The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

Our goal here is to help identify the contextualist’s most worthy competitor to relativism. Recently, some philosophers of language and linguists have argued that, while there are contextualist-friendly semantic theories of deontic modals that fit with the relativist’s challenge data, the best such theories are not Lewis-Kratzer-style semantic theories. If correct, this would be important: It would show that the theory that has for many years enjoyed the status of the default view of modals in English and other languages (...) is in need of revision. Here we defend the default view by showing how a Kratzer-style semantics is able to make available readings of the relevant utterances that fit with the pretheoretical judgments opponents purport it cannot fully capture. Having established this, we turn to considering the more theoretical grounds proponents have offered for preferring their rival contextualist views. Here the question is to what extent such grounds favor semantic over what Korta and Perry call “near-side pragmatic” explanations of our judgments. In particular, we argue that our favored readings figure in near-side pragmatic explanations of those judgments that possess the methodological and theoretical advantages of systematicity and unity at least as well as, if not to a greater extent than, those of opponents who argue for their revised semantic theories on the basis of these advantages. (shrink)

In the preface to this work, Thayer explains that his purpose is to present "the classic writings of pragmatism" defined as "the original and formative expressions of this philosophy articulated by its most eminent spokesmen." The selections are from Peirce, James, and Dewey as well as brief readings from Mead and C. I. Lewis. Each selection is accompanied by a brief introduction. In addition to these selectional introductions, there is also a two-part general introduction. The first part is a (...) short historical piece by Thayer situating pragmatism in the context of western thought. The second part is a 1931 article by Dewey outlining the development of pragmatism in Peirce and James. These informative introductions should be of value to the philosophical novice who finds himself in many anthologies afloat on the sea of primary sources without the aid of the historical context necessary to fix his position. The individual selections have been carefully chosen and well coordinated. Insofar as they cluster about the central theme of the epistemological nature of pragmatism, they avoid the pitfall of attempting to elucidate the entire philosophy of many thinkers in one volume. The Peirce section includes in addition to the usual articles, "The Fixation of Belief" and "How to Make Our Ideas Clear," selections from Peirce's later writings including the 1905 article, "What Pragmatism Is" in which he differentiates his pragmatism from that of James. The section on James incorporates important sections from The Principles of Psychology together with the famous essay "The Will to Believe" and two lectures on the pragmatic concept of meaning and truth from Pragmatism. The Dewey selection provides a judicious collection of his writings from the 1896 article on the "Reflex Arc Concept" advocating the integration of organism and action to the general analysis of intelligent action in his 1938 book, Logic: The Theory of Inquiry. Also included is a chapter from The Quest for Certainty describing the application of pragmatic method to the realm of moral value. The contents of this volume are rounded out with a piece by Mead on social consciousness and the social self and an article by C. I. Lewis on the pragmatic conception of the a priori. Thayer has produced an excellent anthology of pragmatic philosophy well suited to any course in classical American philosophy emphasizing an epistemological approach.--W. J. L. (shrink)

ABSTRACTRecognising identity and emotion conveyed by the face is important for successful social interactions and has thus been the focus of considerable research. Debate has surrounded the extent...

J. L. Austin, in "Ifs and Cans," proclaimed the common hope that we soon "may see the birth, through the joint labors of philosophers, grammarians, and numerous other students of language, of a true and comprehensive science of language." The problem has always been with the "joint labors" part. Philosophers have always been willing to issue linguists dictums and linguists have been happy to teach philosophers "plain facts." Austin’s general view of language, and his particular notion of performative utterance, can (...) be found in the writing of J. R. Firth, the most commanding British linguist of Austin’s generation, but Austin never refers to Firth. In the present volume, however, we find clear and exciting evidence of genuinely joint labors on the part of philosophers and linguists. They stem from a summer conference in 1969 rounded out with contributions from notables. To two thick issues of Synthese the editors have added a dazzling piece by Saul Kripke, two substantial pieces by James McCawley and J. R. Ross, a short paper by Paul Ziff, and a reprint of P. F. Strawson’s "Grammar and Philosophy." This is an invaluable book and the best book among the many now available concerning the interaction of linguistics and philosophy: worth the cost, which the contributors attempted to reduce through foregoing royalties. The philosophers in this volume hold, or hold intriguing, the view that the semantics of a natural language can and must, in effect, be a theory of truth for a language in much the manner that Tarski suggested, and provided, for artificial language: the recursive specification of biconditionals in which the left hand gives the structural description of an object language sentence and the right hand, the truth conditions in the metalanguage. In "homophonic" translation this requirement can be trivially satisfied simply by mentioning the sentence on the left that one uses on the right: one makes the requirement non-trivial by forcing enough into the recursive specification so that one captures the native speaker’s implicit semantic competence. In this volume, the "orthodox" Davidsonian program, which takes the syntax of the metalanguage to be standard predicate logic, is ably argued by John Wallace ; Richard Montague, David Lewis, and Jaakko Hintikka would want an intensional logic covering modality and propositional attitudes. The linguists who find this philosophical climate most appealing are called "generative semanticists": McCawley, Ross, George Lakoff and others argue that any proposed semantic rule will eventually prove necessary to syntax too and that, hence, the deepest level of syntactical form will be equivalent to semantic form. Whatever the ultimate fate of this joint program, it leads here to much exciting interaction between linguists and philosophers: linguists who welcome the machinery and conceptual standards of modern logic, and philosophers who try to grasp the specifics of crucial issues in recent linguistic theory. Even if Quine’s doubts, here sketched, and Chomsky’s currently unpublished more technical objections should be well-founded, nonetheless the joint labor will have been very much worthwhile. Aside from this general debate about semantics, there are several papers covering more specific issues. The papers of J. A. Fodor, Terence Parsons, and Ross concern adverbs and the logical form of action sentences; several papers, particularly B. H. Partee’s, examine "Opacity, Coreference, and Pronouns." In all these papers one notes the fulfillment of Austin’s hope that philosophic and linguistic arguments should become intermixed, if not at times properly indistinguishable. Perhaps the most enjoyable and exciting paper stands aside from linguistics: Saul Kripke’s "Naming and Necessity." Kripke here argues quite informally for the separation of analytic, a priori, and necessary that is required for a Kripke style, S5, modal logic with de re modalities. "Gold is a yellow metal," for example, turns out to be contingent, while "Heat is the motion of particles" is necessary but a posteriori ; and that philosopher’s stone of stones, "The morning star is the evening star," is discovered to be necessary but a posteriori.—J. L. (shrink)

Volume 34, Issue 8, December 2020, Page 1621-1631.

Lewis proposes a solution for bridging the gap between cognitive-psychological and neurobiological theories of emotion in terms of dynamic systems modeling. However, an important brain network is absent in his account: the neuroendocrine system. In this commentary, the dynamic features of the cross-talk between the hypothalamic-pituitary-adrenal (HPA) and gonadal (HPG) axes are discussed within a triple-balance model of emotion.

Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

In an adaptive clinical trial , key trial characteristics may be altered during the course of the trial according to predefined rules in response to information that accumulates within the trial itself. In addition to having distinguishing scientific features, adaptive trials also may involve ethical considerations that differ from more traditional randomized trials. Better understanding of clinical trial experts’ views about the ethical aspects of adaptive designs could assist those planning ACTs. Our aim was to elucidate the opinions of clinical (...) trial experts regarding their beliefs about ethical aspects of ACTs. (shrink)

This book is a collection of secondary essays on America's most important philosophic thinkers—statesmen, judges, writers, educators, and activists—from the colonial period to the present. Each essay is a comprehensive introduction to the thought of a noted American on the fundamental meaning of the American regime.

This article addresses five research questions: What specific behaviors are described in the literature as ethical or unethical? What percentage of business people are believed to be guilty of unethical behavior? What specific unethical behaviors have been observed by bank employees? How serious are the behaviors? Are experiences and attitudes affected by demographics? Conclusions suggest: There are seventeen categories of behavior, and that they are heavily skewed toward internal behaviors. Younger employees have a higher level of ethical consciousness than older (...) employees. The longer one works for a company, the more one may look to job security as a priority; this can lead to rationalizing or overlooking apparently unethical behaviors. More emphasis is needed on internal behaviors with particular attention on the impact that external behaviors have on internal behaviors. (shrink)

Pancreatitis is a complex, progressively destructive inflammatory disorder. Alcohol was long thought to be the primary causative agent, but genetic contributions have been of interest since the discovery that rare PRSS1, CFTR and SPINK1 variants were associated with pancreatitis risk. We now report two associations at genome-wide significance identified and replicated at PRSS1-PRSS2 and X-linked CLDN2 through a two-stage genome-wide study. The PRSS1 variant likely affects disease susceptibility by altering expression of the primary trypsinogen gene. The CLDN2 risk allele is (...) associated with atypical localization of claudin-2 in pancreatic acinar cells. The homozygous CLDN2 genotype confers the greatest risk, and its alleles interact with alcohol consumption to amplify risk. These results could partially explain the high frequency of alcohol-related pancreatitis in men. © 2012 Nature America, Inc. All rights reserved. (shrink)

This, the 21st volume in the Library of Living Philosophers, is more than Sir Alfred Ayer's final word on the philosophical issues that preoccupied him for more than sixty years; the list of contributors is a roll-call of some of the greatest living figures in philosophy, each expertly addressing a key problem arising in Ayer's work. Most of the critical papers are answered directly and in detail by Sir Alfred-he completed his replies to 21 of the 24 papers before his (...) death. Contributors include: A. J. Ayer, Evandro Agazzi, James Campbell, David S. Clarke, Michael Dummett, Elizabeth Eames, John Foster, Dimitri Ginev, Paul Gochet, Martin Hollis, Ted Honderich, Tscha Hung, Peter Kivy, Arne Naess, D. J. O'Connor, Desiree Park, David Pears, Azarya Polikarov, Hilary Putnam, Francisco Miró, Quesada C., A. Anthony Quinton, Emanuele Riverso, Ernest Sosa, T. L. S. Sprigge, Barry Stroud, and David Wiggins. (shrink)

This work should be quite useful as a problem guide to phenomenalist and dualist metaphysics. Professor Yolton is concerned that any system be read both from an internal and an external perspective keeping them as separate and distinct as possible. He also cautions that the external perspective should not presuppose another metaphysic for that has often resulted in gross misreadings of earlier authors. In the first section of the book, phenomenalism, he shows how, for example, D. M. Armstrong and G. (...) Warnock have misread Berkeley and attacks G. Warnock and J. Austin's principle which rules out use of a technical irreducible language by philosophers. Solipsism and idealism as well as Berkeley's sensory phenomenalism are treated. In the second section of the book, dualism, Professor Yolton argues that some "transcendent Meaning Principle" is necessary to make the non-sensual side of dualism intelligible, outlines Plato's dualism as against Protagorian monism, indicates what he considers B. Russell's dualism and tries to show that Russell's treatment of one side is partially completed by C. I. Lewis' treatment of what Professor Yolton considers the other side. In the third section on meaning and truth he tries to establish 1) that there is a large measure of intranslatability between philosophical systems; 2) that meaning involves referrent necessarily; 3) that truth is defined by ontological rules; and 4) that correspondence is the basic truth-relation. Brief discussion is given of certain aspects of the works of P. Strawson, B. Russell, J. S. Mill, G. Ryle, W. V. O. Quine, Meinong, and Eric Tom. Slightly over half of this book is comprised of papers, some slightly modified, published from 1949 to 1961.--J. B. L. (shrink)

Lewis has missed an excellent opportunity to concisely demonstrate that a dynamical system can provide a bridge between emotion theory and neurobiology.

La préface des Principes oppose les quatre premiers degrés d'une sagesse empirique, fondée sur les notions communes, l'expérience sensible et la fréquentation d'autrui dans la conversation ou la lecture (IX, B, 5), à la morale la plus achevée qu'il situe ainsi au sommet du système : " Toute la philosophie est comme un arbre, dont les racines sont la métaphysique, le tronc est la physique et les branches qui sortent de ce tronc sont toutes les autres sciences, qui se réduisent (...) à trois principales, à savoir la médecine, la mécanique et la morale ; j'entends la plus haute et la plus parfaite morale, qui présupposant une entière connaissance des autres sciences, est le dernier degré de la sagesse. ". (shrink)