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)

The strong weak truth table (sw) reducibility was suggested by Downey, Hirschfeldt, and LaForte as a measure of relative randomness, alternative to the Solovay reducibility. It also occurs naturally in proofs in classical computability theory as well as in the recent work of Soare, Nabutovsky, and Weinberger on applications of computability to differential geometry. We study the sw-degrees of c.e. reals and construct a c.e. real which has no random c.e. real (i.e., Ω number) sw-above it.

We show that in the c.e. weak truth table degrees if b < c then there is an a which contains no hypersimple set and b < a < c. We also show that for every w < c in the c.e. wtt degrees such that w is hypersimple, there is a hypersimple a such that w < a < c. On the other hand, we know that there are intervals which contain no hypersimple set.

ABSTRACT:A wide range of research uses patterns of genetic variation to infer genetic similarity between individuals, typically referred to as genetic ancestry. This research includes inference of human demographic history, understanding the genetic architecture of traits, and predicting disease risk. Researchers are not just structuring an intellectual inquiry when using genetic ancestry, they are also creating analytical frameworks with broader societal ramifications. This essay presents an ethics framework in the spirit of virtue ethics for these researchers: rather than focus on (...) rule following, the framework is designed to build researchers’ capacities to react to the ethical dimensions of their work. The authors identify one overarching principle of intellectual freedom and responsibility, noting that freedom in all its guises comes with responsibility, and they identify and define four principles that collectively uphold researchers’ intellectual responsibility: truthfulness, justice and fairness, anti-racism, and public beneficence. Researchers should bring their practices into alignment with these principles, and to aid this, the authors name three common ways research practices infringe these principles, suggest a step-by-step process for aligning research choices with the principles, provide rules of thumb for achieving alignment, and give a worked case. The essay concludes by identifying support needed by researchers to act in accord with the proposed framework. (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)

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)

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.

Dayton's account of lewis' pragmatic contradiction seriously misconstrues this key concept by analyzing it in terms of logical contradiction. this order of analysis is explicitly rejected by lewis as the reverse of the proper order in which the pragmatic concept is foundational to logic and epistemology. i outline a correct account of pragmatic contradiction. then lewis' application of the idea to moral skepticism and the liar paradox is reconsidered, and is seen to vindicate his claim that both (...) skeptic and liar are defeated by a non-fallacious "ad hominem" consisting of a demonstration that each is in pragmatic contradiction. (shrink)

We say that A ≤LR B if every B-random number is A-random. Intuitively this means that if oracle A can identify some patterns on some real γ. In other words. B is at least as good as A for this purpose. We study the structure of the LR degrees globally and locally (i.e., restricted to the computably enumberable degrees) and their relationship with the Turing degrees. Among other results we show that whenever α in not GL₂ the LR degree of (...) α bounds $2^{\aleph _{0}}$ degrees (so that, in particular, there exist LR degrees with uncountably many predecessors) and we give sample results which demonstrate how various techniques from the theory of the c.e. degrees can be used to prove results about the c.e. LR degrees. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:Remembering Lewis E. HahnGeorge C. H. Sun, President, John Howie, Professor Emeritus, Thomas Alexander, Professor and Director of Graduate Studies, Kenneth W. Stikkers, Professor and Chair, Randall Auxier, Professor, Robert Hahn, Professor, Joseph Wu, Professor Emeritus, Elizabeth R. Eames, Professor Emeritus, Martin Lu, Professor of Philosophy, George Kimball Plochmann, Professor Emeritus, Matt Sronkoski, Philosophy Graduate and Academic Adviser, Dave Clarke, Professor Emeritus, Eugenie Gatens-Robinson, Professor Emerita, Hans H. (...) Rudnick, Professor Emeritus, Stephen Bickham, Professor EmeritusPresident, and Don Mikula (bio)The following testimonials were offered on the occasion of a memorial gathering for Dr. Lewis E. Hahn held on February 19, 2005, and were compiled for presentation here by Sharon (Hahn) Crowell.A Tribute to Dr. Lewis E. Hahn (1908-2004) from a Global PerspectiveGeorge C. H. Sun President, Thomé H. Fang Institute, Inc., Mobile, AlabamaAmong the philosophical community in both the East and the West, no word of introduction is needed for our beloved Master, who was the recipient of numerous distinctions and honors, with titles that included "Man of the Year in Philosophy" and "Award of Lifetime Achievement." The very name "Lewis E. Hahn" itself already stands now for genuineness, dedication, and fulfillment.A great work is a dialogue with eternity; a great person is such a work. In less than thirty years he succeeded in developing Carbondale from what had been a small college town in the Midwest into the Mecca of American philosophy. His most important achievements were the Dewey Center and the Pepper Archives that he helped install at SIUC These, among other such institutions, will remain a unique contribution, a glory of American philosophy, and a monument in the history of human thought.For posterity Lewis E. Hahn will remain an object of wonder and amazement. How is it possible for one human being to have accomplished so much, so well, and in so short a span of time—less than one century—in breadth, depth, and diversity? Some one hundred years ago, by bridging the gap between the New World and the Old, William James was hailed as the great genius of international friendship among philosophical thinkers, but we now find a greater genius in Lewis E. Hahn, who succeeded in bringing together the peoples of East and West from at least four continents: Europe, Australia, America (both North and Latin America), and Asia. To my knowledge, few of his predecessors and contemporaries have been half so widely read and liberal-minded as he was, in view of the range and scope of the Library of Living Philosophers that he helped continue after the passing of its founder, Dr. Paul A. Schilpp.What type of man was Hahn, our younger generation will wonder? Only a pluralist approach can help us understand the true character of such a legendary pluralist-contextualist. In short, he was "a full personality." As I recall, while working on my dissertation with him in the 1970s, we had a brief discussion on Confucius, the sage of ancient China. "A full personality!" was his laconic assessment. Suddenly I realized, to quote the Analects: "The Master is talking about himself!" For, as the Buddhists put it, only a Buddha can understand a Buddha. Or, as William James put it, only one who has philosophy can appreciate philosophy. Many friends [End Page 1] of my generation admire him so much; Te Chen of Hong Kong calls him "a great Confucian in America." Those who regret the loss of many precious Confucian virtues in China today have now rediscovered them in the person of Lewis E. Hahn! If Nietzsche called Kant "a great Chinese in Königsberg," it is simply because he had not encountered our own Master.A paradigm of academic leadership, Dr. Hahn is simply irreplaceable—this is a tribute I personally heard in Carbondale in the late 1960s. It is not an exaggeration to say that he was a superb administrator, and he could have been the best Secretary of the State we ever had, for he possessed more in the way of philosophical wisdom than all his predecessors put together! As a great teacher, he was no less "serene, good, learned, wise, and ardent" than... (shrink)

In this paper we examine C. I. Lewis's view on the roleof coherence – what he calls ''congruence'' – in thejustification of beliefs based on memory ortestimony. Lewis has two main theses on the subject. His negativethesis states that coherence of independent items ofevidence has no impact on the probability of a conclusionunless each item has some credibility of its own. Thepositive thesis says, roughly speaking, that coherenceof independently obtained items of evidence – such asconverging memories or testimonies (...) – raises the probabilityof a conclusion to the extent sufficient for epistemicjustification, or, to use Lewis's expression, ''rationaland practical reliance''.It turns out that, while thenegative thesis is essentially correct, astrong positive connection between congruence andprobability – a connection of the kind Lewis ultimatelyneeds in his validation of memory – is contingent on thePrinciple of Indifference. In the final section we assess therepercussions of the latter fact for Lewis's theory in particularand for coherence justification in general. (shrink)

This article aimed to highlight the reasons for a criticism by the Irish writer Clive Staples Lewis towards the direction of youth education in Europe, notably in the United Kingdom, in the 20th century. His criticism gained as his main thesis what the writer called “the abolition of man”, resulting from an educational system that promotes an alleged rationality that prevented the development of an intermediate element in the human being between the cerebral and the visceral. For Lewis, (...) that intermediate element is the emotions that, well trained, endow the intellect with capacities to deal with the mere animal organism. For this purpose, our starting point in this work was outlined by the cut of a broader work, which consists of an exhibition that, in general, highlights some guidelines that point to the composition of a Philosophy of Education in C. S. Lewis. We seek to collect, initially, the elements of a philosophical anthropology, collected directly, by an interpretative procedure, from the vast work of the author in question, particularly The Abolition of Man, Pure and Simple Christianity, The Weight of Glory, Christian Reflections, The Four Loves, Letters from a Devil to His Apprentice, God in the Dock, Ethics to Live Better, Christian Reflections, among others. In addition to these texts used as a direct source, we also take the work of Gabrielle Greggersen, entitled The Philosophical Anthropology of C. S. Lewis, where the author makes an interpretive incursion into the author’s fictional literature texts, as well as the works biographies of Alister MacGrath, Conversing with Lewis and The Life of C. S. Lewis, in which the Irish philosopher’s life and work are richly detailed. Keywords: C. S. Lewis. Philosophy. Education. Philosophy of education. Philosophical anthropology. (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)

This selection of articles by Lewis E. Hahn addresses the philosophical school of contextualism and four contemporary American philosophers: John Dewey, Henry Nelson Wieman, Stephen C. Pepper, and Brand Blanshard. Stressing the relatively recent contextualistic worldview, which he considers one of the best world hypotheses, Hahn seeks to achieve a broad perspective within which all things may be given their due place. After providing a brief outline, Hahn explains contextualism in relation to other philosophies. In his opening chapter, as (...) in later chapters, he expresses contextualism as a form of pragmatic naturalism. In spite of Hahn’s high regard for contextualism, however, he does not think it would be good if we were limited to a single worldview. “The more different views we have and the more different sources of possible light we have, the better our chances that some of these cosmic maps will shed light on our world and our place in it.”. (shrink)

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)

Formulated by Aquinas, commented on by post-Copernican philosophers and theologians, analysed in depth by C.S. Lewis, and deliberated by some contemporary writers, the question of multiple incarnations either within humanity or amongst extra-terrestrial sentient species is all too intermittently examined: ‘Can the Christ be incarnated more than once in our reality, or somewhere else in the universe, or another reality?’ In this paper, we examine the debate and the conclusions: that is, Lewis’s position within his philosophical theology and (...) his analogical narratives; also, some contemporary philosophers of religion and theologians (Karl Rahner, with Christopher L. Fisher and David Fergusson; Sjoerd L. Bonting and William B. Drees; E.L. Mascall and Brian Hebblethwaite; Oliver Crisp and Keith Ward). How do they relate to Aquinas’s handling of the question and how do they compare with Lewis’s approach based on a theology of the imagination (grounded in Augustine and Alice Meynell)? Can Lewis resolve the argument? Could alien species have witnessed wholly different acts, equally unique, costly to God, and necessary to the process of salvation? Any answer or explanation relates to the function and purpose of the incarnation: the Fall, original sin—therefore, how we define the boundaries, limits, of atonement. (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.

This article opposes a view widely accepted in studies concerning the history of modal logic, according to which (i) the approach of C. I. Lewis towards constructing modern modal logic was purely syntactical (i.e. limited to the construction of axiomatic systems S1-S5 of propositional modal logic), and (ii) the notion of a possible world was incorporated into modern logic and philosophy mainly by authors such as Rudolf Carnap and Saul Kripke. The article presents Lewis' definition of a possible (...) world, and his formulation of the truth-conditions of statements containing strict implication as their main connective in terms of possible worlds. The main question of the article is whether it is possible to consider Lewis' work in this area as an early stage of the development of possible world semantics, and if so, in what sense? The article concludes by answering affirmatively, due to soundness and completeness proofs with respect to S5 using Lewis' semantics. (shrink)

Immediate experiences may be found good or bad at the time of occurrence, and this value contributes to the goodness or badness of life in general. In addition, they may continue to affect later experiences to the very end of a lifetime. The final assessment of an experience, therefore, cannot be made until a lifetime has come to an end, at which point one would no longer be in a position to assess. It remains instructive, nevertheless, to apply the standard (...) of an entire lifetime in qualifying the value assessed to any part of that lifetime. Presumably, then, the phrase “a life found good in the living of it,” refers not to a life as it is found in the moments of living it, but to a life as it appears from the vantage point of any moment while looking back over the whole. The finding seems more like finding through reflection or in imagination, than finding yellowness; and the word “living”, therefore, must be used in an unusual and uncommon sense. A life found good in the living of it, is a life which may later have value-qualities attached to it which are different from those which it was originally found to have. A life is lived and re-lived. (shrink)

Arthur Danto is the Johnsonian Professor Emeritus of Philosophy at Columbia University and the most influential philosopher of art in the last half century. As an art critic for The Nation for 25 years and frequent contributor to other widely read outlets such as the New York Review of Books, Danto also has become one of the most respected public intellectuals of his generation. He is the author of some two dozen important books, along with hundreds of articles and reviews (...) which have been the center of both controversy and discussion. In this volume Danto offers his intellectual autobiography and responds to essays by 27 of the keenest critics of his thought from the worlds of philosophy and the arts. The book includes 16 pages of color art reproductions. Danto is the author dozens of books on art, philosophy, the philosophy of art, and art criticism. He is a rare philosopher who is also a public intellectual. (shrink)

The following statement is a report of the Committee on Philosophy in Education of the American Philosophical Association and was approved by the Association's Board of Officers in September, 1959. The Committee was composed of the following: C. W. Hendel, Chairman, H. G. Alexander, R. M. Chisholm, Max Fisch, Lucius Garvin, Douglas Morgan, A. E. Murphy, Charner Perry, and R. G. Turnbull. Primary responsibility for the preparation of this report belonged to a subcommittee composed of Roderick M. Chisholm, Chairman, H. (...) G. Alexander, Lewis Hahn, Paul C. Hayner, and Charles W. Hendel. (shrink)

An inductive method Cλ in the λ-system of Carnap [1] is immodest, on evidence e, iff its estimate, on e, of its own accuracy is higher than its estimate, on e, of the accuracy of any rival method Cλ′. Immodesty seems to be a condition of stable trust: if you trusted a modest Cλ, you should start by trusting its advice to replace it by a rival that it estimates to be more accurate. One might guess that any Cλ would (...) be immodest on any evidence. But in [2] I proved that, under a certain accuracy measure taken from Carnap [1], §§ 20–21, there would be exactly one immodest Cλ. Unfortunately, that one sometimes turns out to be C0 ; and since nobody in his right mind would trust C0 we are then left with no acceptable Cλ. Stephen Spielman [3] has proposed a remedy: an estimate of accuracy, on evidence e, should disregard accuracy under circumstances that are ruled out by e. Spielman proves that if this change is made, any Cλ is immodest on any evidence. (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.

C. S. Lewis reflexionó sobre la filosofía del color de manera accesoria en algunas de sus obras teóricas y les dio cauce narrativo en la Trilogía cósmica. A pesar de ser una cuestión escasamente explorada en la academia, resulta pertinente investigar el valor filosófico y especulativo que concede al color en el ámbito de su teoría de lo real, de inspiración platónica. Esta investigación aspira a analizar e interpretar, desde la cosmología precopernicana, la relevancia ontológica, epistemológica y metafísica del (...) color de las que se hacen eco los tres libros que componen la saga de Ransom a través de una serie de temas recurrentes. El profesor Lewis, además, acompañó estas reflexiones de una interdisciplinariedad que se sustentaba sobre el simbolismo medieval. En la trilogía, los colores de los mundos del espacio profundo revelan la verdadera realidad inteligible y anticipan el fundamento metafísico del cosmos en el marco de una metanarrativa teísta y trascendente. (shrink)

Recent work in the history of philosophy of science details the Kantianism of philosophers often thought opposed to one another, e.g., Hans Reichenbach, C.I. Lewis, Rudolf Carnap, and Thomas Kuhn. Historians of philosophy of science in the last two decades have been particularly interested in the Kantianism of Reichenbach, Carnap, and Kuhn, and more recently, of Lewis. While recent historical work focuses on recovering the threatened-to-be-forgotten Kantian themes of early twentieth-century philosophy of science, we should not elide the (...) differences between the Kantian strands running throughout this work. In this paper, I disentangle a few of these strands in the work of Reichenbach and Lewis focusing especially on their theories of relativized, constitutive a priori principles in empirical knowledge. In particular, I highlight three related differences between Reichenbach and Lewis concerning their motivations in analyzing scientific knowledge and scientific practice, their differing conceptions of constitutivity, and their relativization of constitutive a priori principles. In light of these differences, I argue Lewis’s Kantianism is more similar to Kuhn’s Kantianism than Reichenbach’s, and so might be of more contemporary relevance to social and practice-based approaches to the philosophy of science. (shrink)