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)

Do the rich descriptions and narrative shapings of literature provide a valuable resource for readers, writers, philosophers, and everyday people to imagine and confront the ultimate questions of life? Do the human activities of storytelling and complex moral decision-making have a deep connection? What are the moral responsibilities of the artist, critic, and reader? What can religious perspectives—from Catholic to Protestant to Mormon—contribute to literary criticism? Thirty well known contributors reflect on these questions, including iterary theorists Marshall Gregory, James (...) Phelan, and Wayne Booth; philosophers Martha Nussbaum, Richard Hart, and Nina Rosenstand; and authors John Updike, Charles Johnson, Flannery O'Connor, and Bernard Malamud. Divided into four sections, with introductory matter and questions for discussion, this accessible anthology represents the most crucial work today exploring the interdisciplinary connections between literature, religion and philosophy. (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)

Introduction The philosophy of history has come to be virtually expropriated by Marxism, contributing to the general disesteem in which the subject is now ...

Research on the `meaning of work', especially concerning the Global South, is scarce. This paper aims to reduce this scarcity by applying critical realist meta-theory to the work and life history interviews of workers in Sri Lanka. A key discovery is that finding meaning in life through work is a personal emergent power and that, as such, it explains the way that individuals consciously manoeuvre their life-journeys towards a desired end - a modus vivendi - in a dialectic which involves (...) both emergent structural change (morphogenesis) and agency. This paper also reveals that Margaret Archer's theory of reflexivity, based on interviews with Western individuals, cannot be transferred rigidly to the reflexivity of Global South individuals, and therefore more work on reflexivity within this context is required. This paper therefore makes a theoretical contribution to the existing meaning of work scholarship, and it extends existing understandings of the concepts of reflexivity and emergence. (shrink)

The morality of our distant ancestors bears a remarkable resemblance to the moral experiences of modern athletes. This book brings together stories from today’s sports world and the moral practices of hunter-gatherers to shed new light on both sports and morality and offer a unique interpretation of America’s love affair with sports.

In Book XI of the Confessions Augustine claims that time has its beginning and ending in eternity. In Being and Time, Heidegger claims that death is the ultimate futural possibility for authentic human existence. These two texts, one from the fourth century, the other from the twentieth century, depict two very different perspectives on what limits the human conception of time. Can these perspectives be reconciled? Severson offers a new reading of the Confessions that affirms Augustine's religious quest for understanding (...) while taking into account the constraints of modern criticism. (shrink)

Written by a multi-disciplinary group of leading practitioners, _Sexual Offending Against Children_ provides an account of the practice, policy and management issues involved in the assessment and treatment of adult and adolescent sexual offenders against children. Written for practitioners from all disciplines concerned with this area of work, it is underpinned by a strong theoretical base, giving a practical and detailed description of the management of sexual offenders, as well as the potential impact on service providers.

The philosopher John J. McDermott comes out of the long American tradition that takes the aim of philosophical inquiry to be interpretation of the open meanings of experience, so that we might all live fuller and richer lives. Here, the authors of these nine essays explore his highly original interpretations of philosophy's various questions about our shared existence. How are we to understand the nature of American culture and to carry forward its important contributions? What is the personal importance of (...) embodiment, of living in the realization of death? How does our physical and personal environment nourish bodies and spirits? What does the deliberate pursuit of a morality offer us? How can we carry forward the fundamental tasks of education to enable those who follow us to use our shared past to address their civic and spiritual problems? What are the possibilities for community? Together, these essays offer a clear, multi-layered understanding of the compelling vision that McDermott has presented over the years. In an Afterword, McDermott responds to the authors' queries and concerns, offering a restatement of his understanding of the American philosopher's task. These essays indicate, and McDermott's response confirms, that for him philosophy is not a purely cerebral activity. Philosophy is, rather, an intellectual means of exploring the fullness of human experience, and it functions best when it operates in the context of the broad sweep of the humanities. Similarly, for McDermott the self is no given substantial entity. On the contrary, it is relational, rooted geographically and socially in its place and its fellows, and damaged when these life-giving processes fail. Further, McDermott does not accept any ultimate canopy of meaning. The human journey is a personal project within which provisional meanings must be created to sustain our advance. (shrink)

This paper is intended to contribute to the discussion of the differential level of adoption of Big Data among research communities. Recognising the impracticality of conducting an audit across all forms and uses of Big Data, we have restricted our enquiry to one very specific form of Big Data, namely general purpose taxonomies, of which Mosaic, Acorn and Origins are examples, that rely on data from a variety of Big Data feeds. The intention of these taxonomies is to enable the (...) records of consumers and citizens held on Big Data datasets to be coded according to type of residential neighbourhood or ethno-cultural heritage without any use of questionnaires. Based on our respective experience in the academic social sciences, in government and in the design and marketing of these taxonomies, we identify the features of these classifications which appear to render them attractive or problematic to different categories of potential user or researcher depending on how the relationship is conceived. We conclude by identifying seven classifications of user or potential user who, on account of their background, current position and future career expectations, tend to respond in different ways to the opportunity to adopt these generic systems as aids for understanding social processes. (shrink)

Critic, poet and philosopher Friedrich von Schlegel (1772–1829) was a leading figure of German Romanticism. In the two years before his untimely death, he wrote three cycles of lectures intended as part of a larger project to lay the foundations of a new general philosophy. Two of these cycles, 'Philosophie des Lebens' (given in 1827, published 1828) and 'Philosophie des Sprache und des Wortes' (given in December 1828 and published posthumously), are reissued here in an 1847 English translation. The first (...) presents Schlegel's understanding of philosophy as independent of theology or politics, concerned with the 'inner spiritual life' of humankind. The second explores the nature of communication through language and art. Schlegel argues that full human consciousness cannot be restored by Enlightenment science, but only by divine revelation and redemption. He offers no ready-made solutions, but encourages his listeners to develop their own responses to these questions. (shrink)

The Renaissance was a period of great intellectual change and innovation as philosophers rediscovered the philosophy of classical antiquity and passed it on to the modern age. Renaissance philosophy is distinct both from the medieval scholasticism, based on revelation and authority, and from philosophers of the seventeenth and eighteenth centuries who transformed it into new philosophical systems. Despite the importance of the Renaissance to the development of philosophy over time, it has remained largely understudied by historians of philosophy and professional (...) philosophers. This anthology aims to correct this by providing scholars and students of philosophy with representative translations of the most important philosophers of the Renaissance. Its purpose is to help readers appreciate philosophy in the Renaissance and its importance in the history of philosophy. The anthology includes translations from philosophers from the thirteenth to the seventeenth centuries, and it ranges from works on moral and political philosophy, to metaphysics, epistemology, and natural philosophy, thereby providing historians and students of philosophy with a sense for the nature, breadth, and complexity of philosophy in the Renaissance. Each translation is accompanied by an introduction by a historian of Renaissance philosophy, as well as select secondary sources, in order to encourage further study. (shrink)

Public health ethics, like the field of public health it addresses, traditionally has focused more on practice and particular cases than on theory, with the result that some concepts, methods, and boundaries remain largely undefined. This paper attempts to provide a rough conceptual map of the terrain of public health ethics. We begin by briefly defining public health and identifying general features of the field that are particularly relevant for a discussion of public health ethics.Public health is primarily concerned with (...) the health of the entire population, rather than the health of individuals. Its features include an emphasis on the promotion of health and the prevention of disease and disability; the collection and use of epidemiological data, population surveillance, and other forms of empirical quantitative assessment; a recognition of the multidimensional nature of the determinants of health; and a focus on the complex interactions of many factors—biological, behavioral, social, and environmental—in developing effective interventions. (shrink)

Questions about the relation between identity and discernibility are important both in philosophy and in model theory. We show how a philosophical question about identity and dis- cernibility can be ‘factorized’ into a philosophical question about the adequacy of a formal language to the description of the world, and a mathematical question about discernibility in this language. We provide formal definitions of various notions of discernibility and offer a complete classification of their logical relations. Some new and surprising facts are (...) proved; for instance, that weak dis- cernibility corresponds to discernibility in a language with constants for every object, and that weak discernibility is the most discerning nontrivial discernibility relation. (shrink)

Fourteen philosophers share their experience teaching Peirce to undergraduates in a variety of settings and a variety of courses. The latter include introductory philosophy courses as well as upper-level courses in American philosophy, philosophy of religion, logic, philosophy of science, medieval philosophy, semiotics, metaphysics, etc., and even an upper-level course devoted entirely to Peirce. The project originates in a session devoted to teaching Peirce held at the 2007 annual meeting of the Society for the Advancement of American Philosophy. The session, (...) organized by James Campbell and Richard Hart, was co-sponsored by the American Association of Philosophy Teachers. (shrink)

Theorems of hyperarithmetic analysis occupy an unusual neighborhood in the realms of reverse mathematics and recursion-theoretic complexity. They lie above all the fixed iterations of the Turing jump but below ATR $_{0}$. There is a long history of proof-theoretic principles which are THAs. Until the papers reported on in this communication, there was only one mathematical example. Barnes, Goh, and Shore [1] analyze an array of ubiquity theorems in graph theory descended from Halin’s [9] work on rays in graphs. They (...) seem to be typical applications of ACA $_{0}$ but are actually THAs. These results answer Question 30 of Montalbán’s Open Questions in Reverse Mathematics [19] and supply several other natural principles of different and unusual levels of complexity.This work led in [25] to a new neighborhood of the reverse mathematical zoo: almost theorems of hyperarithmetic analysis. When combined with ACA $_{0}$ they are THAs but on their own are very weak. Denizens both mathematical and logical are provided. Generalizations of several conservativity classes are defined and these ATHAs as well as many other principles are shown to be conservative over RCA $_{0}$ in all these senses and weak in other recursion-theoretic ways as well. These results answer a question raised by Hirschfeldt and reported in [19] by providing a long list of pairs of principles one of which is very weak over RCA $_{0}$ but over ACA $_{0}$ is equivalent to the other which may be strong or very strong going up a standard hierarchy and at the end being stronger than full second-order arithmetic. (shrink)

Deductive Irrationality examines and critiques economic rationalism by assessing the work of influential political philosophers and economic theorists such as Thomas Hobbes, John Locke, Adam Smith, Friedrich Hayek, Gunnar Myrdal, and John F. Muth. It is one of the first serious attempts to investigate the dominant sub-fields in economic theory through the lens of political philosophy.

Thomas Jefferson and Philosophy: Essays on the Philosophical Cast of Jefferson’s Writings is a collection of essays on topics that relate to philosophical aspects of Jefferson’s thinking over the years. Much historical insight is given to ground the various philosophical strands in Jefferson’s thought and writing on topics such as political philosophy, moral philosophy, slavery, republicanism, wall of separation, liberty, educational philosophy, and architecture.

The philosopher John J. McDermott comes out of the long American tradition that takes the aim of philosophical inquiry to be interpretation of the open meanings of experience, so that we might all live fuller and richer lives. Here, the authors of these nine essays explore his highly original interpretations of philosophy's various questions about our shared existence. How are we to understand the nature of American culture and to carry forward its important contributions? What is the personal importance of (...) embodiment, of living in the realization of death? How does our physical and personal environment nourish bodies and spirits? What does the deliberate pursuit of a morality offer us? How can we carry forward the fundamental tasks of education to enable those who follow us to use our shared past to address their civic and spiritual problems? What are the possibilities for community? Together, these essays offer a clear, multi-layered understanding of the compelling vision that McDermott has presented over the years. In an Afterword, McDermott responds to the authors' queries and concerns, offering a restatement of his understanding of the American philosopher's task. These essays indicate, and McDermott's response confirms, that for him philosophy is not a purely cerebral activity. Philosophy is, rather, an intellectual means of exploring the fullness of human experience, and it functions best when it operates in the context of the broad sweep of the humanities. Similarly, for McDermott the self is no given substantial entity. On the contrary, it is relational, rooted geographically and socially in its place and its fellows, and damaged when these life-giving processes fail. Further, McDermott does not accept any ultimate canopy of meaning. The human journey is a personal project within which provisional meanings must be created to sustain our advance. (shrink)

The sounds that make up spoken words are heard in a series and must be mapped rapidly onto words in memory because their elements, unlike those of visual words, cannot simultaneously exist or persist in time. Although theories agree that the dynamics of spoken word recognition are important, they differ in how they treat the nature of the competitor set—precisely which words are activated as an auditory word form unfolds in real time. This study used eye tracking to measure the (...) impact over time of word frequency and 2 partially overlapping competitor set definitions: onset density and neighborhood density. Time course measures revealed early and continuous effects of frequency (facilitatory) and on set based similarity (inhibitory). Neighborhood density appears to have early facilitatory effects and late inhibitory effects. The late inhibitory effects are due to differences in the temporal distribution of similarity within neighborhoods. The early facilitatory effects are due to subphonemic cues that inform the listener about word length before the entire word is heard. The results support a new conception of lexical competition neighborhoods in which recognition occurs against a background of activated competitors that changes over time based on fine-grained goodness-of-fit and competition dynamics. (shrink)

Has moral relativism run its course? The threat of 9/11, terrorism, reproductive technology, and globalization has forced us to ask anew whether there are universal moral truths upon which to base ethical and political judgments. In this timely edited collection, distinguished scholars present and test the best answers to this question. These insightful responses temper the strong antithesis between universalism and relativism and retain sensitivity to how language and history shape the context of our moral decisions. This important and relevant (...) work of contemporary political and social thought is ideal for use in the classroom across many disciplines, including political science, philosophy, ethics, law, and theology. (shrink)

Leading scholars address Paul Ricoeur's last major work, Oneself as Another.

Halin in 1965 proved that if a graph has [Formula: see text] many pairwise disjoint rays for each [Formula: see text] then it has infinitely many pairwise disjoint rays. We analyze the complexity of this and other similar results in terms of computable and proof theoretic complexity. The statement of Halin’s theorem and the construction proving it seem very much like standard versions of compactness arguments such as König’s Lemma. Those results, while not computable, are relatively simple. They only use (...) arithmetic procedures or, equivalently, finitely many iterations of the Turing jump. We show that several Halin-type theorems are much more complicated. They are among the theorems of hyperarithmetic analysis. Such theorems imply the ability to iterate the Turing jump along any computable well ordering. Several important logical principles in this class have been extensively studied beginning with work of Kreisel, H. Friedman, Steel and others in the 1960s and 1970s. Until now, only one purely mathematical example was known. Our work provides many more and so answers Question 30 of Montalbán’s Open Questions in Reverse Mathematics in 2011. Some of these theorems including ones in Halin in 1965 are also shown to have unusual proof theoretic strength as well. (shrink)

The sounds that make up spoken words are heard in a series and must be mapped rapidly onto words in memory because their elements, unlike those of visual words, cannot simultaneously exist or persist in time. Although theories agree that the dynamics of spoken word recognition are important, they differ in how they treat the nature of the competitor set—precisely which words are activated as an auditory word form unfolds in real time. This study used eye tracking to measure the (...) impact over time of word frequency and 2 partially overlapping competitor set definitions: onset density and neighborhood density. Time course measures revealed early and continuous effects of frequency (facilitatory) and on set based similarity (inhibitory). Neighborhood density appears to have early facilitatory effects and late inhibitory effects. The late inhibitory effects are due to differences in the temporal distribution of similarity within neighborhoods. The early facilitatory effects are due to subphonemic cues that inform the listener about word length before the entire word is heard. The results support a new conception of lexical competition neighborhoods in which recognition occurs against a background of activated competitors that changes over time based on fine‐grained goodness‐of‐fit and competition dynamics. (shrink)

We propose that certain forms of chronic illness can be transformative experiences, in the sense described by L.A. Paul.