This paper proposes a generalization of the Kripke semantics of intuitionistic logic IL appropriate for intuitionistic Łukasiewicz logic IŁL — a logic in the intersection between IL and (classical) Łukasiewicz logic. This generalised Kripke semantics is based on the poset sum construction, used in Bova and Montagna (Theoret Comput Sci 410(12):1143–1158, 2009) to show the decidability (and PSPACE completeness) of the quasiequational theory of commutative, integral and bounded GBL algebras. The main idea is that w \Vdash \sigma—which for IL is (...) a relation between worlds w and formulas \sigma, and can be seen as a function taking values in the booleans w \Vdash \sigma \in {B}—becomes a function taking values in the unit interval w \Vdash \sigma \in [0,1]. An appropriate monotonicity restriction (which we call sloping functions) needs to be put on such functions in order to ensure soundness and completeness of the semantics. (shrink)

Most hospitals are considered charities under common law because they were established for the benefit of the public. The law granted them benefits, but also imposed duties. Under the cy-pres doctrine, if a charitable purpose becomes obsolete or incapable of being carried out, the court could modify those purposes to meet current needs of the organization and the community. Modern laws attempt to find a purpose as near as possible to original purposes set up by donors. In the case of (...) hospital conversion, some regulators say assets must be used to support hospital health care, while others say they can be used in the broad sense of health care. That has been a continuing conflict between communities and regulators.Since 1996, 30 conversion statutes have been enacted, covering hospitals, HMOs, and insurers. (shrink)

Most hospitals are considered charities under common law because they were established for the benefit of the public. The law granted them benefits, but also imposed duties. Under the cy-pres doctrine, if a charitable purpose becomes obsolete or incapable of being carried out, the court could modify those purposes to meet current needs of the organization and the community. Modern laws attempt to find a purpose as near as possible to original purposes set up by donors. In the case of (...) hospital conversion, some regulators say assets must be used to support hospital health care, while others say they can be used in the broad sense of health care. That has been a continuing conflict between communities and regulators.Since 1996, 30 conversion statutes have been enacted, covering hospitals, HMOs, and insurers. (shrink)

The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (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 expression “AI” has become as commonplace as “computer.” While many people have a relatively clear idea of what an AI system or a computer does or can do, fewer have an idea of how precisely th...

Clinical ethics consultation is largely outside the scope of regulation and oversight, despite its importance. For decades, the bioethics community has been unable to reach a consensus on whether there should be accountability in this work, as there is for other clinical activities that influence the care of patients. The American Society for Bioethics and Humanities, the primary society of bioethicists and scholars in the medical humanities and the organizational home for individuals who perform CEC in the United States, has (...) initiated a two‐step quality attestation process as a means to assess clinical ethics consultants and help identify individuals who are qualified to perform this role. This article describes the process. (shrink)

Although clinical ethics consultation is a high-stakes endeavor with an increasing prominence in health care systems, progress in developing standards for quality is challenging. In this article, we describe the results of a pilot project utilizing portfolios as an evaluation tool. We found that this approach is feasible and resulted in a reasonably wide distribution of scores among the 23 submitted portfolios that we evaluated. We discuss limitations and implications of these results, and suggest that this is a significant step (...) on the pathway to an eventual certification process for clinical ethics consultants. (shrink)

Engineering the Climate: The Ethics of Solar Radiation Management is a wide-ranging and expert analysis of the ethics of the intentional management of solar radiation. This book will be a useful tool for policy-makers, a provocation for ethicists, and an eye-opening analysis for both the scientist and the general reader with interest in climate change.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (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)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

Ayn Rand's first novel, We the Living, offers an early form of the author's nascent philosophy—the philosophy Rand later called Objectivism. Robert Mayhew's collection of entirely new essays brings together pre-eminent scholars of Rand's writing. In part a history of We the Living, from its earliest drafts to the Italian film later based upon it, Mayhew's collection goes on to explore the enduring significance of Rand's first novel as a work both of philosophy and of literature.

The study of anarchism as a philosophical, political, and social movement has burgeoned both in the academy and in the global activist community in recent years. Taking advantage of this boom in anarchist scholarship, Nathan J. Jun and Shane Wahl have compiled twenty-six cutting-edge essays on this timely topic in New Perspectives on Anarchism.

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 and X-linked CLDN2 through a two-stage genome-wide study. The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is (...) associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men. © 2012 Nature America, Inc. All rights reserved. (shrink)

The development of symbolic logic is often presented in terms of a cumulative story of consecutive innovations that led to what is known as modern logic. This narrative hides the difficulties that this new logic faced at first, which shaped its history. Indeed, negative reactions to the emergence of the new logic in the second half of the nineteenth century were numerous and we study here one case, namely logic at Oxford, where one finds Lewis Carroll, a mathematical teacher (...) who promoted symbolic logic, and John Cook Wilson, the Wykeham Professor of Logic who notoriously opposed it. An analysis of their disputes on the topic of logical symbolism shows that their opposition was not as sharp as it might look at first, as Cook Wilson was not so much opposed to the « symbolic » character of logic, but the intrusion of mathematics and what he perceived to be the futility of some of its problems, for logicians and philosophers alike. (shrink)

The Great Chain of Being has been recognized for fifty years as the masterpiece of the History of Ideas movement in America. Lovejoy's work stimulated deeper research into our heritage, which has demonstrated that the idea of the chain of being has not lost its vitality. However, Lovejoy would probably be surprised that hierarchy is now defended in philosophy of science, in ontology and metaphysics, in ethics and aesthetics, and in philosophical anthropology. This volume presents concepts of hierarchy and the (...) great chain of being from Plato, Aristotle, Plotinus, medieval and Renaissance thinkers, Hindu philosophy, and authors of the twentieth century. This volume represents the ideas of twenty scholars, among whom are Dominic O'Meara, Ronald Hathaway, Ewert Cousins, John Sommerfeldt, Lewis Ford, David Blumenthal, and Marion and Paul Kuntz. The editors have compiled a bibliography of four hundred and fifty items and an index of names, places, and concepts which allow the reader immediate access to the variety as well as the unity of ideas. (shrink)

Recently, the practice of deciding legal cases on purely statistical evidence has been widely criticised. Many feel uncomfortable with finding someone guilty on the basis of bare probabilities, even though the chance of error might be stupendously small. This is an important issue: with the rise of DNA profiling, courts are increasingly faced with purely statistical evidence. A prominent line of argument—endorsed by Blome-Tillmann 2017; Smith 2018; and Littlejohn 2018—rejects the use of such evidence by appealing to epistemic norms (...) that apply to individual inquirers. My aim in this paper is to rehabilitate purely statistical evidence by arguing that, given the broader aims of legal systems, there are scenarios in which relying on such evidence is appropriate. Along the way I explain why popular arguments appealing to individual epistemic norms to reject legal reliance on bare statistics are unconvincing, by showing that courts and individuals face different epistemic predicaments (in short, individuals can hedge when confronted with statistical evidence, whilst legal tribunals cannot). I also correct some misconceptions about legal practice that have found their way into the recent literature. (shrink)

Smith proposes an account of how languages developed. He did so not as historian, but as a philosopher with a special concern about how a nominalist could account for general terms. Names for individuals are taken as fairly unproblematic – say ‘Thames’ and ‘Avon’ for each of the respective rivers. But whence the word ‘river,’ applicable to more than one, if all that exist are particular objects? Smith’s view is not the usual one, according to which people deploy (...) a powerful ability to abstract mentally, and subsequently affix a label to a general concept. He resisted this because he granted that such robust mental processes themselves presuppose the use of words. Rather, what holds the class together is the word itself, a “single appellation.”. (shrink)

I distinguish paradoxes and hypodoxes among the conundrums of time travel. I introduce ‘hypodoxes’ as a term for seemingly consistent conundrums that seem to be related to various paradoxes, as the Truth-teller is related to the Liar. In this article, I briefly compare paradoxes and hypodoxes of time travel with Liar paradoxes and Truth-teller hypodoxes. I also discuss Lewis’ treatment of time travel paradoxes, which I characterise as a Laissez Faire theory of time travel. Time travel paradoxes are impossible (...) according to Laissez Faire theories, while it seems hypodoxes are possible. (shrink)

Drawing on models of communication due to Lewis and Skyrms, I contrast sender-receiver systems as they appear within and between organisms, and as they function in the bridging of space and time. Within the organism, memory can be seen as the sending of messages over time, communication between stages as opposed to spatial parts. Psychological memory and genetic memory are compared with respect to their relations to a sender-receiver model. Some puzzles about “genetic information” can be resolved by seeing (...) the genome as a cell-level memory with no sender. (shrink)

In responding to three reviews of Evolution in Four Dimensions (Jablonka and Lamb, 2005, MIT Press), we briefly consider the historical background to the present genecentred view of evolution, especially the way in which Weismann’s theories have influenced it, and discuss the origins of the notion of epigenetic inheritance. We reaffirm our belief that all types of hereditary information—genetic, epigenetic, behavioural and cultural—have contributed to evolutionary change, and outline recent evidence, mainly from epigenetic studies, that suggests that non-DNA heritable variations (...) are not rare and can be quite stable. We describe ways in which such variations may have influenced evolution. The approach we take leads to broader definitions of terms such as ‘units of heredity’, ‘units of evolution’, and ‘units of selection’, and we maintain that ‘information’ can be a useful concept if it is defined in terms of its effects on the receiver. Although we agree that evolutionary theory is not undergoing a Kuhnian revolution, the incorporation of new data and ideas about hereditary variation, and about the role of development in generating it, is leading to a version of Darwinism that is very different from the gene-centred one that dominated evolutionary thinking in the second half of the twentieth century. (shrink)