Review of Aesthetics of Religion: A Connective Concept, eds. Alexandra Grieser and Jay Johnston, Religion and Reason, 58.

The sublime evokes our awe, our terror, and our wonder. Applied first in ancient Greece to the heights of literary expression, in the 18th-century the sublime was extended to nature and to the sciences, enterprises that viewed the natural world as a manifestation of God's goodness, power, and wisdom. In The Scientific Sublime, Alan Gross reveals the modern-day sublime in popular science. He shows how the great popular scientists of our time--Richard Feynman, Stephen Hawking, Steven Weinberg, Brian Greene, Lisa (...) Randall, Rachel Carson, Stephen Jay Gould, Steven Pinker, Richard Dawkins, and E. O. Wilson--evoke the sublime in response to fundamental questions: How did the universe begin? How did life? How did language? These authors maintain a tradition initiated by Joseph Addison, Edmund Burke, Immanuel Kant, and Adam Smith, towering 18th-century figures who adapted the literary sublime first to nature, then to science--though with one crucial difference: religion has been replaced wholly by science. In a final chapter, Gross explores science's attack on religion, an assault that attempts to sweep permanently under the rug two questions science cannot answer: What is the meaning of life? What is the meaning of the good life? (shrink)

Ontologies are being used increasingly to promote the reusability of scientific information by allowing heterogeneous data to be integrated under a common, normalized representation. Definitions play a central role in the use of ontologies both by humans and by computers. Textual definitions allow ontologists and data curators to understand the intended meaning of ontology terms and to use these terms in a consistent fashion across contexts. Logical definitions allow machines to check the integrity of ontologies and reason over data annotated (...) with ontology terms to make inferences that promote knowledge discovery. Therefore, it is important not only to include in ontologies multiple types of definitions in both formal and in natural languages, but also to ensure that these definitions meet good quality standards so they are useful. While tools such as Protégé can assist in creating well-formed logical definitions, producing good definitions in a natural language is still to a large extent a matter of human ingenuity supported at best by just a small number of general principles. For lack of more precise guidelines, definition authors are often left to their own personal devices. This paper aims to fill this gap by providing the ontology community with a set of principles and conventions to assist in definition writing, editing, and validation, by drawing on existing definition writing principles and guidelines in lexicography, terminology, and logic. (shrink)

This paper proposes a reformulation of the treatment of boundaries, at parts and aggregates of entities in Basic Formal Ontology. These are currently treated as mutually exclusive, which is inadequate for biological representation since some entities may simultaneously be at parts, boundaries and/or aggregates. We introduce functions which map entities to their boundaries, at parts or aggregations. We make use of time, space and spacetime projection functions which, along the way, allow us to develop a simple temporal theory.

We have begun work on two separate but related ontologies for the study of neurological diseases. The first, the Neurological Disease Ontology (ND), is intended to provide a set of controlled, logically connected classes to describe the range of neurological diseases and their associated signs and symptoms, assessments, diagnoses, and interventions that are encountered in the course of clinical practice. ND is built as an extension of the Ontology for General Medical Sciences — a high-level candidate OBO Foundry ontology that (...) provides a set of general classes that can be used to describe general aspects of medical science. ND is being built with classes utilizing both textual and axiomatized definitions that describe and formalize the relations between instances of other classes within the ontology itself as well as to external ontologies such as the Gene Ontology, Cell Ontology, Protein Ontology, and Chemical Entities of Biological Interest. In addition, references to similar or associated terms in external ontologies, vocabularies and terminologies are included when possible. Initial work on ND is focused on the areas of Alzheimer’s and other diseases associated with dementia, multiple sclerosis, and stroke and cerebrovascular disease. Extensions to additional groups of neurological diseases are planned. The second ontology, the Neuro-Psychological Testing Ontology (NPT), is intended to provide a set of classes for the annotation of neuropsychological testing data. The intention of this ontology is to allow for the integration of results from a variety of neuropsychological tests that assay similar measures of cognitive functioning. Neuro-psychological testing is an important component in developing the clinical picture used in the diagnosis of patients with a range of neurological diseases, such as Alzheimer’s disease and multiple sclerosis, and following stroke or traumatic brain injury. NPT is being developed as an extension to the Ontology for Biomedical Investigations. (shrink)

The Protein Ontology provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set has (...) allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (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.

ABSTRACT In this article, we first document the virtually complete absence of infectious disease examples and concerns at the time bioethics emerged as a field. We then argue that this oversight was not benign by considering two central issues in the field, informed consent and distributive justice, and showing how they might have been framed differently had infectiousness been at the forefront of concern. The solution to this omission might be to apply standard approaches in liberal bioethics, such as autonomy (...) and the harm principle, to infectious examples. We argue that this is insufficient, however. Taking infectious disease into account requires understanding the patient as victim and as vector. Infectiousness reminds us that as autonomous agents we are both embodied and vulnerable in our relationships with others. We conclude by applying this reunderstanding of agency to the examples of informed consent and distributive justice in health care. (shrink)

The prelims comprise: Seeing Infectious Disease as Central The Birth of Bioethics Amid the Decline of Infectious Disease The Shifting Concerns of Public Health Bioethics and Public Health: How the Twain Didn't Meet The Case of HIV Bridging the Gap: Seeing Bioethics in Terms of the Patient as Victim and Vector An Ordinary Example Summing Up: Autonomous Agency in the Context of Infectious Disease Notes.

ABSTRACT In this article, we first document the virtually complete absence of infectious disease examples and concerns at the time bioethics emerged as a field. We then argue that this oversight was not benign by considering two central issues in the field, informed consent and distributive justice, and showing how they might have been framed differently had infectiousness been at the forefront of concern. The solution to this omission might be to apply standard approaches in liberal bioethics, such as autonomy (...) and the harm principle, to infectious examples. We argue that this is insufficient, however. Taking infectious disease into account requires understanding the patient as victim and as vector. Infectiousness reminds us that as autonomous agents we are both embodied and vulnerable in our relationships with others. We conclude by applying this reunderstanding of agency to the examples of informed consent and distributive justice in health care. (shrink)

In this international and interdisciplinary collection of critical essays, distinguished contributors examine a crucial premise of traditional readings of Plato's dialogues: that Plato's own doctrines and arguments can be read off the statements made in the dialogues by Socrates and other leading characters. The authors argue in general and with reference to specific dialogues, that no character should be taken to be Plato's mouthpiece. This is essential reading for students and scholars of Plato.

To understand what ontologies do through their definitions, we propose a theoretical explanation of the functions of definitions in ontologies backed by empirical neuropsychological studies. Our goal is to show how these functions should motivate (i) the systematic inclusion of definitions in ontologies and (ii) the adaptation of definition content and form to the specific context of use of ontologies.

Joseph Conrad’s ‘The secret sharer’ has often been associated with what can be called initiation stories. However, in this article I argue that Conrad’s text is more than that. It can, I suggest, be read as an allegory of the inaccessibility to reveal the essence of being in command, being in education, and also the inaccessibility of the essence of the meaning of the text itself. It keeps its secret by allegorically staging alternative readings. This inaccessibility gives rise to a (...) feeling of strangeness, of the uncanny, that must be faced in order to pass through the initiation into the unknown that all the possible allegorical meanings of the text produce. In other words, ‘The secret sharer’ has an educational value that goes beyond the act of merely using it to exemplify a certain type of initiation. In this way I connect Conrad’s text to the themes of strangeness and the stranger and show how they mutually can involve a reading of education and literature as two distinct discourses of learning. (shrink)

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology – QHIO. We apply QHIO to breast cancer hot-spot detection with (...) the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. (shrink)

A power of attorney for healthcare (POAHC) form gives designated individuals legal status to make healthcare decisions when patients are unable to convey their decisions to medical staff. Completion of a POAHC form is crucial in the provision of comprehensive healthcare, since it helps to ensure that patients’ interests, values, and preferences are represented in decisions about their medical treatment. Because increasing numbers of people suffer from debilitating illness and cognitive deficits, healthcare systems may be called upon to navigate the (...) complexities of patients’ care without clear directives from the patients themselves. Hence, the healthcare industry encourages all individuals to complete a POAHC form to ensure that persons who have the patients’ trust are able to act as their surrogate decision makers. However, sometimes POAHC agents, even when they are patients’ trusted agents, lack the capacity to make fully informed decisions that are in the patients’ best interests. We describe designated surrogate decision makers who have impaired or diminished judgment capacity as incapacitated surrogates. Decision making that is obviously flawed or questionable is a significant impediment to providing timely and appropriate care to patients. Moreover, failure to redress these issues in a timely and efficient manner can result in significant costs to an institution and a diminished quality of patient care. The authors offer a legal, ethical, and interdisciplinary framework to help navigate cases of incapacitated surrogates. (shrink)

In this view from 2007–2009, the ethical challenges facing a potential global effort to control infectious disease are explored; they provide sobering insight into the challenges of later decades. Despite the devastating pandemic of HIV/AIDS that erupted in the early 1980s, despite the failure to eradicate polio and the emergence of resistant forms of tuberculosis that came into focus in the 1990s, and despite newly emerging diseases like Severe Acute Respiratory Syndrome (SARS) in 2003 and the fearsome prospect of human-to-human (...) avian flu, it is nevertheless a time of some excitement over prospects for effective control of much of infectious disease. Funded by national and international governmental and nongovernmental organizations (NGOs), private foundations, and even popular entertainers, large-scale new efforts are under way to address global killers like AIDS, tuberculosis, and malaria, among others. This “marvelous momentum” can be seen as part of a continuing effort from the time of Jenner onward. Extrapolating from this, we explore the notion of a “comprehensive global effort for the eradication, elimination or control of infectious disease”, with particular attention to the ethical issues that arise. This is to “think big” about disease-control efforts that are now often done in piecemeal ways. This chapter identifies five tracks along which such efforts need to be pursued: (1) national and international organizations and the development of collective will; (2) epidemiological and health care infrastructure; (3) scientific development; (4) religious, social, and cultural considerations; (5) legal and social protections for individuals and groups. Each of these poses significant ethical issues which, we argue, should be viewed in a comprehensive way, to ensure that practice, research, and policy in each of these areas understands the person with communicable infectious disease as both victim and (potential) vector. (shrink)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

Untoward injuries are unacceptably common in medical treatment, at times with tragic consequences for patients. The phrases 'an epidemic of error' and 'the medical toll' have been coined to describe this problem of 'iatrogenic harm', which it has been suggested may have contributed to 98,000 deaths per year in the US. Some of these incidents are the result of negligence on the part of doctors, but more usually they are no more than inevitable concomitants of the complexity of modern healthcare. (...) This book is fundamentally about distinguishing the former from the latter. Although medicine is used as the book's primary example, the points made apply equally to aviation, industrial activities, and many other fields of human endeavour. The book advocates a more informed alternative to the blaming culture which has increasingly come to dominate our response to accidents, whether in the medical field or elsewhere. (shrink)

Reason and Value collects fifteen brand-new papers by leading contemporary philosophers on themes from the moral philosophy of Joseph Raz. The subtlety and power of Raz's reflections on ethical topics - including especially his explorations of the connections between practical reason and the theory of value - make his writings a fertile source for anyone working in this area. The volume honours Raz's accomplishments in the area of ethical theorizing, and will contribute to an enhanced appreciation of the significance of (...) his work for the subject. (shrink)

This paper examines the characteristics of infectious diseases that raise special medical and social ethical issues, and explores ways of integrating both current bioethical and classical public health ethics concerns. Many of the ethical issues raised by infectious diseases are related to these diseases' powerful ability to engender fear in individuals and panic in populations. We address the association of some infectious diseases with high morbidity and mortality rates, the sense that infectious diseases are caused by invasion or attack on (...) humans by foreign micro-organisms, the acute onset and rapid course of many infectious diseases, and, in particular, the communicability of infectious diseases. The individual fear and community panic associated with infectious diseases often leads to rapid, emotionally driven decision making about public health policies needed to protect the community that may be in conflict with current bioethical principles regarding the care of individual patients. The discussion includes recent examples where dialogue between public health practitioners and medical-ethicists has helped resolve ethical issues that require us to consider the infected patient as both a victim with individual needs and rights and as a potential vector of disease that is of concern to the community. (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)

This paper examines the characteristics of infectious diseases that raise special medical and social ethical issues, and explores ways of integrating both current bioethical and classical public health ethics concerns. Many of the ethical issues raised by infectious diseases are related to these diseases’ powerful ability to engender fear in individuals and panic in populations. We address the association of some infectious diseases with high morbidity and mortality rates, the sense that infectious diseases are caused by invasion or attack on (...) humans by foreign micro‐organisms, the acute onset and rapid course of many infectious diseases, and, in particular, the communicability of infectious diseases. The individual fear and community panic associated with infectious diseases often leads to rapid, emotionally driven decision making about public health policies needed to protect the community that may be in conflict with current bioethical principles regarding the care of individual patients. The discussion includes recent examples where dialogue between public health practitioners and medical‐ethicists has helped resolve ethical issues that require us to consider the infected patient as both a victim with individual needs and rights and as a potential vector of disease that is of concern to the community. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

We began with the observation that language is often held to enact the world. We have examined several instances of this notion, beginning with a discussion of the folk etymology of certain words, moving through an example of Freud, to Morgenstern, Lettvin, and Stevens. The method shared by these examples assumes that words are literally saturated with meaning; that what appears arbitrary or senseless in them can be made to render up its sense and its motivation through a kind of (...) inspired analysis. Our intent has been to show how this principle of folk etymology lies behind some sophisticated creative thinking. In Freud, it is hypothesized to be a psychological mechanism of some depth. In Morgenstern and Lettvin, it forms the basis for a resonant poetic joke, while in Stevens it appears to have the same major status as the mythic principle of creation-through-language illustrated in our first examples from Egyptian mythology and from Genesis. Stevens, of course, uses the principle to create poetry, not religion; for as he says in section 5 of "The Man with the Blue Guitar": Poetry Exceeding music must take the placeOf empty heaven and its hymns . . . Samuel Jay Keyser, head of the department of linguistics and philosophy at the Massachusetts Institute of Technology and editor of Linguistic Inquiry, is the coauthor of English Stress: Its Form, Its Growth and Its Role in Verse and of Beginning English Grammar. Alan Prince, an assistant professor of linguistics at the University of Massachusetts at Amherst, has written on stress and linguistic rhythm and is currently working, with Keyser, on the poetry of Wallace Stevens. (shrink)

This work has been selected by scholars as being culturally important, and is part of the knowledge base of civilization as we know it. This work was reproduced from the original artifact, and remains as true to the original work as possible. Therefore, you will see the original copyright references, library stamps (as most of these works have been housed in our most important libraries around the world), and other notations in the work. This work is in the public domain (...) in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work.As a reproduction of a historical artifact, this work may contain missing or blurred pages, poor pictures, errant marks, etc. Scholars believe, and we concur, that this work is important enough to be preserved, reproduced, and made generally available to the public. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

Experience has recently reemerged as an important analytical category for historians of the Old Regime and the French Revolution. Reacting against the perceived excesses of discourse analysis, which made political language independent of any social determinants, certain post-revisionists are now seeking to contextualize political language by relating it to the experience of those who use it. Political agency, in these analyses, is understood to be the effect of particular formative experiences. This article suggests that the search for an experiential antidote (...) to discourse is misconceived because it perpetuates an untenable dichotomy between thought and reality. Access to the phenomenon of historical agency should be pursued not through experience or discourse but through the category of consciousness, since the make-up of the subject's consciousness determines how he/she engages the world and decides to attempt changing it. After a brief discussion of an important study that exemplifies both the allure and the functionality of the notion of experience, Timothy Tackett's Becoming a Revolutionary, the article focuses on the evolving political consciousness of a man who became a revolutionary agitator in 1789, J.-M.-A. Servan. Analysis of his writings between 1769 and 1789 shows that the way in which his perspective was constructed, rather than the lessons of experience per se, determined the shape of his revolutionary intentions in 1789. (shrink)

Since testing for HIV infection became possible in 1985, testing of pregnant women has been conducted primarily on a voluntary, ‘opt-in’ basis. Faden, Geller and Powers, Bayer, Wilfert, and McKenna, among others, have suggested that with the development of more reliable testing and more effective therapy to reduce maternal-fetal transmission, testing should become either routine with ‘opt-out’ provisions or mandatory. We ask, in the light of the new rapid tests for HIV, such as OraQuick, and the development of antiretroviral treatment (...) that can reduce maternal-fetal transmission rates to <2%, whether that time is now. Illustrating our argument with cases from the United States (US), Kenya, Peru, and an undocumented Mexican worker in the US, we show that when testing is accompanied by assured multi-drug therapy for the mother, the argument for opt-out or mandatory testing for HIV in pregnancy is strong, but that it is problematic where testing is accompanied by adverse events such as spousal abuse or by inadequate intrapartum or follow-up treatment. The difference is not a ‘double standard’, but reflects the presence of conflicts between the health interests of the mother and the fetus – conflicts that would be abrogated by the assurance of adequate, continuing multi-drug therapy. In light of these conflicts, where they still occur, careful processes of informed consent are appropriate, rather than opt-out or mandatory testing. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

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

In 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)

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