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.

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)

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

This work has been selected by scholars as being culturally important, and is part of the knowledge base of civilization as we know it. This work was reproduced from the original artifact, and remains as true to the original work as possible. Therefore, you will see the original copyright references, library stamps (as most of these works have been housed in our most important libraries around the world), and other notations in the work. This work is in the public domain (...) in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work. As a reproduction of a historical artifact, this work may contain missing or blurred pages, poor pictures, errant marks, etc. Scholars believe, and we concur, that this work is important enough to be preserved, reproduced, and made generally available to the public. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (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)

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 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.

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)

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 ...

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)

Fix a countable nonstandard model M of Peano arithmetic. Even with some rather severe restrictions placed on the types of minimal cofinal extensions N≻M that are allowed, we still find that there are 2ℵ0 possible theories of (N,M) for such N’s.

In this paper I argue for a computational theory of thinking that does not eliminate the mind. In doing so, I will defend computationalism against the arguments of John Searle and James Fetzer, and briefly respond to other common criticisms.

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)

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)

James H. Donelan describes how two poets, a philosopher, and a composer - Hölderlin, Wordsworth, Hegel, and Beethoven - developed an idea of self-consciousness based on music at the turn of the nineteenth century. This idea became an enduring cultural belief: the understanding of music as an ideal representation of the autonomous creative mind. Against a background of political and cultural upheaval, these four major figures - all born in 1770 - developed this idea in both metaphorical and actual (...) musical structures, thereby establishing both the theory and the practice of asserting self-identity in music. Beethoven still carries the image of the heroic composer today; this book describes how it originated in both his music and in how others responded to him. Bringing together the fields of philosophy, musicology, and literary criticism, Donelan shows how this development emerged from the complex changes in European cultural life taking place between 1795 and 1831. (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 ..

If a concept, or thought, is not only something one can be aware of but also something which, unlike everything else, can be the same for every thinker, then language is a problem for thinkers. Although a linguistic sign is not itself a concept, but rather is only used to signify a concept, signs are required to think concepts—or, at least, to think the relations of concepts—and the use of linguistic signs may sometimes lead to confusion, for two signs may (...) be used to signify one concept, and one sign may be used to signify two concepts. A thinker may attempt to avoid confusion by using only one sign to signify one concept, but it may be that in any given language there is only one sign with which to signify two concepts. In this case the thinker may borrow a sign from a foreign language or invent a new sign to signify one of the two concepts. A similar problem arises for a thinker who discovers a concept, and may signify it by either using a sign in the given language, borrowing a sign from a foreign language, or inventing a new sign. Even with all these precautions, however, a thinker may occasionally lapse into using one sign to signify two concepts, and this presents a problem for anyone interpreting the thinker’s utterances and written texts. (shrink)