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)

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.

Historian James H. Jones published the first edition of Bad Blood, the definitive history of the Tuskegee Syphilis Experiment, in 1981. Its clear-eyed examination of that research and its implications remains a bioethics classic, and the 30-year anniversary of its publication served as the impetus for the reexamination of research ethics that this symposium presents. Recent revelations about the United States Public Health Service study that infected mental patients and prisoners in Guatemala with syphilis in the late 1940s in (...) order to determine the efficacy of treatment represent only one of the many attestations to the persistence of ongoing, critical, and underaddressed issues in research ethics that Bad Blood first explored. Those issues include, but are not limited to: the complex and contested matters of the value of a given research question, the validity of the clinical trial designed to address it, and the priorities of science. (shrink)

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

Perhaps no technological innovation has so dominated the second half of the twentieth century as has the introduction of the programmable computer. It is quite difficult if not impossible to imagine how contemporary affairs—in business and science, communications and transportation, governmental and military activities, for example—could be conducted without the use of computing machines, whose principal contribution has been to relieve us of the necessity for certain kinds of mental exertion. The computer revolution has reduced our mental labors by means (...) of these machines, just as the Industrial Revolution reduced our physical labor by means of other machines. (shrink)

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 ...

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)

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)

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.

Taking Brian Cantwell Smith’s study, “Limits of Correctness in Computers,” as its point of departure, this article explores the role of models in computer science. Smith identifies two kinds of models that play an important role, where specifications are models of problems and programs are models of possible solutions. Both presuppose the existence of conceptualizations as ways of conceiving the world “in certain delimited ways.” But high-level programming languages also function as models of virtual (or abstract) machines, while low-level programming (...) languages function as models of causal (or physical) machines. The resulting account suggests that sets of models embedded within models are indispensable for computer programming. (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)

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 purpose of this essay is to investigate the properties of singular causal systems and their population manifestations, with special concern for the thesis of methodological individualism, which claims that there are no properties of social groups that cannot be adequately explained exclusively by reference to properties of individual members of those groups, i.e., at the level of individuals. Individuals, however, may be viewed as singular causal systems, i.e., as instantiations of (arrangements of) dispositional properties. From this perspective, methodological individualism (...) appears to be an ambiguous thesis: some properties of collections of (independent) systems of the same kind are reducible, but other properties of collections of (dependent) systems of the same kind are not. In cases of the first kind, therefore, methodological individualism is true, but trivial; while in cases of the second kind, it is significant, but false. Hence, if the arguments that follow are correct, at least some of the properties of social groups should qualify as emergent. (shrink)

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 ..

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.

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.

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)

The music of Christoph Willibald von Gluck was a revolution for Paris operagoers when his work premiered there in 1774. In a setting known for its restive and often rowdy spectators, Alceste, Iphigénie en Aulide, and Orpheé et Eurydice seized audiences with unprecedented force. They shed silent tears or sobbed openly, and some cried out in sympathy with the sufferers onstage. “Oh Mama! This is too painful!” three girls called out as Charon led Alcestis to the underworld, and a boy (...) pleaded with his father to take him home. A woman who watched the same performance described falling on her knees in her opera-box as the march of the priests of Apollo began, staying in this position “suppliant and with my hands clasped until the end of the piece.”Gluck's streamlined musical language was one reason for these emotional responses. He and his librettist Ranieri de’ Calzabigi simplified the conventions by eliminating extraneous subplots, abandoning the repetitive da capo form, and replacing trills and runs with simpler melodies meant to convey passion. Another reason was the widespread culture of sentimentalism, which equated virtue with sincerity and judged tears to be the natural sign of an open heart. Painters depicted tender and tumultuous family scenes, and friends pledged trembling vows of fidelity. Listeners were also readers, and many described similar tearful responses when they read the century's bestseller, Rousseau's novel Julie; or, The New Heloise.Everist, a musicologist, takes up the story of Gluck in France in the nineteenth century, when the German composer remained a presence in repertoires. No longer prone to tears, the public was often indifferent and sometimes hostile to his works. Conductors and composers nevertheless persisted in promoting Gluck's music. Between 1828 and 1870, operatic excerpts appeared roughly twice a year in performances of the prestigious Société des Concerts, and the charismatic conductor Jules Pasdeloup regularly programmed his music. Many listeners remained unconvinced. A writer in 1861 described the “sepulchral boredom that reigned the length of all five acts” of Alceste. The periodical Monde dramatique used the same language to characterize Gluck's music: it was “profoundly boring.” After a high point of performances in the middle of Napoleon III's reign, Gluck disappeared from the Paris opera and concert stage for some thirty years.Everist's aim in this slim book is to isolate the “agents” involved in the French reception of Gluck. Traditional reception histories might begin with Gluck and his aims, identifying musical features, particular responses of audiences, critics’ accounts, and perhaps the more elusive temper of the times. Everist focuses instead on less conspicuous networks of impresarios, theater directors, and publishers. In his telling, such agents also include journalists and writers of fiction. The avowed effort is to decenter the artist and his art to emphasize the limited role that composers and librettists play in the performance of an opera. A quoted passage in the book reminds us that without parking attendants, stagehands, and ticket sellers the show could not go on. True enough. Genealogies of Music and Memory therefore provides tables listing Gluck arias in anthologies, particular singers’ performances, works by composers other than Gluck who also drew themes from classical antiquity, and works by other foreign-born composers. A section on “material culture” lists paintings and sculptures of Gluck in Paris theaters and museums.As a “genealogy,” the book is a salutary reminder of the web of amateurs and professionals who discuss, promote, and perform works that others have created. Writers such as E. T. A. Hoffmann, Mme de Staël, and Hippolyte Taine held up Gluck as the embodiment of German music. Hector Berlioz wrote frequently and enthusiastically about Gluck, although he was less keen to program his music. The singers François Delsarte and Pauline Viardot aroused temporary interest in Gluck by regularly including his arias in their recitals. Musical anthologies for the bourgeois household included piano arrangements of his best-known arias. Some nineteenth-century adaptations of his works were scored for the military band.Genealogies of Music and Memory is musicology with very little music. Everist's reliance on networks of actors, agents, publishers, pedagogical practices, and archival environments leads him to assert that “multiple agency is endemic in the story told here.” Unfortunately, it is often unclear just what the story is. Carelessness in writing and editing throughout—including a subject-verb clash in the book's final sentence—has rendered key passages obscure. Everist describes Delsarte's voice as feeble, broken, veiled, and ready to be extinguished twice in the same paragraph, first as a paraphrase and again in a quotation (with a misplaced comma).Decentering artists and their work to elevate others responsible for its reception brings attention to the unseen and often unsung. In the absence of particular performance histories, musical analyses and description, or sustained accounts of shared tastes or critical responses, however, conclusions remain piecemeal. Everist claims to have revealed a “Geertzian web of culture” in his study. A more modest account would describe it as an enumeration of references, revivals, editions, excerpts, and arrangements. (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)

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)