Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Library of Living Philosophers volume on Hilary Putnam with critical essays, Putnam's autobiography and his replies.

The Oxford Handbook of Religious Conversion offers a comprehensive exploration of the dynamics of religious conversion, which for centuries has profoundly shaped societies, cultures, and individuals throughout the world. Scholars from a wide array of religions and disciplines interpret both the varieties of conversion experiences and the processes that inform this personal and communal phenomenon.This volume examines the experiences of individuals and communities who change religions, those who experience an intensification of their religion of origin, and those who encounter new (...) religions through colonial intrusion, missionary work, and charismatic and revitalization movements. The thirty-two innovative essays provide overviews of the history of particular religions, including Hinduism, Buddhism, Confucianism, Taoism, Sikhism, Islam, Christianity, Judaism, indigenous religions, and new religious movements. The essays also offer a wide range of disciplinary perspectives-psychological, sociological, anthropological, legal, political, feminist, and geographical-on methods and theories deployed in understanding conversion, and insight into various forms of deconversion. (shrink)

The scope of Philosophy in Multiple Voices provides the reader with eight philosophical streams of thought-African-American, Afro-Caribbean, Asian-American, Feminist, Latin-American, Lesbian, Native-American and Queer-that introduce readers to alternative, complex philosophical questions concerning gendered, sexed, racial and ethnic identities, canon formation, and meta-philosophy. The overriding theme of the text is that philosophy is pluralistic in voice, rich in diversity, and ought to valorize democratic intellectual spaces of philosophical engagement.

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.

Plagiarism strikes at the heart of academe, eroding the fundamental value of academic research. Recent evidence suggests that acts of plagiarism and awareness of these acts are on the rise in academia. To address this issue, a vein of research has emerged in recent years exploring plagiarism as an area of academic inquiry. In this new academic subject, case studies and analysis have been one of the most influential methodologies employed. Case studies provide a venue where acts of plagiarism can (...) be discussed and analyzed in a constructive manner, and that is the primary purpose of this article. Unlike previous studies, however, we focus on the role of the publisher, a key player in dealing with acts of plagiarism, but one who has received little attention in the academic literature. Specifically, we examine how an academic publisher addressed allegations of plagiarism and how the publisher’s decision-making affected the outcome. We analyze the case by applying the guidelines from different frameworks and ethical theory and develop recommendations from the lessons evidenced, the second main objective of our article. This analysis advances the dialog on academic plagiarism by exploring the role of the publisher from a deontological perspective of ethical absolutism. (shrink)

This volume consists of an intellectual autobiography by world-renowned philosopher Hilary Putnam, 26 critical or descriptive essays, 26 replies by Arthur C. Danto, and a bibliography listing all of Putnam's published writings.

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)

The Search for the Legacy of the USPHS Syphilis Study at Tuskegee is a collection of essays from experts in a variety of fields seeking to redefine the legacy of the infamous Tuskegee Syphilis Study. The essayists place the legacy of the study within the evolution of racial and ethnic relations in the United States. Contributors include two leading historians on the study, two former United States Surgeons General, and other prominent scholars from a wide range of fields.

Until recently, psychologists have conceptualised and studied trust in God (TIG) largely in isolation from contemporary work in theology, philosophy, history, and biblical studies that has examined the topic with increasing clarity. In this article, we first review the primary ways that psychologists have conceptualised and measured TIG. Then, we draw on conceptualizations of TIG outside the psychology of religion to provide a conceptual map for how TIG might be related to theorised predictors and outcomes. Finally, we provide a research (...) agenda for future empirical work in this area, as well as practical applications for counsellors and religious leaders. (shrink)

This article develops a multidimensional approach for the investigation of the ethical codes of professional associations. The authors: (a) examine various ethical frameworks to identify ethical constructs, (b) select ethical constructs to apply to the assessment of professional codes of ethics, (c) content analyze conceptual and descriptive similarities and differences across a large sample of professional codes of ethics, (d) address organizational variables that affect the development of ethical codes, and (e) investigate through survey research the beliefs and attitudes of (...) association leadership toward ethical code issues. The content analysis and survey research results have implications for association leadership, its membership, public policy makers, the general public and for future research. (shrink)

Few figures of the Middle Ages command the attention of so many modern disciplines as Robert Grosseteste (c. 1170-1253). Theology, Philosophy, History, and Science are all areas which his life and thought continue to have significance and to inspire re-interpretation. Accompanied by a series of original commentaries, this new edition of Grosseteste's work, with English translation, draws together the perspectives of modern scientists and medieval specialists. Volume I of a six volume series, Knowing and Speaking presents two of the earliest (...) of Grosseteste's works, the treatises On the Liberal Arts and On the Generation of Sounds. These are accompanied by a significant Middle English treatise on the Seven Liberal Arts whose anonymous fifteenth-century author translated and excerpted passages from Grosseteste's treatises in a re-imagining of their structure and function.0Each work is treated separately within the volume, which is constructed in three parts. On the Liberal Arts sets Grosseteste's thoughts on the arts subjects and emphasises moral concerns about the purpose of learning. On the Generation of Sounds builds on the theories and statements of On the Liberal Arts in connection to the production of sound, elaborating the earlier position, relating the generation of sounds to human vocal and speech production. (shrink)

Researchers from diverse disciplines, including organismal and cellular physiology, sports science, human nutrition, evolution and ecology, have sought to understand the causes and consequences of the surprising variation in metabolic rate found among and within individual animals of the same species. Research in this area has been hampered by differences in approach, terminology and methodology, and the context in which measurements are made. Recent advances provide important opportunities to identify and address the key questions in the field. By bringing together (...) researchers from different areas of biology and biomedicine, we describe and evaluate these developments and the insights they could yield, highlighting the need for more standardisation across disciplines. We conclude with a list of important questions that can now be addressed by developing a common conceptual and methodological toolkit for studies on metabolic variation in animals. (shrink)

We say that A≤LRB if every B-random set is A-random with respect to Martin–Löf randomness. We study this relation and its interactions with Turing reducibility, classes, hyperimmunity and other recursion theoretic notions.

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)

In this paper we investigate nonnormal modal systems in the vicinity of the Lewis system S1. It might be claimed that Lewis's modal systems are the starting point of modern modal logics. However, our interests in the Lewis systems and their relatives are not historical. They possess certain syntactical features and their frames certain structural properties that are of interest to us. Our starting point is not S1, but a weaker logic S1$^0$. We extend it to S1$^0$D, (...) which can be considered as a deontic counterpart of the alethic S1. Soundness and completeness of these systems are then demonstrated within a prenormal idiom. We conclude with some philosophical remarks on the interpretation of our deontic logic. (shrink)

In this paper we investigate nonnormal modal systems in the vicinity of the Lewis system S1. It might be claimed that Lewis's modal systems (S1, S2, S3, S4, and S5) are the starting point of modern modal logics. However, our interests in the Lewis systems and their relatives are not (merely) historical. They possess certain syntactical features and their frames certain structural properties that are of interest to us. Our starting point is not S1, but a weaker (...) logic S1 (S1 without the schema [T]). We extend it to S1D, which can be considered as a deontic counterpart of the alethic S1. Soundness and completeness of these systems are then demonstrated within a prenormal idiom. We conclude with some philosophical remarks on the interpretation of our deontic logic. (shrink)

The effectiveness of information retrieval technology in electronic discovery (E-discovery) has become the subject of judicial rulings and practitioner controversy. The scale and nature of E-discovery tasks, however, has pushed traditional information retrieval evaluation approaches to their limits. This paper reviews the legal and operational context of E-discovery and the approaches to evaluating search technology that have evolved in the research community. It then describes a multi-year effort carried out as part of the Text Retrieval Conference to develop evaluation methods (...) for responsive review tasks in E-discovery. This work has led to new approaches to measuring effectiveness in both batch and interactive frameworks, large data sets, and some surprising results for the recall and precision of Boolean and statistical information retrieval methods. The paper concludes by offering some thoughts about future research in both the legal and technical communities toward the goal of reliable, effective use of information retrieval in E-discovery. (shrink)

By theword problemfor some class of algebraic structures we mean the problem of determining, given a finite setEof equations between words and an additional equationx=y, whetherx=ymust hold in all structures satisfying each member ofE. In 1947 Post [P] showed the word problem for semigroups to be undecidable. This result was strengthened in 1950 by Turing, who showed the word problem to be undecidable forcancellation semigroups,i.e. semigroups satisfying thecancellation propertyNovikov [N] eventually showed the word problem for groups to be undecidable.In 1966 (...) Gurevich [G] showed the word problem to be undecidable forfinitesemigroups. However, this result on finite structures has not been extended to cancellation semigroups or groups; indeed it is easy to see that a finite cancellation semigroup is a group, so both questions are the same. We do not here settle the word problem for finite groups, but we do show that the word problem is undecidable for finite semigroups with zero satisfying an approximation to the cancellation property. (shrink)

The general tenor of this introductory text is metaphilosophical, perhaps too much so for an introduction to twentieth century philosophy. The book is divided into sections on Realism, Idealism, Pragmatism, Existentialism, and Analysis. Each of these sections has an introduction of twenty or so pages which traces the currents in the history of philosophy which gave rise to Realism, Idealism, etc. in the twentieth century. Two spokesmen or "voices" for the general position or for some methodological consequences of the position (...) are then presented by means of reasonably lengthy and self-contained selections from their writings: Lovejoy and Montague on Realism, Blanshard and Joachim on Idealism, Dewey and Lewis on Pragmatism, Sartre and Tillich on Existentialism, and Schlick and Austin on Analysis. Each section concludes with a good annotated guide for further reading. There are dangers in the "isms" approach to philosophy on any, let alone an introductory, level. The editors seem aware of these dangers in their general introduction, but the format of their book works against their own admonitions, and the instructor who adopts this text will have to provide considerable supplementation.—E. A. R. (shrink)

Addis contributes the slightly longer essay, "Ryle's Ontology of Mind," while Lewis's contribution is titled "Moore's Realism," in this, the second volume of the Iowa Publications in Philosophy. After overcoming an initial wave of incredulity that it would ever occur to anyone to include mention of Ryle, Moore, and ontology in the same breath, the reader—with an apprehensive eye on the place of publication—might resign himself to wading through the carnage created by the wild wielding of a metaphysical ax (...) whetted on a Bergmannian stone. Happily, this is not the case. Both authors are convinced that Moore and Ryle need an ontology to solve the problems they have set their analyses to work upon ; and neither author has any compunction about attributing an implicit substance ontology to both Moore and Ryle. It need hardly be added that Lewis and Addis do Moore and Ryle the courtesy of explicitating this ontology and subsequently showing its inadequacies from a basically Bergmannian point of view. But all of this is carried out in a deft and scholarly fashion, as with a scalpel and not an ax. The net results are a penetrating critique of two important philosophers and a challenging display of the virtues of a method of analysis that does not stop at a linguistic or phenomenological level.—E. A. R. (shrink)

The editors of this book of readings have packed in a wealth of material in a way which evinces an imaginative conception of, as well as an ambitious program for a course in the philosophy of education. There are forty-three selections of varying completeness from thirty-six different authors; among the philosophers included are Kierkegaard, Schlick, Kant, Ayer, Blanshard, Scheffler, Stace, Moore, Feigl, Russell, Lewis, Dewey, James, Royce, and Peirce. Plato is the only pre-Kantian philosopher to make an appearance. Half (...) of the selections do not concern education or the philosophy of education directly. Rather, they consider one or more of the four main problem areas of philosophy which the editors have decided gear into problems in the philosophy of education most directly. These areas are the nature of philosophy, metaphysics or the nature of reality, the nature of knowledge, and the nature of value. The section on metaphysics is epistemologically slanted, as might be expected where the concern is for the relation of teaching and learning to the nature of reality. The statements of the philosophers on the general philosophical problems are given at the beginning of each of the sections and then followed by applications of the philosophical position by philosophers, once again, and educational theorists to the field of education. Since too often the philosophy of education is taught in the education rather than the philosophy department, the liberal dose of straight philosophy should prove extremely helpful to the student of education who is accustomed to receiving the philosophy appropriate to the philosophy of education in a highly diluted form.—E. A. R. (shrink)

Selections from "twentieth century sources" which include Moore, Broad, Price, Paul, Lewis, Chisholm, and Warnock. Sense data and phenomenalism are the most heavily represented topics. The choice is substantial, and the editor has skillfully arranged selections in pairs which take up opposite sides of the same problem. This appears to be the best buy in paper on this subject.—E. A. R.

Addis contributes the slightly longer essay, "Ryle's Ontology of Mind," while Lewis's contribution is titled "Moore's Realism," in this, the second volume of the Iowa Publications in Philosophy. After overcoming an initial wave of incredulity that it would ever occur to anyone to include mention of Ryle, Moore, and ontology in the same breath, the reader—with an apprehensive eye on the place of publication—might resign himself to wading through the carnage created by the wild wielding of a metaphysical ax (...) whetted on a Bergmannian stone. Happily, this is not the case. Both authors are convinced that Moore and Ryle need an ontology to solve the problems they have set their analyses to work upon ; and neither author has any compunction about attributing an implicit substance ontology to both Moore and Ryle. It need hardly be added that Lewis and Addis do Moore and Ryle the courtesy of explicitating this ontology and subsequently showing its inadequacies from a basically Bergmannian point of view. But all of this is carried out in a deft and scholarly fashion, as with a scalpel and not an ax. The net results are a penetrating critique of two important philosophers and a challenging display of the virtues of a method of analysis that does not stop at a linguistic or phenomenological level.—E. A. R. (shrink)

This chapter outlines David Lewis's favored foundational account of linguistic representation, and outlines and briefly evaluates variations and modifications. It gives an opinionated exegesis of Lewis's work on the foundations of reference: his interpretationism. The author looks at the way that the metaphysical distinction between natural and non‐natural properties came to play a central role in his thinking about language. Lewis's own deployment of this notion has implausible commitments. The chapter briefly considers a buck‐passing strategy involving fine‐grained (...) linguistic conventions. Lewis was no fan of primitive intentionality. Much of the Lewisian framework remains attractive. The overall select‐and‐project method, with its promise to deal even‐handedly with all linguistic intentionality, and its epistemic tractability, should be retained. Post‐Lewisian interpretationism results from emphasizing and retaining some of the virtues of Lewis's original proposal promises (e.g. universality and epistemic tractability), while compromising on others (e.g. metaphysical principle). (shrink)

The twenty-sixth volume in the highly acclaimed Library of Living Philosophers series is devoted to the work of British philosopher of logic and metaphysician, P. F. Strawson. Following the Library of Living Philosophers series format, the volume contains an intellectual autobiography, twenty critical and descriptive essays by leading philosophers from around the world, Strawson's replies to the essays, and a bibliography of Strawson's works. Born in 1919, Strawson was a leading proponent of ordinary language philosophy. He is the author of (...) the early and extremely influential paper "On Referring" in which he criticized Russell's theory of definite descriptions. His most influential book, Individuals, helped to raise the status of metaphysics as a philosophical enterprise. Themes first addressed in this book continued to be of concern to him in his later work, including the possibility of objective knowledge, the subject-predicate distinction, the ontological status of persons, and the problem of individuation. Contributors to the book include: Ruth Garrett Millikan, Susan Haack, E. M. Adams, Panayot Butchvarov, Richard Behling, John McDowell, Simon Blackburn, Tadeusz Szubka, David Frederick Haight, Joseph S. Wu, Andrew G. Black, David Pears, Robert Boyd, Hilary Putnam, Paul F. Snowdon, Arindam Chakrabarti, Wenceslao J. Gonzalez, Ernest Sosa, Chung-M. Tse, John R. Searle, P. F. Strawson. (shrink)