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)

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.

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)

This handbook presents a comprehensive introduction to the core areas of philosophy of education combined with an up-to-date selection of the central themes. It includes 95 newly commissioned articles that focus on and advance key arguments; each essay incorporates essential background material serving to clarify the history and logic of the relevant topic, examining the status quo of the discipline with respect to the topic, and discussing the possible futures of the field. The book provides a state-of-the-art overview of philosophy (...) of education, covering a range of topics: Voices from the present and the past deals with 36 major figures that philosophers of education rely on; Schools of thought addresses 14 stances including Eastern, Indigenous, and African philosophies of education as well as religiously inspired philosophies of education such as Jewish and Islamic; Revisiting enduring educational debates scrutinizes 25 issues heavily debated in the past and the present, for example care and justice, democracy, and the curriculum; New areas and developments addresses 17 emerging issues that have garnered considerable attention like neuroscience, videogames, and radicalization. The collection is relevant for lecturers teaching undergraduate and graduate courses in philosophy of education as well as for colleagues in teacher training. Moreover, it helps junior researchers in philosophy of education to situate the problems they are addressing within the wider field of philosophy of education and offers a valuable update for experienced scholars dealing with issues in the sub-discipline. Combined with different conceptions of the purpose of philosophy, it discusses various aspects, using diverse perspectives to do so. Contributing Editors: Section 1: Voices from the Present and the Past: Nuraan Davids Section 2: Schools of Thought: Christiane Thompson and Joris Vlieghe Section 3: Revisiting Enduring Debates: Ann Chinnery, Naomi Hodgson, and Viktor Johansson Section 4: New Areas and Developments: Kai Horsthemke, Dirk Willem Postma, and Claudia Ruitenberg. (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.

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)

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)

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.

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.

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)

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.

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)

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)

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)

An adequate theory of rights ought to forbid the harming of animals to promote trivial interests of humans, as is often done in the animal-user industries. But what should the rights view say about situations in which harming some animals is necessary to prevent intolerable injustices to other animals? I develop an account of respectful treatment on which, under certain conditions, it’s justified to intentionally harm some individuals to prevent serious harm to others. This can be compatible with recognizing the (...) inherent value of the ones who are harmed. My theory has important implications for contemporary moral issues in nonhuman animal ethics, such as the development of cultured meat and animal research. (shrink)

In lieu of an abstract, here is a brief excerpt of the content:The Controversy Between Schelling and Jacobi LEWIS S. FORD SCHELLING, ALONGWITH FICHTE, has suffered the fate of being labelled one of tIegel's predecessors. Richard Kroner provides the classic expression of this viewpoint in his monumental study, Von Kant bis Hegel, which examines Schelling's thought primarily for its contribution to Hegel's final synthesis.I In English we have Josiah Royce's sympathetic and lively account of Schelling's early romantic exuberance, regarded (...) as a transitional stage in the development of German idealism. 2 But this emphasis on the early ScheUing has led to an unfortunate neglect of his work subsequent to the break with Hegel in 1807. Schelling's romanticism, so ably documented by E. D. Hirsch, Jr., 3 can only be regarded as one phase in the total sweep of his thought, for, after the break with Hegel, Schelling produced at least three major works: the essay •ber das Wesen der menschlichen Freiheit,4 wrestling with the problem of evil and human freedom, the fragmentary Weltalter, 5 which in scope and dialectical intricacy should be compared with Hegel's Logic, and the Philosophie der Mythologie und Offenbarung, 6 furnishing a fundamental critique of the whole dialectical enterprise. Save for the essay on human freedom, however, none of these works were published during his lifetinm, as Schelling withdrew from the public eye after his controversies with Hegel and Jacobi. Thus the publishing histories of Schelling and Hegel are exactly reverse. Schelling rushed into print his early speculative gropings, while Hegel suppressed his/making the Ph~nomenologic des Geistes his first major publication. Then while Hegel's Logic and Encyclopedia were being publicly acclaimed, Schelling remained silent. This accident of history is largely responsible for the illusion that Schelling is the older of the two x (Tiibingen: J. C. B. Mohr, 1921-24),2 vols. 2The Spirit of Modern Philosophy (Boston: Houghton Mifflin, 1892), Lecture VI, 164-189. Wordsworth and ScheUing, A Typological Study of Romanticism (New Haven: Yale University Press, 1960),Yale Studies in English, Vol. CXLV. 4Friedrich Wilhelm Joseph yon Sehelling, Philosophische Untersuchungen i~berdas Wesen der menschlichen Freyheit und die damit zusaramenhdngenden Gegenstdnde, 1809. Reprinted in the Sdmmtliche Werke, Erste Abtheilung, VII. Band (Stuttgart und Augsburg: J. G. Cotta, 1856), 331-416. English translation by James Gutmann: Of Human Freedom (Chicago: Open Court, 1936). 5Three fragmentary versions of the Weltalter have been published. The Urfassungen of 1811 and 1813were edited by Manfrcd SehrSter and published as a separate Naehlassband to the M~nchener Jubildumsausgabe of the collected works: Die Weltalter, Fragmente (Munich: Biederstein, Leibniz, 1946). A later version is published in S.W. I: 8, pp. 195-344,which has been translated by Frederick de Wolfe Bolman, Jr. : The Ages of the World (NewYork: Columbia University Press, 1942). 6Philosophie der Mythologie is published in S.W. II: 1-2; Philosophie der Offenbarung in S.W. II: 3-4. These essays were first collected and published by Herman Nohl in Hegels theologische Jugendschriften (Tiibingen: 1907).T. M. Knox translated them into English, with an introduction by Richard Kroner: GeorgWilhelm Friedrich Hegel, Early Theological Writings (Chicago: University of Chicago Press, 1948). [75] 76 HISTORY OF PHILOSOPHY thinkers (actually he was five years Hegel's junior), who retired from the philosophical scene after making his contribution to the Hegelian synthesis. Paul Tillich's doctoral dissertations s and Ernst Cassirer's studies in post-Kantian thought 9 made serious inroads on this conception, yet the iIInsion persisted. Their insistence on the importance of the later Schelling has been brilliantly sustained by two recent studies: Horst Fuhrmans's Schellings Philosophie der Weltalter1~and Walter Schulz's Die Vollendung des deutschen Idealismus in der Spdtphilosophie Schellings, ~ and we may hope that the conventional estimate of Schelling will be drastically revised. Fuhrmans has demonstrated that the split between the early and the later Schelling must be placed in the year 1806 when he came in contact with Franz yon Bander in Munich, who encouraged him to delve deeper into the theological and cosmological ramifications of Jacob Boehme's thought. TM The reorientation this caused is apparent in the essay on human freedom, published in 1809, but it was not fully exploited until the... (shrink)

Greek and Roman Philosophy After Aristotle brings together over twenty-five of the most important works of Western philosophy written from 322 B.C.E. — the death of Aristotle — to the close of the third century C.E. Eminent philosopher Jason Saunder's choices for this concise volume emphasize the range and significance of the leading philosophers of the Hellenistic Age. Supplemented by Dr. Saunder's enlightening introduction, descriptive notes, and extensive bibliography, these readings provide an essential introduction for students and general readers alike (...) to the enormous influence of Greek philosophy on the formative years of Christianity as well as the early Christians' distrust of it. Published initially in 1966 as part of The Free Press paperback series Readings in the History of Philosophy, this affordable volume introduces Lucretius, Epicurus, Epictetus and Stoicism, Sextus Empiricus, Lucian, Philo of Alexanderia, and Plotinus, as well as seminal figures from early Christian thought, including St. Paul and Clement of Alexandria. JASON L. SAUNDERS held positions in philosophy at the University of California at San Diego, and at The City College of New York. Dr. Saunders was the author of The History and Philosophy of Ancient and Renaissance Stoicism, Greek and Latin Philosophy of Aristotle, Philosophy of Neo Stoicism, and Justus Lipsius: The Philosopher of Renaissance Stoicism. [Back cover text from 1994 reprint.]. (shrink)

In The Case for Animal Rights, Tom Regan argues that although all subjects-of-a-life have equal inherent value, there are often differences in the value of lives. According to Regan, lives that have the highest value are lives which have more possible sources of satisfaction. Regan claims that the highest source of satisfaction, which is available to only rational beings, is the satisfaction associated with thinking impartially about moral choices. Since rational beings can bring impartial reasons to bear on decision making, (...) Regan maintains that they have an additional possible source of satisfaction that nonrational beings do not have and, consequently, the lives of rational beings turn out to have greater value.. (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)

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)

Recent discussions in the just war literature suggest that soldiers have a duty to assume certain risks in order to protect the lives of all innocent civilians. I challenge this principle of risk by arguing that it is justified neither as a principle that guides the conduct of combat soldiers, nor as a principle that guides commanders in the US military. I demonstrate that the principle of risk fails on the first account because it requires soldiers both to violate their (...) strict duty of obedience and loyalty and to exceed their special obligations to protect their fellow comrades, the state, the state's constituents and other protected civilians. I then illustrate that the principle of risk fails on the second account since it conflicts with the commander's primary obligation to protect and promote the welfare and lives of his or her soldiers. I conclude by arguing that we cannot reasonably expect soldiers and commanders to adhere to the principle of risk until there is a radical, institutional-level transformation of militaristic goals, values, strategies, policies, warrior codes and expectations of service members in the US Armed Forces. (shrink)

Alister McGrath has written to great acclaim on both Richard Dawkins and C. S. Lewis. Here he brings these two intriguing and well-known writers into a conversation. They could hardly have more different perspectives! Engaging with their views is a brilliant way of sharpening up our own thinking on the meaning of life.

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)

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)