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)

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)

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

The ideas of the late Donald Davidson are beginning to be appreciated beyond their origin in Analytic philosophy of language. Davidson doesn’t make appropriation easy. He was an Analytic philosopher’s philosopher, intricately technical, indifferent to questions outside a narrow specialization. As prose, Davidson is elegant, spare, subtle, and indirect. A great deal is left unsaid. If Quine were H. L. Mencken, Davidson would be Henry James. To follow the argument carefully, you need a course in logic, maybe more than (...) one. The effort is worth it. It’s been a long time since there was a really new idea about truth. Philosophers have recycled between Plato and Protagoras for two thousand years. Davidson credits logician Alfred Tarski, but without Davidson the ideas would have been lost, for Tarski himself didn’t see the most important thing, and would have learned as much from Davidson as the rest of us have. Before Tarski it seemed inevitable to think of truth in terms of relations extending beyond language. With Tarski truth becomes an artifact of the logic of language. The only way to explain what it is for a sentence to be true is to show how it relates to an infinite set of other sentences. The account never strays from relations of language to language. The result is an idea of truth that’s as unconditional as any purist could ask for, yet supports no metaphysical interpretation. Instead, metaphysical ideas of truth stand exposed as extravagantly superfluous. Davidson’s question in these lectures is the point of is. What’s this particle doing in language? There’s no obvious answer. He decides that we never know exactly what is means because we never know what is true means. We would know both if only we knew what our language is, but we never will. (shrink)

This paper is about the similarity between the appreciation of a piece of art, such as a cherished music album, and the loving appreciation of a person whom one knows well. In philosophical discussion about the rationality of love, the Qualities View (QV) says that love can be justified by reference to the qualities of the beloved. I argue that the oft-rehearsed trading-up objection fails to undermine the QV. The problems typically identified by the objection arise from the idea that (...) love-worthy qualities could be coarse-grained, when in fact they must be fine-grained. The analogy with appreciation of aesthetic qualities helps to draw out this point. Once the fine-grained nature of love-worthy qualities is properly understood, it is clear that critics of the QV cannot rely on the trading-up objection to motivate its rejection. Moreover, the paper’s core argument helps to illuminate the persistently aesthetic nature of interpersonal affections. (shrink)

We applaud the spirit of MacNeilage's attempts to better explain the evolution and cortical control of speech by drawing on the vast literature in nonhuman primate neurobiology. However, he oversimplifies motor cortical fields and their known individual functions to such an extent that he undermines the value of his effort. In particular, MacNeilage has lumped together the functional characteristics across multiple mesial and lateral motor cortex fields, inadvertantly creating two hypothetical centers that simply may not exist.

A lineage of prominent philosophers who have discussed the second-person relation can be regarded as advancing structural accounts. They posit that the second-person relation effects one transformative change to the structure of practical reasoning. In this paper, I criticise this orthodoxy and offer an alternative, substantive account. That is, I argue that entering into second-personal relations with others does indeed affect one's practical reasoning, but it does this not by altering the structure of one's agential thought, but by changing what (...) reasons can become available. The importance of second-personal thought for action is heterogenous. Second-person relations make possible the emergence of a wide variety of different kinds of practical reasons: creating some, revealing others. Recognising this diminishes the appeal of the traditional, structural accounts of the practical significance of such second-personal relations. Moving away from structural accounts facilitates a more thorough understanding of the intersubjective form of action. (shrink)

Recent discussions in the various circles of feminism, postmodernism, and environmentalism have begun to make clear that ontology and epistemology without ethics is deadly - oppressive to women, oppressive to men, oppressive to the earth. In response to this crisis of reason in modernity, this collection of essays suggests the importance of knowing other-wise, non-rational ways of knowing which are wise to the "other" - a spiritual knowing of the heart with the passionate eye of love. Knowing Otherwise calls into (...) question the Western philosophical tradition of giving pride of place to reason in the acquisition of knowledge. Reasoning is only one of many ways in which we engage, i.e. know, the world. We know more than we think. We know by touch, by feel, by taste, by sight, by sounds, by smell, by symbols, by sex, by trust - by means of every modality of human experience. Philosophy becomes, in the fashion of Levinas, "the wisdom of love at the service of love. Tracing connections between epistemology, ethics, and spirituality - between "knowing" and the "other," between an other and the Other - all the essays serve as points of convergence between postmodern discussions and the Calvinian spirituality which is the home for writers in this collection. In particular, this collection explores the contributions of feminist thought and thinkers such as Emmanuel Levinas, Richard Rorty, Jacqes Derrida, and John D. Caputo to a spiritually and ethically sensitive knowing. (shrink)

Introduction: and a pop quiz -- Administrative ethics: ideas, sources, and development -- Refining the sense of duty: responsibilities of public administrators and the issue of agency -- Reinforcing and enlarging duty: philosophical bases of ethical behavior and the ethics triangle -- Codifying duty and ethical perspectives: professional codes of ethics -- Undermining duty: challenges to the ethical behavior of public administrators -- Deciding how to meet obligations and act responsibly: ethical analysis and problem solving -- Acting on duty in (...) the face of uncertainty and risk: responsible whistleblowing -- Elevating ethical behavior in the organization -- Mandating duty: external measures to promote ethics -- Conclusion: the duties of public administrators. (shrink)

The book uses Zen Buddhism as the opening wedge for an extraordinarily wide-ranging exploration of consciousness.

Kant's philosophy of arithmetic / by Charles Parsons -- Visual geometry / by James Hopkins -- The proof-structure of Kant's transcendental deduction / by Dieter Henrich -- Imagination and perception / by P.F. Strawson -- Kant's categories and their schematism / by Lauchlan Chipman -- Transcendental arguments / by Barry Stroud -- Strawson on transcendental idealism / by H.E. Matthews -- Self-knowledge / by W.H. Walsh -- The age and size of the world / by Jonathan Bennett.

Wilkie proved in 1977 that every countable model ${\mathcal M}$ of Peano Arithmetic has an elementary end extension ${\mathcal N}$ such that the interstructure lattice $\operatorname {\mathrm {Lt}}({\mathcal N} / {\mathcal M})$ is the pentagon lattice ${\mathbf N}_5$. This theorem implies that every countable nonstandard ${\mathcal M}$ has an elementary cofinal extension ${\mathcal N}$ such that $\operatorname {\mathrm {Lt}}({\mathcal N} / {\mathcal M}) \cong {\mathbf N}_5$. It is proved here that whenever ${\mathcal M} \prec {\mathcal N} \models \mathsf {PA}$ and (...) $\operatorname {\mathrm {Lt}}({\mathcal N} / {\mathcal M}) \cong {\mathbf N}_5$, then ${\mathcal N}$ must be either an end or a cofinal extension of ${\mathcal M}$. In contrast, there are ${\mathcal M}^* \prec {\mathcal N}^* \models \mathsf {PA}^*$ such that $\operatorname {\mathrm {Lt}}({\mathcal N}^* / {\mathcal M}^*) \cong {\mathbf N}_5$ and ${\mathcal N}^*$ is neither an end nor a cofinal extension of ${\mathcal M}^*$. (shrink)

This sequel to the widely read Zen and the Brain continues James Austin's explorations into the key interrelationships between Zen Buddhism and brain research. In Zen-Brain Reflections, Austin, a clinical neurologist, researcher, and Zen practitioner, examines the evolving psychological processes and brain changes associated with the path of long-range meditative training. Austin draws not only on the latest neuroscience research and new neuroimaging studies but also on Zen literature and his personal experience with alternate states of consciousness.Zen-Brain Reflections takes (...) up where the earlier book left off. It addresses such questions as: how do placebos and acupuncture change the brain? Can neuroimaging studies localize the sites where our notions of self arise? How can the latest brain imaging methods monitor meditators more effectively? How do long years of meditative training plus brief enlightened states produce pivotal transformations in the physiology of the brain? In many chapters testable hypotheses suggest ways to correlate normal brain functions and meditative training with the phenomena of extraordinary states of consciousness.After briefly introducing the topic of Zen and describing recent research into meditation, Austin reviews the latest studies on the amygdala, frontotemporal interactions, and paralimbic extensions of the limbic system. He then explores different states of consciousness, both the early superficial absorptions and the later, major "peak experiences." This discussion begins with the states called kensho and satori and includes a fresh analysis of their several different expressions of "oneness." He points beyond the still more advanced states toward that rare ongoing stage of enlightenment that is manifest as "sage wisdom."Finally, with reference to a delayed "moonlight" phase of kensho, Austin envisions novel links between migraines and metaphors, moonlight and mysticism. The Zen perspective on the self and consciousness is an ancient one. Readers will discover how relevant Zen is to the neurosciences, and how each field can illuminate the other. (shrink)

This sequel to the widely read Zen and the Brain continues James Austin's explorations into the key interrelationships between Zen Buddhism and brain research. In Zen-Brain Reflections, Austin, a clinical neurologist, researcher, and Zen practitioner, examines the evolving psychological processes and brain changes associated with the path of long-range meditative training. Austin draws not only on the latest neuroscience research and new neuroimaging studies but also on Zen literature and his personal experience with alternate states of consciousness.Zen-Brain Reflections takes (...) up where the earlier book left off. It addresses such questions as: how do placebos and acupuncture change the brain? Can neuroimaging studies localize the sites where our notions of self arise? How can the latest brain imaging methods monitor meditators more effectively? How do long years of meditative training plus brief enlightened states produce pivotal transformations in the physiology of the brain? In many chapters testable hypotheses suggest ways to correlate normal brain functions and meditative training with the phenomena of extraordinary states of consciousness.After briefly introducing the topic of Zen and describing recent research into meditation, Austin reviews the latest studies on the amygdala, frontotemporal interactions, and paralimbic extensions of the limbic system. He then explores different states of consciousness, both the early superficial absorptions and the later, major "peak experiences." This discussion begins with the states called kensho and satori and includes a fresh analysis of their several different expressions of "oneness." He points beyond the still more advanced states toward that rare ongoing stage of enlightenment that is manifest as "sage wisdom."Finally, with reference to a delayed "moonlight" phase of kensho, Austin envisions novel links between migraines and metaphors, moonlight and mysticism. The Zen perspective on the self and consciousness is an ancient one. Readers will discover how relevant Zen is to the neurosciences, and how each field can illuminate the other. (shrink)

A personal story of the ways in which persistence, chance, and creativity interact in biomedical research. This first book by the author of Zen and the Brain examines the role of chance in the creative process. James Austin tells a personal story of the ways in which persistence, chance, and creativity interact in biomedical research; the conclusions he reaches shed light on the creative process in any field. Austin shows how, in his own investigations, unpredictable events shaped the outcome (...) of his research and brought about novel results. He then goes beyond this story of serendipity to propose a new classification of the varieties of chance, drawing on his own research and examples from the history of science—including the famous accidents that led Fleming to the discovery of penicillin. Finally, he explores the nature of the creative process, considering not only the environmental and neurophysiological correlates of creativity but also the role of intuition in both scientific discoveries and spiritual quests. This updated MIT Press paperback edition includes a new introduction and recent material on medical research, creativity, and spirituality. (shrink)

The relationship of Grundy and chromatic numbers of graphs in the context of Reverse Mathematics is investi-gated.

1. WHAT IS ARTIFICIAL INTELLIGENCE? One of the fascinating aspects of the field of artificial intelligence (AI) is that the precise nature of its subject ..

Based on the Zen philosophy about focusing away from the self, a guide to "neural Zen" meditative practices draws on recent findings in brain research to outline recommendations for various methods of pursuing a balanced, selfless state of ...

We need to clarify at least four aspects of selfhood if we are to reach a better understanding of consciousness in general, and of its alternate states. First, how did we develop our self-centred psychophysiology? Second, can the four familiar lobes of the brain alone serve, if only as preliminary landmarks of convenience, to help understand the functions of our many self-referent networks? Third, what could cause one's former sense of self to vanish from the mental field during an extraordinary (...) state of consciousness? Fourth, when a person's physical and psychic self do drop off briefly, how has conscious experience then been transformed? In particular, what happens to that subject's personal sense of time? Our many-sided self arose in widely distributed brain networks. Since infancy, these self-oriented circuits have been over-conditioned by limbic biases. Selfhood then seems to have evolved along lines suggesting at least in shorthand the operations of a kind of ‘I-Me-Mine’ complex. But what happens when this egocentric triad briefly dissolves? Novel states of consciousness emerge. Two personally-observed states are discussed: insight-wisdom ; internal absorption. How do these two states differ phenomenologically? The physiological processes briefly suggested here emphasize shifts in deeper systems, and pivotal roles for thalamo-cortical interactions in the front and back of the brain. (shrink)

The development of science has been a distinctive feature of human history in recent times, especially in the seventeenth and eighteenth centuries. In light of the problems that define the philosophy of science today, James Fetzer provides a foundation for inquiry into the nature of science, the history of science, and the relationship between the two. In Philosophy of Science, Fetzer investigates the aim and methods of empirical science and examines the importance of methodological commitments to the study of (...) science and the significance of interpretations of probability for understanding laws of nature and scientific explanations. This book offers a welcome framework for investigating the most recent work and the most promising solutions to the central problems that arise within this discipline. The result is a timely introduction to an increasingly important field. -- Publisher description. (shrink)

If the decades of the forties through the sixties were dominated by discussion of Hempel's “covering law“ explication of explanation, that of the seventies was preoccupied with Salmon's “statistical relevance” conception, which emerged as the principal alternative to Hempel's enormously influential account. Readers of Wesley C. Salmon's Scientific Explanation and the Causal Structure of the World, therefore, ought to find it refreshing to discover that its author has not remained content with a facile defense of his previous investigations; on the (...) contrary, Salmon offers an original account of different kinds of explications, advances additional criticisms of various alternative theories, and elaborates a novel “two-tiered“ analysis of explanation that tacitly depends upon a “two-tiered” account of homogeneity. Indeed, if the considerations that follow are correct, Salmon has not merely refined his statistical relevance account but has actually abandoned it in favor of a “causal/mechanistic“ construction. This striking development suggests that the theory of explanation is likely to remain as lively an arena of debate in the eighties as it has been in the past. (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.

The purpose of this paper is to explore three alternative frameworks for understanding the nature of language and mentality, which accent syntactical, semantical, and pragmatical aspects of the phenomena with which they are concerned, respectively. Although the computational conception currently exerts considerable appeal, its defensibility appears to hinge upon an extremely implausible theory of the relation of form to content. Similarly, while the representational approach has much to recommend it, its range is essentially restricted to those units of language that (...) can be understood in terms of undefined units. Thus, the only alternative among these three that can account for the meaning of primitive units of language is one emphasizing the basic role of skills, habits, and tendencies in relating signs and dispositions. (shrink)

This is not the usual kind of self-help book. Indeed, its major premise heeds a Zen master's advice to be _less_ self-centered. Yes, it is "one more book of words about Zen," as the author concedes, yet this book explains meditative practices from the perspective of a " _neural_ Zen." The latest findings in brain research inform its suggestions. In _Meditating Selflessly_, James Austin -- Zen practitioner, neurologist, and author of three acclaimed books on Zen and neuroscience -- guides (...) readers toward that open awareness already awaiting them on the cushion and in the natural world. Austin offers concrete advice -- often in a simplified question-and-answer format -- about different ways to meditate. He clarifies both the concentrative and receptive styles of meditation. Drawing widely from the exciting new field of contemplative neuroscience, Austin helps resolve an ancient paradox: why both insight wisdom _and_ selflessness arise simultaneously during enlightened states of consciousness. (shrink)

Does ethical content in organizational mission statements make a difference? Research regarding the effectiveness and results of mission statements is mixed. Krohe concluded that much of the good results do not come from the mission statements themselves but from the strategic re-education that happens in producing one. We attempted to discover whether universities that explicitly state their ethical orientation and vision in their mission statements had students with higher perceived character trait importance and activities that reinforce character than universities that (...) did not. While the faculty and administration may receive benefits from mission statement development through strategic re-education as Krohe suggested, do the statements influence the students at the university who may have had no role in its creation? Using a sample of senior business students at 16 universities we found that students at universities with ethical statements in their mission statements had significantly higher perceived character trait importance and character reinforcement than those at universities whose missions lacked ethical statements. This research suggests that schools that explicitly stated ethical content in their mission statements do influence student ethical orientation. (shrink)

[opening paragraph]: On page 2 of this volume our co-editors set admirable goals. They seek ‘method- ologies that can provide an open link to objective, empirically based description'. Moreover, they want ‘explicit examples of practical knowledge, in case studies'. My comments will address these words and goals. I too prefer the case-method approach, and seek practical ways to access states of consciousness. Then, at the top of page 4, Professors Varela and Shear define ‘nonconscious phenomena’ as those the subject is (...) not aware of. In order to comment further on this issue of awareness and non-awareness, I'll first need to pick up on their other key word -- ‘blindness’ -- as introduced in their section VII. I'll then redirect it. For surely a central topic to confront is our own self-imposed blindfold. Which subterranean region of consciousness are we most unaware of? What thwarts our efforts to study all of its regions? Our own covert self. (shrink)

Far more than just a dance, the dynamic choreography of the Yup’ik provides an illuminating window into the morality, social organization, and colonial history of this indigenous people. In Yupiit Yurayarait, anthropologist Ann Fienup-Riordan begins with a brief historical overview of the colonization and development of Alaska from the Yup'ik point of view. Then, armed with oral history testimony spanning thirty years, she shows how singing and dancing are interconnected and imbued with meaning in this complex ritual. Accompanied by one (...) hundred and fifty original photographs, this volume marks the first in-depth look at the Yup’ik people through the lens of interpretive dance. (shrink)