Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.

Thomas Garrigue Masaryk, later founder and President of the Republic of Czechoslovakia, studied philosophy in the University of Vienna from 1872 to 1876, where he came under the powerful influence of Franz Brentano. We survey the role of Brentano’s philosophy, and especially of his ethics, in Masaryk’s life and work.

Examining the historical development of scientific concepts is important for understanding the structured routines within which these concepts are currently used as goal-directed tools in experiments. To illustrate this claim, I will outline how the concepts of mental imagery and hallucinations each draw on an older interdependent set of associations that, although nominally-discarded, continues to structure their current independent uses for pursuing discrete experimental goals. In doing so, I will highlight how three strands of literature offer mutually instructive insights for (...) understanding how the uses of our current scientific concepts contribute to experimental practices. The first strand of literature includes recent scholarship examining how the uses of scientific concepts can enable scientific practices (e.g., Boon 2012; Brigandt 2012; Feest 2010; Steinle 2012). In this context, scientific concepts have been described as tools that function in ways that contribute to empirical knowledge; contributions that extend beyond their traditionally recognized roles in mental and linguistic representation. The second strand of literature can be glimpsed within the technoscientific studies focus on non-human agency; a focus that supports an account of the disciplined routines within which concepts are used as acting in analogous ways to the routinized participation of machines in experiments (Pickering 1995). The third strand of the literature draws attention to how the functions of concepts are grounded by the set of historically-contingent experimental practices (e.g., Canguilhem 2008; Tiles 1984). Although maintaining valuable differences, the focus of these three strands of literature are mutually instructive. Together, they offer a view of the uses of concepts as taken-for-granted tools that function within networks of subterranean associations; associations that are grounded by historically contingent experimental practices that structure how they act (in concert with human and material participants) within the temporally dynamic processes of scientific practice. Through examples drawn from a comparison of the concepts of mental imagery and hallucinations, I aim to demonstrate the value that the converging insights of these three strands of literature offer for studying the role of scientific concepts in experimental practices. (shrink)

Evidential Uniqueness is the thesis that, for any batch of evidence, there’s a unique doxastic state that a subject with that evidence should have. One of the most common kinds of objections to views that violate Evidential Uniqueness are arbitrariness objections – objections to the effect that views that don’t satisfy Evidential Uniqueness lead to unacceptable arbitrariness. The goal of this paper is to examine a variety of arbitrariness objections that have appeared in the literature, and to assess the extent (...) to which these objections bolster the case for Evidential Uniqueness. After examining a number of different arbitrariness objections, I’ll conclude that, by and large, these objections do little to bolster the case for Evidential Uniqueness. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

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)

In this paper, we defend Socratic studies as a research programme against several recent attacks, including at least one recently published in Polis . Critics have argued that the study of Socrates, based upon evidence mostly or entirely derived from some set of Plato's dialogues, is founded upon faulty and indefensible historical or hermeneutical technique. We begin by identifying what we believe are the foundational principles of Socratic studies, as the field has been pursued in recent years, and we then (...) show how the research programme that derives from accepting these principles is not defeated by any of the most common recent criticisms of it. Specifically, we argue that challenges to sorting Plato's dialogues by date, more general challenges to historicist interpretations of Plato's dialogues, as well as recent literary criticisms of Socratic studies all fail to undermine the research programme. We conclude with some thoughts about how and why Socratic studies has proved itself a valuable and fruitful research programme. (shrink)

Define teleology as the view that requirements hold in virtue of facts about value or goodness. Teleological views are quite popular, and in fact some philosophers (e.g. Dreier, Smith) argue that all (plausible) moral theories can be understood teleologically. I argue, however, that certain well-known cases show that the teleologist must at minimum assume that there are certain facts that an agent ought to know, and that this means that requirements can't, in general, hold in virtue of facts about (...) value or goodness. I then show that even if we grant those 'ought's teleology still runs into problems. A positive justification of teleology looks like it will require an argument of this form: O(X); if X, then O(Y); therefore O(Y). But this form of argument isn't in general valid. I conclude by offering two positive suggestions for those attracted to a teleological outlook. (shrink)

Tennenbaum's Theorem yields an elegant characterisation of the standard model of arithmetic. Several authors have recently claimed that this result has important philosophical consequences: in particular, it offers us a way of responding to model-theoretic worries about how we manage to grasp the standard model. We disagree. If there ever was such a problem about how we come to grasp the standard model, then Tennenbaum's Theorem does not help. We show this by examining a parallel argument, from a simpler model-theoretic (...) result. (shrink)

Simon Blackburn has not shied away from the use of vivid imagery in developing, over a long and prolific career, a large-scale philosophical vision. Here one might think, for instance, of ‘Practical Tortoise Raising’ or ‘Ramsey's Ladder’ or ‘Frege's Abyss’. Blackburn develops a ‘quasi-realist’ account of many of our philosophical and everyday commitments, both theoretical (e.g., modality and causation) and practical (e.g., moral judgement and normative reasons). Quasi-realism aims to provide a naturalistic treatment of its targeted phenomena while earning the (...) right to deploy all of the ‘trappings’ of realism—i.e., while eschewing any idea that our normal thought and talk about such phenomena are pervasively in error. The quasi-realist project is that of explaining how (as Huw Price puts it here) ‘the folk come to “talk the realist talk” without committing ourselves—us theorists, as it were—to “walking the metaphysical walk”’ (p. 136). Quasi-realism, too, can speak of truth, facts, properties, belief, knowledge, and so on. The imagery in this collection also abounds, though, in capturing a different view of quasi-realism: No fewer than three of the contributors picture Blackburn as wanting to have his cake and eat it too (Louise Antony asking, in addition, ‘Who doesn't? It's cake’ [p. 19]). (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)

What is sexual orientation? The contemporary consensus among philosophers is that it is a disposition. Unsurprisingly, recent debates about the metaphysics of sexual orientation are almost entirely intramural. Behavioral dispositionalists argue that sexual orientation is a disposition to behave sexually. Desire dispositionalists argue that it is a disposition to desire sexually. We argue that sexual orientation is not best understood in terms of dispositions to behave or dispositions to desire before arguing that dispositions tout court fail to illuminate sexual orientation. (...) We then introduce and defend the idea that sexual orientation is best understood in terms of categorical phenomenal properties of sexual arousal. (shrink)

There is a need recognized by the National Institute of Dental & Craniofacial Research and the National Cancer Institute to advance basic, translational and clinical saliva research. The goal of the Salivaomics Knowledge Base (SKB) is to create a data management system and web resource constructed to support human salivaomics research. To maximize the utility of the SKB for retrieval, integration and analysis of data, we have developed the Saliva Ontology and SDxMart. This article reviews the informatics advances in saliva (...) diagnostics made possible by the Saliva Ontology and SDxMart. (shrink)

Translation of "Von der Armut am Geiste; ein Dialog des jungen Lukács," by Ágnes Heller. This translation originally appeared in The Philosophical Forum, Spring-Summer 1972.

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)

Sensations can occur in the absence of perception and yet be experienced ‘as if’ seen, heard, tasted, or otherwise perceived. Two concepts used to investigate types of these sensory-like mental phenomena (SLMP) are mental imagery and hallucinations. Mental imagery is used as a concept for investigating those SLMP that merely resemble perception in some way. Meanwhile, the concept of hallucinations is used to investigate those SLMP that are, in some sense, compellingly like perception. This may be a difference of degree. (...) Attempts to reliably differentiate between instances of each type of SLMP remain unresolved. Despite this, the concepts of mental imagery and hallucinations are each routinely used independently of the other. These uses are especially interesting in those published accounts of experiments where equivalent findings about the neuroanatomical correlates of SLMP are reported in support of diverging knowledge-claims about the role of SLMP in neurocognitive processes. This practice presents a puzzle. To examine one aspect of this puzzle, I compare the uses of these two scientific concepts in three ways: examining their roles in differentiating between types of SLMP; exploring how their respective historical developments intersect; and analysing their contributions in neuroimaging experiments. In presenting this series of comparative analyses, I will draw on three themes from historical, philosophical, and social studies of scientific practices: interest in material contributions to knowledge; accounts of how concepts are used in experiments; and explorations of the historical conditions within which current practices emerge. Building on this literature, my comparative analyses supports five related claims. My first claim is that the concepts of mental imagery and hallucinations are each used as independent tools in neuroimaging experiments. My second claim is that, as experimental tools, the concepts of mental imagery and hallucinations are each used for investigating discrete epistemic goals. My third claim is that there are implicit interdependent associations that structure the uses of these two concepts as tools for independently investigating these discrete epistemic goals in neuroimaging experiments. This third claim rests on my analyses of both past and present uses of each concept. Firstly, as seen in their intersecting histories, there are disciplined performances of using the concepts of mental imagery and hallucinations that carry-along shared associations about the mediating role of SLMP in thought. Secondly, these interdependent ‘mediator-view’ associations continue to structure the independent uses of each concept as a tool for investigating SLMP in pursuit of specific goals. Taking this further, my fourth claim is that recognising the structured uses of the concepts of mental imagery and hallucinations can help to account for how equivalent SLMP-neuro-correlates are generated in support of diverging knowledge-claims. Finally, my fifth claim is that the structured uses of these concepts as tools can contribute to experiments in ways analogous to, yet not equivalent with, the active contributions of material instruments. Bringing these claims together, I argue that the concepts of mental imagery and hallucinations operate as structured tools that can actively contribute to the knowledge generated by neuroimaging experiments. In presenting this argument I seek to demonstrate that examining the structured uses of concepts as tools can complement existing approaches to studying how the heterogeneous dynamics of experimental practices can come to contribute to scientific knowledge in unintended ways. (shrink)

The scientific concepts of mental imagery and hallucinations are each used independently of the other in experiments; uses that simultaneously evoke and obscure their historical connections. To highlight one of these connections, I will begin by sketching episodes from the largely separate developmental trajectories of each concept. Considering these historical sketches side-by-side, I will argue that the independent uses of these concepts each inherited a shared set of interdependent associations. In doing so, I seek to illustrate the value of examining (...) historical connections between mental imagery and hallucinations for studying the current uses of these two concepts in neuroimaging experiments. (shrink)

Commentary on: Olaf Blanke, Thomas Metzinger, Full-body illusions and minimal phenomenal selfhood, Trends in Cognitive Sciences, Volume 13, Issue 1, January 2009, Pages 7-13, ISSN 1364-6613, DOI: 10.1016/j.tics.2008.10.003.

A gas in a box is perhaps the most important model system studied in thermodynamics and statistical mechanics. Usually, studies focus on the gas, whereas the box merely serves as an idealized confinement. The present article focuses on the box as the central object and develops a thermodynamic theory by treating the geometric degrees of freedom of the box as the degrees of freedom of a thermodynamic system. Applying standard mathematical methods to the thermody- namics of an empty box allows (...) equations with the same structure as those of cosmology and classical and quantum mechanics to be derived. The simple model system of an empty box is shown to have interesting connections to classical mechanics, special relativity, and quantum field theory. (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)

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)

Examining tensions between the past and present uses of scientific concepts can help clarify their contributions as tools in experimental practices. This point can be illustrated by considering the concepts of mental imagery and hallucinations: despite debates over their respective referential reliabilities remaining unresolved within their interdependent histories, both are used as independently stable concepts in neuroimaging experiments. Building on an account of how these concepts function as tools structured for pursuit of diverging goals in experiments, this paper explores this (...) tension by re-examining the continued reliance of each concept on inverse characterisations inherited from the nominally-discarded ‘mediator-view’ of sensory-like mental phenomena (SLMP). In doing so, I seek to demonstrate how examining unresolved tensions can help highlight that entrenched associations can remain both integral to, and obscured by, the uses of concepts as goal-directed tools within experimental practices. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

Ethical decision-making frameworks assist in identifying the issues at stake in a particular setting and thinking through, in a methodical manner, the ethical issues that require consideration as well as the values that need to be considered and promoted. Decisions made about the use, sharing, and re-use of big data are complex and laden with values. This paper sets out an Ethics Framework for Big Data in Health and Research developed by a working group convened by the Science, Health and (...) Policy-relevant Ethics in Singapore Initiative. It presents the aim and rationale for this framework supported by the underlying ethical concerns that relate to all health and research contexts. It also describes a set of substantive and procedural values that can be weighed up in addressing these concerns, and a step-by-step process for identifying, considering, and resolving the ethical issues arising from big data uses in health and research. This Framework is subsequently applied in the papers published in this Special Issue. These papers each address one of six domains where big data is currently employed: openness in big data and data repositories, precision medicine and big data, real-world data to generate evidence about healthcare interventions, AI-assisted decision-making in healthcare, public-private partnerships in healthcare and research, and cross-sectoral big data. (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.

Advocates of psychedelic drugs argue that they can induce experiences that are of great spiritual and philosophical value, and that they have the potential to ‘expand consciousness.’ But can drugs, as William James (1842-1910), Aldous Huxley (1894- 1963), and Timothy Leary (1920- 1996) argue, allow us to see beyond the horizon of ordinary perception — that is, see things as they really are? To put the philosophical question more generally, can an artificial change (by the means of drugs, electrical stimuli, (...) or psychosurgery) to the brain— to the mind’s material foundations — reveal knowledge through the resulting experience? And could such a change actually provide an authentic religious experience, or rather, knowledge of what it is like to have an authentic religious experience? Or are such claims of instant enlightenment merely a mystical façade? (shrink)

Scholars have traditionally taken the Marquis de Sade to be a straightforward advocate of immoral hedonism. Without rejecting outright this view, I argue that Sade also presents an insightful theory of the psychology of pleasure, placing him amongst the more insightful psychological thinkers of the late 18th century. This paper outlines Sade’s description of the immoral will, in particular his account of how an agent can come to enjoy the humiliation, torture and murder of others. I argue for the following (...) claims: firstly, that Sade, perhaps despite himself, suggests that the sadistic will is pathological; secondly, that Sade’s work gives a far less flattering view of the sadistic will than is commonly supposed. (shrink)

This study aimed to unveil the sentiments of college students' feedback on their teacher's teaching performance during online classes. The research utilized a qualitative approach, explicitly employing text mining. Orange software determined the most frequently used words illustrating teachers' teaching performance during online courses. Moreover, Latent Semantic Indexing (LSI) was utilized to reveal how those frequently used words were structured. Meanwhile, the study showed that the words "teacher," "class," "us," "student," "online," "teaching," "happy," "learning," "understand," and "good" were most frequently (...) used in college students' sentiments regarding their teacher's performance during online classes. The study also indicated that most students have positive feedback on their teachers' teaching performance in online courses. Therefore, the findings suggest that teachers have the abilities and knowledge to successfully impart lessons to their students despite the enormous dilemma the pandemic has brought about in every sector, especially in education. (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)

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 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)

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)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

This study sought to investigate the Human Resource and Management (HRM) Program of a preschool hereinafter referred to as the Early Years Learning Center (EYLC) in Mandaluyong City for purposes of this research study. This is a qualitative case study that delved particularly into the issue of employee retention, especially of seasoned teachers and staff of the subject learning center. It used the interview method to generate an in-depth analysis as it revisited its HRM Program. To triangulate the data gathered, (...) documents from websites and social media as well as artifacts were also utilized. There is a dearth of research on the Human Resource and Management Program in preschool education. Most studies are from India and China. In terms of the HRM Program in education, SWOT analysis was frequently used to help improve the program. There were negligible sources that used the balanced scorecard at the preschool level. Hence, a combination of the SWOT analysis and the Balanced Scorecard method were utilized - the SWOT Analysis to determine the problems the learning center faces vis-à-vis its HRM Program, and the balanced scorecard in the search for a solution or strategy to help solve the problem. Based on the study, these combined tools proved to be effective in revisiting the HRM Program of schools. After interviewing the Directress of EYLC, findings disclosed that to be able to improve the retention of employees in the learning center, the focus should be given to the hiring policies and procedures keeping in mind the job security of its targeted employees. This brings forward concerns over advertising schemes utilizing different venues and platforms as well as issues involving the provision of seasoned employees with a retirement package, comprehensive Health Management Organization (HMO), and a continuing professional development program. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

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)

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

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)

In this article, we propose the Fair Priority Model for COVID-19 vaccine distribution, and emphasize three fundamental values we believe should be considered when distributing a COVID-19 vaccine among countries: Benefiting people and limiting harm, prioritizing the disadvantaged, and equal moral concern for all individuals. The Priority Model addresses these values by focusing on mitigating three types of harms caused by COVID-19: death and permanent organ damage, indirect health consequences, such as health care system strain and stress, as well as (...) economic destruction. It proposes proceeding in three phases: the first addresses premature death, the second long-term health issues and economic harms, and the third aims to contain viral transmission fully and restore pre-pandemic activity. -/- To those who may deem an ethical framework irrelevant because of the belief that many countries will pursue "vaccine nationalism," we argue such a framework still has broad relevance. Reasonable national partiality would permit countries to focus on vaccine distribution within their borders up until the rate of transmission is below 1, at which point there would not be sufficient vaccine-preventable harm to justify retaining a vaccine. When a government reaches the limit of national partiality, it should release vaccines for other countries. -/- We also argue against two other recent proposals. Distributing a vaccine proportional to a country's population mistakenly assumes that equality requires treating differently situated countries identically. Prioritizing countries according to the number of front-line health care workers, the proportion of the population over 65, and the number of people with comorbidities within each country may exacerbate disadvantage and end up giving the vaccine in large part to wealthy nations. (shrink)

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)

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)

Psychopaths routinely disregard social norms by engaging in selfish, antisocial, often violent behavior. Commonly characterized as mentally disordered, recent evidence suggests that psychopaths are executing a well-functioning, if unscrupulous strategy that historically increased reproductive success at the expense of others. Natural selection ought to have favored strategies that spared close kin from harm, however, because actions affecting the fitness of genetic relatives contribute to an individual’s inclusive fitness. Conversely, there is evidence that mental disorders can disrupt psychological mechanisms designed to (...) protect relatives. Thus, mental disorder and adaptation accounts of psychopathy generate opposing hypotheses: psychopathy should be associated with an increase in the victimization of kin in the former account but not in the latter. Contrary to the mental disorder hypothesis, we show here in a sample of 289 violent offenders that variation in psychopathy predicts a decrease in the genetic relatedness of victims to offenders; that is, psychopathy predicts an increased likelihood of harming non-relatives. Because nepotistic inhibition in violence may be caused by dispersal or kin discrimination, we examined the effects of psychopathy on (1) the dispersal of offenders and their kin and (2) sexual assault frequency (as a window on kin discrimination). Although psychopathy was negatively associated with coresidence with kin and positively associated with the commission of sexual assault, it remained negatively associated with the genetic relatedness of victims to offenders after removing cases of offenders who had coresided with kin and cases of sexual assault from the analyses. These results stand in contrast to models positing psychopathy as a pathology, and provide support for the hypothesis that psychopathy reflects an evolutionary strategy largely favoring the exploitation of non-relatives. (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)

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.

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.

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)

Climate change appears to be a classic aggregation problem, in which billions of individuals perform actions none of which seem to be morally wrong taken in isolation, and yet which combine to drive the global concentration of greenhouse gases (GHGs) ever higher toward environmental (and humanitarian) catastrophe. When an individual can choose between actions that will emit differing amounts of GHGs―such as to choose a vegan rather than carnivorous meal, to ride a bike to work rather than drive a car, (...) or to take a reusable bag to the supermarket rather than send another plastic bag to landfill―does she have any reason to choose the lower-emitting actions? In this chapter I'll reject the claim that individuals don't make a difference when it comes to climate change. I first discuss making a difference with every action, as a way of getting clearer about how individuals' actions impact causally on the harms resulting from climate change, making a distinction so far overlooked in the climate ethics discussion between 'macro' thresholds like ice-cap melt, and 'micro' thresholds like severe weather events. I set aside making a difference with every action as implausible, and then move on to discuss both low probability of major difference, and high probability of minor difference. I argue that both of these are plausible characterizations of individuals' causal contributions to climate change. I conclude by noting some policy implications of having (probabilistic) individual difference-making back in play. (shrink)

Die Entwicklung der Philosophie in Österreich unterscheidet sich in markanter Weise von der Hauptlinie der philosophischen Entwicklung in Deutschland. Dabei fällt bei der österreichischen Philosophie vor allem die konsequente Orientierung an den Wissenschaften auf. In der philosophiegeschichtlichen Forschung sind für diese Besonderheit der österreichischen Philosophie z. B. von Otto Neurath, Rudolf Haller, Friedrich Stadier und J.C. Nyiri verschiedene Erklärungen vorgeschlagen worden. In diesen spielen in jeweils unterschiedlicher Weise Faktoren der spezifisch österreichischen Entwicklungen in historischer, institutioneller, politischer und religiöser Hinsicht eine (...) Rolle. Der vorliegende Aufsatz kritisiert demgegenüber bereits die diese Erklärungsversuche tragende Fragestellung: Die philosophischen Entwicklungen in Österreich bedürfen - so lautet die neue These - gar nicht einer besonderen Erklärung; denn sie stellen den geistesgeschichtlichen Normalfall dar. Vielmehr ist eine Erklärung dafür notwendig, daß sich die wissenschaftliche Philosophie und die mit ihr verbundenen Charakterzüge stilistischer Klarheit, technischer Kompetenz, systematischer Orientierung, Spezialisierung und Professionalisierung im gleichen Zeitraum nicht auch in Deutschland entwickelt haben. Eine solche Erklärung läßt sich - so eine weitere These des Aufsatzes - ziemlich leicht aus der besonderen Rolle der (traditionellen idealistischen) Philosophie im deutschen Nationalbewußtsein herleiten. (shrink)

What should we do when we won't do as we ought? Suppose it ought to be that the procrastinating professor accept the task of reviewing a book, and actually review the book. It seems clear that given he won't review it, he ought not to accept the task. That is a genuine moral obligation in light of less than perfect circumstances. I want to entertain the possibility that a set of such obligations form something like a 'practical morality'; that which (...) we ought to do given that we're unlikely or unwilling to do much of what ideal morality demands. If it is possible to give a coherent account of these kinds of obligations, then it is possible to entertain the idea that these obligations are in fact what morality demands. The conceptual truths about justice (good, right, fairness) that come from ideals are one thing; the actions that morality demands of people given their actual circumstances are quite another. In this paper I will ask about the kinds of facts that can be used to establish a more circumscribed set of obligations than we get from the orthodox view about moral obligation. (shrink)