The God of classical Christian faith is radically transcendent--utterly beyond understanding and words. So if God is to be known it must be in the luminous darkness of unknowing. Drawing on a wide range of primary sources--biblical, patristic, and medieval--Barry D. Smith identifies and explores seven ways of expressing the otherness of God in classical Christian thinking. By allowing historical theologians to speak for themselves, he shows how an aversion to ontotheology long precedes postmodernism. The book first lays out (...) the Old Testament and New Testament foundations for subsequent Christian reflections on divine transcendence. These were the teachings that the early church assumed and, with the assistance of Greek philosophy, further refined with their own set of apophatic conceptual tools. The main focus of the book is a sevenfold exposition of that theological refinement. Smith concludes by looking towards possible future theological developments within this apophatic tradition. Drawing on the theological methodology of historic Christianity, he indicates how a synthesis of the biblical teaching on the otherness of God with philosophical traditions other than those inherited from Greek philosophy is also possible. (shrink)

Embryogenesis requires the precise movement and reorganization of many cell and tissue types. Presumably, cell surface receptors allow cells to interact selectively with adjacent cells and with the extracellular environment, as well as initiate differentiative events by transducing appropriate signals across the plasma membrane. One cell surface component that serves as a receptor during a variety of cellular interactions is β1,4‐galactosyltransferase. Cell surface galactosyltransferase participates in diverse cellular interactions by binding its specific glycoconjugate substrate on adjacent cell surfaces or in (...) the extracellular matrix. Biochemical, immunological, and molecular probes are being used to better define cell surface galactosyl‐transferase functional in cellular interactions during fertilization, intercellular adhesion, cell migration, and growth control. (shrink)

The chief sources of groundwater contamination on farms come from point sources and diffuse sources. Possible point sources are feedlots, poorly-sited manure piles, septic sewage-treatment systems—all of which can release nitrate, phosphates and bacteria— and sites of chemical spills. Diffuse sources are typified by excess fertilizer leaching from a number of arable fields. The basis of quality standards for drinking-water is discussed in relation to common contaminants present on farms. Samples of drinking-water were collected in 1991–1992 from wells on about (...) 1,200 farms in order to study the quality of rural groundwater in Ontario. Analysis showed that approximately one third of wells were contaminated with bacteria, 14% were contaminated with nitrate, two wells were contaminated with pesticide, but 40% were considered unsafe because of the presence of at least one contaminant. These values were similar to those reported for similar regions in the U.S. There was no significant effect of agricultural practice on the proportion of contaminated samples. One response of Ontario's farmers to information on water quality has been to initiate their own program, the Environmental Farm Plan, which has 23 modules by which the risk of environmental contamination can be assessed. Government policies for agriculture can be expected to influence farming practices. However, the literature suggests that the consequences of policies aimed at reducing environmental contamination are poorly understood, not least because the instruments used for implementation can have widely differing impacts. The need for discussions on the ethics surrounding the relationship between food producers and consumers with regard to environmental contamination is identified. (shrink)

Abstractβ1,4‐galactosyltransferase is unusual among the glycosyltransferases in that it is found in two subcellular compartments where it performs two distinct functions. In the trans‐Golgi complex, galactosyltransferase participates in oligosaccharide biosynthesis, as do the other glycosyltransferases. On the cell surface, however, galactosyltransferase associates with the cytoskeleton and functions as a receptor for extracellular oligosaccharide ligands. Although we now know much regarding galactosyltransferase function in these two compartments, little is known about how it is targeted to these different sites. By cloning the (...) galactosyltransferase gene products, certain features of the protein have been identified that may be critical for its expression on the cell surface or retention within the Golgi complex. This article discusses recent studies which suggest that a cytoplasmic sequence unique to one galactosyltransferase isoform is required for targeting a portion of this protein to the plasma membrane, enabling it to function as a cell adhesion molecule. These findings allow one to manipulate surface galactosyltransferase expression, either positively or negatively, and perturb galactosyltransferase‐dependent cellular interactions during fertilization and development. (shrink)

The question of what the relevant entities or units of analysis for studying the dynamics of R&D are is central not only for adequate characterizations of the system of scientific and technological knowledge production but also for determining the correct focus for evaluation of R&D activities. Typically, R&D performance evaluations have focused not only on the wrong thing but have looked in the wrong place. Most evaluations have been project or program based. Often this focus is misleading. This article presents (...) a “knowledge value” framework as an alternative focus for understanding and evaluating scientific and technical work. This framework consists of two core concepts: the Knowledge Value Collective and the Knowledge Value Alliance. On the basis of the analysis of twenty-eight case studies of research activities, the authors present a typology of KVAs and conclude that they are a better object of evaluation than discipline-based projects. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

This research illustrates dangers inherent in the gap created when organizations decouple ethics program adoption from implementation. Using a sample of 182 professionals in the pharmaceutical and financial services industries, we examine the relationship between structural decoupling of formal ethics programs and individual-level perceptions and behavior. Findings strongly support the hypothesized relationships between decoupling and organizational members’ legitimacy perceptions of the ethics program, psychological contract breach, organizational cynicism, and unethical behavior.

In the past the law relating to involuntary manslaughter has been the subject of much criticism and controversy, though surprisingly it has received comparatively little attention during the recent review of the homicide law by the Law Commission and the Ministry of Justice. As far as the authors are aware, there has hitherto been no objective empirical research into cases of involuntary manslaughter in England and Wales. Based on data collected from case files maintained by HM Court Service and the (...) Crown Prosecution Service, this article provides a brief analysis of a sample of 127 recent cases. As well as the usual criminological analysis (of offender and offence characteristics), the article focuses on the variations in offenders’ moral culpability for causing death; the relationship between murder and manslaughter (especially those manslaughters at the ‘upper end’ of the seriousness scale); the categorization of different species of involuntary manslaughter, and the sentencing of convicted manslayers. (shrink)

This article draws on the sociology of expectations to examine the construction of expectations of ‘ethical AI’ and considers the implications of these expectations for communication governance. We first analyse a range of public documents to identify the key actors, mechanisms and issues which structure societal expectations around artificial intelligence and an emerging discourse on ethics. We then explore expectations of AI and ethics through a survey of members of the public. Finally, we discuss the implications of our findings for (...) the role of AI in communication governance. We find that, despite societal expectations that we can design ethical AI, and public expectations that developers and governments should share responsibility for the outcomes of AI use, there is a significant divergence between these expectations and the ways in which AI technologies are currently used and governed in large scale communication systems. We conclude that discourses of ‘ethical AI’ are generically performative, but to become more effective we need to acknowledge the limitations of contemporary AI and the requirement for extensive human labour to meet the challenges of communication governance. An effective ethics of AI requires domain appropriate AI tools, updated professional practices, dignified places of work and robust regulatory and accountability frameworks. (shrink)

The notion of function is indispensable to our understanding of distinctions such as that between being broken and being in working order (for artifacts) and between being diseased and being healthy (for organisms). A clear account of the ontology of functions and functioning is thus an important desideratum for any top-level ontology intended for application to domains such as engineering or medicine. The benefit of using top-level ontologies in applied ontology can only be realized when each of the categories identified (...) and defined by a top-level ontology is integrated with the others in a coherent fashion. Basic Formal Ontology (BFO) has from the beginning included function as one of its categories, exploiting a version of the etiological account of function that is framed at a level of generality sufficient to accommodate both biological and artifactual functions. This account has been subjected to a series of criticisms and refinements. We here articulate BFO’s account of function, provide some reasons for favoring it over competing views, and defend it against objections. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is of (...) particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

This study investigated attitudes toward the use of deception in negotiation, with particular attention to the distinction between deception regarding the informational elements of the interaction (e.g., lying about or misrepresenting needs or preferences) and deception about emotional elements (e.g., misrepresenting one's emotional state). We examined how individuals judge the relative ethical appropriateness of these alternative forms of deception, and how these judgments relate to negotiator performance and long-run reputation. Individuals viewed emotionally misleading tactics as more ethically appropriate to use (...) in negotiation than informational deception. Approval of deception predicted negotiator performance in a negotiation simulation and also general reputation as a negotiator, but the nature of these relationships depended on the kind of deception involved. (shrink)

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 paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (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)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

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)