised by the military use of genomics that is compellingly grounded in both the contemporary civilian and military ethics of medical research, arguing that military commanders must be bound by the two principles of paternal- ism and proportionality. I agree fully. But I argue here that this is a much higher bar than we may fully realize. Just as the principle of proportionality relies upon a thorough assessment of harms (...) caused and military advantage gained, the use of genomic research, on Mehlman and Li’s view, will require an accurate understanding of the connection between genotypes and phenotypes – accurate enough to ameliorate the risk undertaken by our armed forces in being subject to such research. Recent conceptual work in evolutionary theory and the philosophy of biology, however, renders it doubtful that such knowledge is forthcoming. The complexity of the relationship between genotypic factors and realized traits (the so-called ‘G→P map’) makes the estimation of potential military advantage, as well as potential harm to our troops, incredibly challenging. Such fundamental conceptual challenges call into question our ability to ever satisfactorily satisfy the demands of a sufficiently rigorous ethical standard. (shrink)

Bertrand Russell was a meta-ethical pioneer, the original inventor of both emotivism and the error theory. Why, having abandoned emotivism for the error theory, did he switch back to emotivism in the 1920s? Perhaps he did not relish the thought that as a moralist he was a professional hypocrite. In addition, Russell's version of the error theory suffers from severe defects. He commits the naturalistic fallacy and runs afoul of his own and Moore's arguments against subjectivism. These defects could be (...) repaired, but only by abandoning Russell's semantics.Russell preferred to revert to emotivism. (shrink)

The concept of self has preeminently been asserted (in its many versions) as a core component of anti-reductionist, antinaturalistic philosophical positions, from Descartes to Husserl and beyond, with the exception of some hybrid or intermediate positions which declare rather glibly that, since we are biological entities which fully belong to the natural world, and we are conscious of ourselves as 'selves', therefore the self belongs to the natural world (this is characteristic e.g. of embodied phenomenology and enactivism). Nevertheless, from Cudworth (...) and More’s attacks on materialism all the way through twentieth-century argument against naturalism, the gulf between selfhood and the world of Nature appears unbridgeable. In contrast, my goal in this paper is to show that early modern materialism could yield a theory of the self according to which (1) the self belongs to the world of external relations (Spinoza), such that no one fact, including supposedly private facts, is only accessible to a single person; (2) the self can be reconstructed as a sense of “organic unity” which could be a condition for biological individuality (a central text here is Diderot’s 1769 Rêve de D’Alembert); yet this should not lead us to espouse a Romantic concept of organism as foundational or even ineffable subjectivity (a dimension present in Leibniz and made explicit in German idealism); (3) what we call 'self' might simply be a dynamic process of interpretive activity undertaken by the brain. This materialist theory of the self should not neglect the nature of experience, but it should also not have to take at face value the recurring invocations of a better, deeper “first-person perspective” or “first-person science.”. (shrink)

Peter Corning: The Fair Society: The science of human nature and the pursuit of social justice Content Type Journal Article Category Review Essay Pages 1-8 DOI 10.1007/s10539-011-9304-0 Authors Holly Lawford-Smith, Centre for Applied Ethics and Public Philosophy, Charles Sturt University, Canberra, Australia Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867.

Table of contents for MONSTERS AND PHILOSOPHY, edited by Charles T. Wolfe (London 2005) -/- List of Contributors iii Acknowledgments vii List of Abbreviations ix -/- Introduction xi Charles T. Wolfe The Riddle of the Sphinx: Aristotle, Penelope, and 1 Empedocles Johannes Fritsche Science as a Cure for Fear: The Status of Monsters in 21 Lucretius Morgan Meis Nature and its Monsters During the Renaissance: 37 Montaigne and Vanini Tristan Dagron Conjoined Twins and the Limits of our Reason (...) 61 Annie Bitbol-Hespériès Degeneration and Hybridism in the Early Modern Species 109 Debate: Towards the Philosophical Roots of the Creation-Evolution Controversy Justin E. H. Smith Leibniz on the Unicorn and Various other Curiosities 131 Roger Ariew The Creativity of God and the Order of Nature: 153 Anatomizing Monsters in the Early Eighteenth Century Anita Guerrini The Status of Anomalies in the Philosophy of Diderot 169 Annie Ibrahim The Materialist Denial of Monsters 187 Charles T. Wolfe Cerebral Assymetry, Monstrosities and Hegel. 205 On the Situation of the Life Sciences in 1800 Michael Hagner The Lady Knight of the Perilous Place 217 Elfriede Jelinek Monster: More than a Word. . . From Portent to Anomaly, 231 the Extraordinary Career of Monsters Beate Ochsner Index 281 . (shrink)

How does Locke contribute to the development of 18th-century projects for a science of the mind, even though he seems to reject or at least bracket off such an idea himself? Contrary to later understandings of empiricism, Locke goes out of his way to state that his project to investigate and articulate the ‘logic of ideas’ is not a scientific project: “I shall not at present meddle with the Physical consideration of the Mind” (Essay, I.i.2). Locke further specifies that this (...) means his analysis of mental processes will not engage with knowledge of the brain (e.g. in terms of corpuscles and animal spirits), even though he had been the student of Thomas Willis. Now, Kant seemed to make an elementary mistake, given such a clear statement on Locke’s part, when he claimed that Locke’s project was a “physiology of the understanding” (in the Preface to the A edition of the first Critique). One can ask of course what this physiology of the understanding was, and if it existed, in or out of the Lockean intellectual world (as I have sought to investigate in a 2016 paper). This leads me to inquire into the outcome of his empiricism for a scientific treatment of the mind, including in the sense of a ‘naturalization’ of the mind (with implications also for our understanding of empiricism: Anstey’s influential distinction between experimental and speculative philosophy does not seem useful here). Because if Kant made this charge, there were also many 18th-century thinkers who positively treated Locke as their great forerunner in psychology and related fields: Charles Bonnet and Joseph Priestley among them, just as some prominent physicians such as Cabanis claimed to be ‘finishing the job’ that Locke had started in, e.g. their materialist theories of the passions. What one might term ‘the Locke Problem’ here is: how can one reconcile empiricism and claims about cerebral processes, while seeking to remain a Lockean? Differently put, what is the process of naturalization, a naturalization of? (shrink)

Phenomenological realism, in the tradition of Dietrich von Hildebrand, is advanced as a promising methodology for a theistic philosophy of divine and human agency. Phenomenological realism is defended in contrast to the practice of historicalism -- the view that a philosophy of mind and God should always be done as part of a thoroughgoing history of philosophy, e.g. the use of examples in analytic theology should be subordinated to engaging the work of Kant and other great philosophers. The criticism of (...) theism based on forms of naturalism that give exclusive authority to the physical sciences is criticized from a phenomenological, realist perspective. (shrink)

Despite the recent advances in information and communication technology that have increased our ability to store and circulate information, the task of ensuring that the right sorts of information gets to the right sorts of people remains. We argue that the many efforts underway to develop efficient means for sharing information across healthcare systems and organizations would benefit from a careful analysis of human action in healthcare organizations. This in turn requires that the management of information and knowledge within healthcare (...) organizations be combined with models of resources and processes of patient care that are based on a general ontology of social interaction. The Health Level 7 (HL7) is one of several ANSI-accredited Standards Developing Organizations operating in the healthcare arena. HL7 has advanced a widely used messaging standard that enables healthcare applications to exchange clinical and administrative data in digital form. HL7 focuses on the interface requirements of the entire healthcare system and not exclusively on the requirements of one area of healthcare such as pharmacy, medical devices, imaging or insurance transactions. This has inspired the development of a powerful abstract model of patient care called the Reference Information Model (RIM). The present paper begins with an overview of the core classes of the HL7 (Version 3) RIM and a brief discussion of its “actcentered” view of healthcare. Central to this account is what is called the life cycle of events. A clinical action may progress from defined, through planned and ordered, to executed. These modalities of an action are represented as the mood of the act. We then outline the basis of an ontology of organizations, starting from the theory of speech Acts, and apply this ontology to the HL7 RIM. Special attention is given to the sorts of preconditions that must be satisfied for the successful performance of a speech act and to the sorts of entities to which speech acts give rise (e.g. obligations, claims, commitments, etc.). Finally we draw conclusions for the efficient communication and management of medical information and knowledge within and between healthcare organizations, paying special attention to the role that medical documents play in such organizations. (shrink)

Public attitudes towards cognitive enhancement––e.g., using stimulants like Adderall and Ritalin to improve mental functioning––are mixed. Attitudes vary by context and prompt ethical concerns about fairness, obligation, and authenticity/character. While people may have strong views about the morality of cognitive enhancement, how these views are affected by the physical characteristics of enhancers is unknown. Visible facial anomalies (e.g., scars) bear negatively on perceptions of moral character. This pre-registered study (osf[dot]io/uaw6c/) tested the hypothesis that such negative biases against people with facial (...) anomalies extend to moral beliefs surrounding their use of cognitive enhancement. In an online survey, 941 participants made moral judgments in response to a vignette about a person who had to decide whether or not to enhance. The vignette was accompanied by a face photograph that ostensibly depicted the potential enhancer and either did or did not have visible anomalies. Participants then learned whether the person ultimately decided to enhance. Next, participants played a modified Trust Game with, they were told, the person from the photograph/vignette. Participants judged enhancement to be less fair and enhancers less authentic if they had facial anomalies, while effects on judgments of moral obligation and on behavior were not detected. These findings extend previous work showing that people with visible differences are subject to an “anomalous-is-bad” stereotype that has negative consequences for perceptions of their moral character. While anomalous faces were judged more harshly, these judgments did not appear to affect behavior. These results are discussed in relation to discrimination and policy. (shrink)

While there has been significant discussion in the health sciences and ethics literatures about problems associated with publication practices (e.g., ghost- and gift-authorship, conflicts of interest), there has been relatively little practical guidance developed to help researchers determine how they should fairly allocate credit for multi-authored publications. Fair allocation of credit requires that participating authors be acknowledged for their contribution and responsibilities, but it is not obvious what contributions should warrant authorship, nor who should be responsible for the quality and (...) content of the scientific research findings presented in a publication. In this paper, we review arguments presented in the ethics and health science literatures, and the policies or guidelines proposed by learned societies and journals, in order to explore the link between author contribution and responsibility in multi-author multidisciplinary health science publications. We then critically examine the various procedures used in the field to help researchers fairly allocate authorship. (shrink)

The history of philosophy can be seen either as a contribution to history or a contribution to philosophy or perhaps as a bit of both. Hutchinson fail on both counts. The book is bad: bad in itself (since it quite definitely ought not to be) and bad as a companion to Principia (since it sets students a bad example of slapdash, lazy and pretentious philosophizing and would tend to put them off reading Moore). As a conscientious reviewer I ploughed through (...) every page and I have to say that I resented every minute of my life that I wasted on the book. Don’t waste any of yours. (shrink)