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)

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.

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 ..

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)

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)

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

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)

The notion of program verification appears to trade upon an equivocation. Algorithms, as logical structures, are appropriate subjects for deductive verification. Programs, as causal models of those structures, are not. The success of program verification as a generally applicable and completely reliable method for guaranteeing program performance is not even a theoretical possibility.

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)

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)

Some reasons are thought to depend on relations between people, such as that of a promiser to a promisee. It has sometimes been assumed that all reasons that are relational in this way are moral obligations. I argue, via a counter example, that there are non-obligatory relational reasons. If true, this has ramifications for relational theories of morality.

Technological revolutions are dissected into three stages: the introduction stage, the permeation stage, and the power stage. The information revolution is a primary example of this tripartite model. A hypothesis about ethics is proposed, namely, ethical problems increase as technological revolutions progress toward and into the power stage. Genetic technology, nanotechnology, and neurotechnology are good candidates for impending technological revolutions. Two reasons favoring their candidacy as revolutionary are their high degree of malleability and their convergence. Assuming the emerging technologies develop (...) into mutually enabling revolutionary technologies, we will need better ethical responses to cope with them. Some suggestions are offered about how our approach to ethics might be improved. (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)

The purpose of this paper is to provide a systematic defense of the single-case propensity account of probabilistic explanation from the criticisms advanced by Hanna and by Humphreys and to offer a critical appraisal of the aleatory conception advanced by Humphreys and of the deductive-nomological-probabilistic approach Railton has proposed. The principal conclusion supported by this analysis is that the Requirements of Maximal Specificity and of Strict Maximal Specificity afford the foundation for completely objective explanations of probabilistic explananda, so long as (...) they are employed on the basis of propensity criteria of explanatory relevance. (shrink)

Being able to ask others to do things, and thereby giving them reasons to do those things, is a prominent feature of our interpersonal lives. In this paper, I discuss the distinctive normative status of requests – what makes them different from commands and demands. I argue for a theory of this normative phenomenon which explains the sense in which the reasons presented in requests are a matter of discretion. This discretionary quality, I argue, is something that other theories cannot (...) accommodate, though it is a significant aspect of the relations that people stand in to one another, and the kinds of practical reasons that flow from those relations. (shrink)

Significant structural, developmental, and financial constraints exist in Scottish soccer that may predicate a different approach to talent identification and development. To our knowledge, no published reports exist evaluating the prevalence of the relative age effect in Scottish soccer players. Consequently, the aim of this study was to investigate the prevalence of the RAE among varied playing levels and ages of male Scottish youth soccer players. Birthdates of male youth players from U10 to U17 age groups and from playing levels: (...) “Amateur”, “Development”, and “Performance”, alongside a group of male Scottish senior professional players were recorded and categorized into quartiles and semesters from the start of the selection year. Birthdates were analyzed for: each playing level and each age group irrespective of playing level. For the varied playing levels examined, an RAE was evident in “Development” and “Performance” playing levels only at youth level. When examining each age group, an RAE was observed in U12–U17 players only. While there was a slight asymmetry favoring Q1 born senior professional players, the RAE was not present within this group of our sample. Results from our study suggest that a bias in selecting individuals born earlier in the selection year may exist within male soccer academy structures, but not at amateur level. The asymmetry favoring chronologically older players at youth but not professional level questions the efficacy of this conscious bias within male Scottish soccer players. (shrink)

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)

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 idea that human thought requires the execution of mental algorithms provides a foundation for research programs in cognitive science, which are largely based upon the computational conception of language and mentality. Consideration is given to recent work by Penrose, Searle, and Cleland, who supply various grounds for disputing computationalism. These grounds in turn qualify as reasons for preferring a non-computational, semiotic approach, which can account for them as predictable manifestations of a more adquate conception. Thinking does not ordinarily require (...) the execution of mental algorithms, which appears to be at best no more than one rather special kind of thinking. (shrink)

Luciano Floridi (2003) offers a theory of information as a “strongly semantic” notion, according to which information encapsulates truth, thereby making truth a necessary condition for a sentence to qualify as “information”. While Floridi provides an impressive development of this position, the aspects of his approach of greatest philosophical significance are its foundations rather than its formalization. He rejects the conception of information as meaningful data, which entails at least three theses – that information can be false; that tautologies are (...) information; and, that “It is true that...” is non-redundant – appear to be defensible. This inquiry offers various logical, epistemic, and ordinary-language grounds to demonstrate that an account of his kind is too narrow to be true and that its adoption would hopelessly obscure crucial differences between information, misinformation, and disinformation. (shrink)

It is common for people to be sensitive to aesthetic qualities in one another’s speech. We allow the loveliness or unloveliness of a person’s voice to make impressions on us. What is more, it is also common to allow those aesthetic impressions to affect how we are inclined to feel about the speaker. We form attitudes of liking, trusting, disliking or distrusting partly in virtue of the aesthetic qualities of a person’s speech. In this paper I ask whether such attitudes (...) could ever be legitimate. This is a microcosm of the broader issue of whether people’s aesthetic qualities in general can justify the interpersonal valuing-attitudes that they so often cause. I draw from recent discussions of body aesthetics to articulate a pair of challenges. One challenge says that aesthetic judgements of speech are reliant on unjustifiable prejudices. The other holds that a person’s aesthetic qualities are irrelevant to whether they should be liked. Against these challenges I argue that some speech can bear aesthetic qualities which are not reliant on prejudice and which are relevant to whether the speaker should be liked. I develop this argument through an analysis of the concept of lyricism. (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.

The standard interpretation of the imitation game is defended over the rival gender interpretation though it is noted that Turing himself proposed several variations of his imitation game. The Turing test is then justified as an inductive test not as an operational definition as commonly suggested. Turing's famous prediction about his test being passed at the 70% level is disconfirmed by the results of the Loebner 2000 contest and the absence of any serious Turing test competitors from AI on the (...) horizon. But, reports of the death of the Turing test and AI are premature. AI continues to flourish and the test continues to play an important philosophical role in AI. Intelligence attribution, methodological, and visionary arguments are given in defense of a continuing role for the Turing test. With regard to Turing's predictions one is disconfirmed, one is confirmed, but another is still outstanding. (shrink)

Bounded lattices (that is lattices that are both lower bounded and upper bounded) form a large class of lattices that include all distributive lattices, many nondistributive finite lattices such as the pentagon lattice N₅, and all lattices in any variety generated by a finite bounded lattice. Extending a theorem of Paris for distributive lattices, we prove that if L is an ℵ₀-algebraic bounded lattice, then every countable nonstandard model ������ of Peano Arithmetic has a cofinal elementary extension ������ such that (...) the interstructure lattice Lt(������ / ������) is isomorphic to L. (shrink)

Let ℳ be a countable, recursively saturated model of Peano Arithmetic, and let Aut be its automorphism group considered as a topological group with the pointwise stabilizers of finite sets being the basic open subgroups. Kaye proved that the closed normal subgroups are precisely the obvious ones, namely the stabilizers of invariant cuts. A proof of Kaye's theorem is given here which, although based on his proof, is different enough to yield consequences not obtainable from Kaye's proof.