Arsenic and phosphorus are group 15 elements with similar chemical properties. Is it possible that arsenate could replace phosphate in some of the chemicals that are required for life? Phosphate esters are ubiquitous in biomolecules and are essential for life, from the sugar phosphates of intermediary metabolism to ATP to phospholipids to the phosphate backbone of DNA and RNA. Some enzymes that form phosphate esters catalyze the formation of arsenate esters. Arsenate esters hydrolyze very rapidly in aqueous solution, which makes (...) it improbable that phosphorous could be completely replaced with arsenic to support life. Studies of bacterial growth at high arsenic:phosphorus ratios demonstrate that relatively high arsenic concentrations can be tolerated, and that arsenic can become involved in vital functions in the cell, though likely much less efficiently than phosphorus. Recently Wolfe‐Simon et al. 1 reported the isolation of a microorganism that they maintain uses arsenic in place of phosphorus for growth. Here, we examine and evaluate their data and conclusions. (shrink)

Leonid Martynov and Boris Slutsky began to write during Stalin's reign and were aware of the contemporary official pressure to make literature more broadly accessible as well as of the highly experimental, and thus more difficult, poetry that had come into vogue during the years leading up to the Bolshevik revolution. Martynov's response was to create verse marked by ambiguity; he employs the graphic layout and internal rhyme to avoid predictability and easy interpretation, especially in a poem's opening lines. Slutsky, (...) in contrast, often lacks the sense of rhythmic order that usually emerges in Martynov's poems. He may disrupt the rhythm unexpectedly or vary it so frequently that no overarching pattern appears. Both, whether by unsettling the rhythm or complicating its perception, manage to recall the freer and more experimental artistic milieu of the early twentieth century. (shrink)

Healing Makes Our Hearts Happy: Spirituality and Cultural Transformation among the Kalaharilu/'hoansi Richard Katz Megan Biesele and Verna St Denis Rochester Vermont: Inner Traditions, 1997. 214pp. $29.95.

For live-related kidney donation, the current UK guidance specifies that the donor has a right to know the recipient’s HIV status. This guidance may prevent some potential recipients from asking friends or family to donate, as they do not wish them to know they are HIV positive. Currently, it is felt necessary that the donor should know the HIV status of the recipient in order to give fully informed consent to the operation. However, the specific medical details are not required (...) in order to allow for donor informed consent. This consent requires knowledge of the general expectation for survival of a graft and the specific expectation for survival of this graft in the recipient; it does not require specific knowledge of the recipient’s medical condition. (shrink)

A critical survey of the major philosophical arguments that have been used to justify the institutions and policies of contemporary welfare states considers the claims of rights theory, egalitarianism, and citizenship and communitarian doctrines. It finds that these arguments are both internally confused and inconsistent with conventional welfare policies. It is argued that the welfare state itself has serious ambiguities: it claims to cater for the needy, as part of its ?public good?; obligations, yet in practice it delivers a range (...) of private goods, e.g., health, housing, education and pensions, often irrespective of need. Yet classical liberal theories of state welfare, which favor simple cash payments, are flawed in theory and potentially costly in practice, while neocon?servative theories, by imposing ?values?; on welfare recipients, undermine liberal pluralism. The author concludes that welfare philosophy should be concerned with two neglected areas: the possibility that welfare be provided outside the familiar market and state categories, and the construction of constitutional rules to prevent the middle?class ?capture?; of existing welfare states. (shrink)

Discusses Anglo-American capitalism, exemplified by the commercial and financial systems of Wall Street and the City of London and including the ethics of the stock market, the morality of takeovers, and the problem of business and the environment.

Intersectionality theory explores the special sorts of disadvantage that arise as the result of occupying multiple disadvantaged demographic categories. One significant methodological problem for the quantitative study of intersectionality is the difficulty of acquiring data sets large enough to produce significant results when one is looking for intersectional effects. For this reason, we argue, simulation methods may be particularly useful to this branch of theorizing because they can generate precise predictions and causal dependencies in a relatively cheap way, and can (...) thus guide future empirical work. We illustrate this point through models which show that intersectional oppression can arise under conditions where social groups are disadvantaged in the emergence of bargaining norms. As we show, intersectional disadvantage can arise even when actors from all social categories are completely identical in terms of preferences and abilities. The conditions necessary to derive such disadvantage are relatively minimal. And when actors behave in ways that reflect stronger intersectional identities, the potential for disadvantage increases. (shrink)

First published in 1987. Towards the end of the twentieth century there was a resurgence of thinking about politics, economics and society referred to variously as the 'New Right', the radical right, neo-conservatism, economic liberalism or libertarianism. Although the New Right is not a single coherent movement it represented a clear alternative to the prevailing social-democratic consensus and had had considerable influence on government policy in both America and Britain. This book presents an introductory survey of the New Right worldwide. (...) It examines the varieties of free-market and 'monetarist' economic thought and introduces the reader to the public-choice critique of public policy. In political philosophy the book analyses American and British conservative thought and compares conservatism with neo-liberalism. The author pays particular attention to the New Right's analysis of constitutionalism and its critique of the dominance of 'politics' over 'economics' during the high-point of the consensus period. The author assesses the success which the different schools of the New Right have had in influencing public opinion and in the formation of government policy. He does not argue for or against the New Right but presents a dispassionate survey from which the reader can draw his or her own conclusions. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

This paper describes and critically reflects on a participatory policy process which resulted in a government decision not to introduce genetically modified cotton in farmers’ fields in Mali. In January 2006, 45 Malian farmers gathered in Sikasso to deliberate on GM cotton and the future of farming in Mali. As an invited policy space convened by the government of Sikasso region, this first-time farmers' jury was unique in West Africa. It was known as l’ECID—Espace Citoyen d’Interpellation Démocratique —and it had (...) an unprecedented impact on the region. In this Deliberative and Inclusive Process, the ECID combined the citizens’ jury method with indigenous methods for debate and dialogue, including the traditional African palaver. The ECID brought together male and female producers representing every district in the Sikasso region of southern Mali, specialist witnesses from various continents and a panel of independent observers, as well as resource persons and members of the national and international press and media. As an experiment in deliberative democracy, the ECID of Sikasso aimed to give men and women farmers the opportunity to share knowledge on the benefits and risks of GM cotton, and make policy recommendations on the future of GM technology in Malian agriculture. Designed as a bottom-up and participatory process, the ECID’s outcomes significantly changed national policy on the release of GM technology and have had an enduring influence in Mali. In this paper, we describe our positionality as action researchers and co-organisers of the ECID. We explain the methodology used for the ECID of Sikasso and critically reflect on the safeguards that were put in place to ensure a balanced and trustworthy deliberative process. The ECID and its key outcomes are discussed in the context of the political economy of GM cotton in West Africa. Last, we briefly highlight the relevance of the ECID for current international debates on racism in the theory and practice deliberative democracy; the production of post-normal transdisciplinary knowledge for technology risk-assessments; and the politics of knowledge in participatory policy-making for food and agriculture. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

This review emphasizes the worldwide and U.S. evolving population demographics and the need for the dental profession to exercise its professional and ethical duty to expand its traditional patient base to provide needed services.

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)

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

This project investigates critical issues and events related to Trek Therapeutics experience as a public benefit corporation. We will present and discuss how Trek differentiates itself in an industry where the attention is on high prices supporting high investor returns. Trek’s benefit corporation status helped it garner favorable attention in some respects, but has also presented challenges, particularly when it comes to attracting new capital.

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)

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)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

(Report assembled for the Workshop of the AMIA Working Group on Formal Biomedical Knowledge Representation in connection with AMIA Symposium, Washington DC, 2005.) Best practices in ontology building for biomedicine have been frequently discussed in recent years. However there is a range of seemingly disparate views represented by experts in the field. These views not only reflect the different uses to which ontologies are put, but also the experiences and disciplinary background of these experts themselves. We asked six questions related (...) to biomedical ontologies to what we believe is a representative sample of ontologists in the biomedical field and came to a number conclusions which we believe can help provide an insight into the practical problems which ontology builders face today. (shrink)

Psychological contracts represent perceived reciprocal obligations between an employer and an employee. Most research has focused on employee or employer rights (the entitlement side of the obligation equation). We examine the responsibilities inherent in psychological contracts. After reviewing the moral aspect of psychological contracts, we use the issue of tenure as a discussion point for this topic.

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.

The appeal of materialism lies precisely in this, in its claim to be natural metaphysics within the bounds of science. That a doctrine which promises to gratify our ambition (to know the noumenal) and our caution (not to be unscientific) should have great appeal is hardly something to be wondered at. (Putnam (1983), p.210) Materialism says that all facts, in particular all mental facts, obtain in virtue of the spatio- temporal distribution, and properties, of matter. It was, as Putnam says, (...) “metaphysics within the bounds of science”, but only so long as science was thought to say that the world is made out of matter.1 In this century physicists have learned that there is more in the world than matter and, in any case, matter isn’t quite what it seemed to be. For this reason many philosophers who think that metaphysics should be informed by science advocate physicalism in place of materialism. Physicalism claims that all facts obtain in virtue of the distribution of the fundamental entities and properties –whatever they turn out to be- of completed fundamental physics. Later I will discuss a more precise formulation. But not all contemporary philosophers embrace physicalism. Some- and though a minority not a small or un-influential one- think that physicalism is rather the metaphysics for an unjustified scientism; i.e. it is scientistic metaphysics. Those among them that think that physicalism can be clearly formulated think that it characterizes a. (shrink)