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)

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)

Those who have had the benefit of a reasonably lengthy familiarity with the philosophy of religion, and more particularly with the God question, may be so kind to a speaker long in exile from philosophy and only recently returned, as to subscribe, initially at least, to the following rather enormous generalization: meaning and truth, which to most propositions are the twin forces by which they are maintained, turn out in the case of claims about God, to be the centrifugal forces (...) by which they disintegrate. In simpler language, the greater the amount of intelligible meaning that can be given to the idea of God, the less grounds there would appear to be for assuming let alone asserting, that God exists, at least as a being distinguishable from all the things in this empirical world which are the source of the range of meanings available to us; on the other hand, the more we insist that God exists, a being over and above the things that make up this empirical world the less the amount of commonly available meaning we appear to be able to apply to God. Or, to put this in a manner which might obviate an obvious objection to it; either everything we know is tout ensemble , God, and then nothing in the world that we know is distinctively divine; or else nothing in this world is God, and then nothing that we appear to be able to know is God. That same formulation will work, it should be noted, even if we substitute for ‘things in the world’, ‘an aspect or aspects of things in the world’. (shrink)

James P. Sterba offers something that philosophers have long sought: an argument showing that morality is rationally required. Furthermore he argues that morality requires substantial equality. Even libertarian perspectives, which would seem to require minimal enforcement of morality, are shown to lead to a requirement of equality.

Using yet untapped resources from moral and political philosophy, this book seeks to answer the question of whether an all good God who is presumed to be all powerful is logically compatible with the degree and amount of moral and natural evil that exists in our world. It is widely held by theists and atheists alike that it may be logically impossible for an all good, all powerful God to create a world with moral agents like ourselves that does not (...) also have at least some moral evil in it. James P. Sterba focuses on the further question of whether God is logically compatible with the degree and amount of moral and natural evil that exists in our world. The negative answer he provides marks a new stage in the age-old debate about God's existence. (shrink)

In this unique work, James P. Sterba argues that traditional ethics has yet to confront the three significant challenges posed by environmentalism, feminism, and multiculturalism. He maintains that while traditional ethics has been quite successful at dealing with the problems it faces, it has not addressed the possibility that its solutions to these problems are biased in favor of humans, men, and Western culture. In Three Challenges to Ethics: Environmentalism, Feminism, and Multiculturalism, Sterba examines each of these challenges. In (...) the case of environmentalism, he argues that traditional ethics must incorporate conflict resolution principles that favor nonhumans over humans in a significant range of cases. In terms of feminism, he maintains that traditional ethics should rule out gendered family structures and implement an ideal of androgyny. In regard to multiculturalism, he contends that traditional ethics must endorse an ethics that is secular in character and that can survive an extensive comparative evaluation of both Western and non-Western moral ideals and cultures. The only textbook devoted to this topic, Three Challenges to Ethics is an engaging text for introductory courses in ethics and moral problems and is also interesting and provocative reading for scholars and general readers. (shrink)

Almost no systematic theorizing is generality-free. Scientists test general hypotheses; set theorists prove theorems about every set; metaphysicians espouse theses about all things of any kind. But do we ever succeed in theorizing about absolutely everything? Not according to generality relativism, which J.P. Studd defends in this book.

This book conveys the breadth and interconnectedness of questions of justice - a rarity in contemporary moral and political philosophy. James P. Sterba argues that a minimal notion of rationality requires morality, and that a minimal libertarian morality requires the welfare and equal opportunity endorsee by welfare liberals and the equality endorsed by socialists, as well as a full feminist agenda. Feminist, racial, homosexual, and multicultural justice, are also shown to be mutually supporting. The author further shows the compatibility (...) between anthropocentric and biocentric environmental ethics, as between just war and pacifist theories. Finally, he spells out when normal politics, legal protest, civil disobedience, revolutionary action, and criminal disobedience are morally permitted by justice for here and now. This highly original and potentially controversial book is ideal for courses in moral and political philosophy, applied ethics, women's studies, environmental studies, and peace studies. (shrink)

ABSTRACT I explore the viability of a Galilean relational theory of space-time—a theory that includes a three-place collinearity relation among its stock of basic relations. Two formal results are established. First, I prove the existence of a class of dynamically possible models of Newtonian mechanics in which collinearity is uninstantiated. Second, I prove that the dynamical properties of Newtonian systems fail to supervene on their Galilean relations. On the basis of these two results, I argue that Galilean relational space-time is (...) too weak of a structure to support a relational interpretation of classical mechanics. 1.Introduction 2.Completeness 3.Leibnizian Relationalism 4.Galilean Relationalism 5.Inverse-Cube Force Laws 5.1Warm-up 5.2Model 1: Zero angular momentum 5.3Model 2: Non-zero angular momentum 6.Supervenience 7.Incompleteness 8.Conclusion. (shrink)

This book combines the two most common approaches used to introduce students or general readers to ethics: the historical and the applied. Using these approaches, Sterba examines traditional ethical theories and disagreements, exploring Aristotelian, Kantian, and utilitarian ethics, as well as their contemporary defenders. But rather than focusing on formal aspects of these views, Sterba applies the best practical arguments from each of these perspectives to a variety of moral problems, such as sexual harassment, affirmative action, and international terrorism and (...) the second Iraqi war. (shrink)

In this introduction, I summarize the main themes of my book, particularly those that my critics have focused on in their papers that follow. I also argue that I could not have reached the conclusions that I have if I hadn’t employed a peacemaking rather than a warmaking way of doing philosophy. I provide a characterization of a peacemaking way of doing philosophy and show how the conclusions of my book depend on doing philosophy in that way.

Thousands of texts discuss Egytpain cosmology and cosmogony. James Allen has selected sixteen to translate and discuss in order to shed light on one of the questions that clearly preoccupied ancient intellectuals; the origins of the world.

BackgroundPlagiarism is common and threatens the integrity of the scientific literature. However, its detection is time consuming and difficult, presenting challenges to editors and publishers who are entrusted with ensuring the integrity of published literature.MethodsIn this study, the extent of plagiarism in manuscripts submitted to a major specialty medical journal was documented. We manually curated submitted manuscripts and deemed an article contained plagiarism if one sentence had 80 % of the words copied from another published paper. Commercial plagiarism detection software (...) was utilized and its use was optimized.ResultsIn 400 consecutively submitted manuscripts, 17 % of submissions contained unacceptable levels of plagiarized material with 82 % of plagiarized manuscripts submitted from countries where English was not an official language. Using the most commonly employed commercial plagiarism detection software, sensitivity and specificity were studied with regard to the generated plagiarism score. The cutoff score maximizing both sensitivity and specificity was 15 % (sensitivity 84.8 % and specificity 80.5 %).ConclusionsPlagiarism was a common occurrence among manuscripts submitted for publication to a major American specialty medical journal and most manuscripts with plagiarized material were submitted from countries in which English was not an official language. The use of commercial plagiarism detection software can be optimized by selecting a cutoff score that reflects desired sensitivity and specificity. (shrink)

Among the distinguished contributors to the series are fellows of the Institute, past and present, Leonard E. Boyle, Jocelyn Hillgarth, Edouard Jeauneau, James K. McConica, M. Michèle Mulchahey, Joseph Owens, Walter H. Principe, James P. ...

What will it take for business to improve lives? Many think we need a theoretically sound meta-narrative to articulate the proper place for business in our lives. Important as that is, this meta-narrative will only come to life when everyone articulates his and her personal narrative, shares it with others, and ultimately fine-tunes it into a personal theory-in-use, one that guides everyday decision-making. Hoping that the Humanistic Management Association willsoon find room on its webpage for those of us in business (...) and business education to share our values and beliefs with each other, I thought I would start usoff by sharing mine here. (shrink)

We investigate the notion of relevance as it pertains to ‘commonsense’, subjunctive conditionals. Relevance is taken here as a relation between a property (such as having a broken wing) and a conditional (such as birds typically fly). Specifically, we explore a notion of ‘causative’ relevance, distinct from ‘evidential’ relevance found, for example, in probabilistic approaches. A series of postulates characterising a minimal, parsimonious concept of relevance is developed. Along the way we argue that no purely logical account of relevance (even (...) at the metalevel) is possible. Finally, and with minimal restrictions, an explicit definition that agrees with the postulates is given. (shrink)

Drawing on and inspired by Paul Taylor’s Respect for Nature, I develop a view which I call “biocentric pluralism,” which, I claim, avoids the major criticisms that have been directed at Taylor’s account. In addition, I show that biocentric pluralism has certain advantages over biocentric utilitarianism (VanDeVeer) and concentric circle theories (Wenz and Callicott).

Skeptical theists hold that we should be skeptical about our ability to know the reasons that God would have for permitting evil, at least in particular cases. They argue for their view by setting aside actions that are wrong in themselves and focusing their attention on actions that are purportedly right or wrong simply in terms of their consequences. However, I argue in this paper that once skeptical theists are led to take into account actions that are wrong in themselves, (...) as they must, they cannot escape the conclusion that there is a logical contradiction between the existence of an all-good, all-powerful God and what would have to be God’s permission of the significant and horrendous evil consequences of immoral actions found in our world. (shrink)

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The Pursuit of Justice: A Personal Philosophical History is a collection of renowned scholar and philosopher James P. Sterba’s finest works - essays spanning the full spectrum of his illustrious career along with new scholarship on the enduring struggle for justice we face as a society, and as individuals in the modern world. That struggle, or pursuit, may be ongoing, but – as this book details – it has come a long way, and that progress, however frustrating it may (...) be to obtain and secure, is a testament to the work to which scholars like Sterba have devoted their lives and careers. (shrink)

This volume provides an introduction to word and paradigm models of morphology and the general perspectives on linguistic morphology that they embody. The recent revitalization of these models is placed in the larger context of the intellectual lineage that extends from classical grammars to current information-theoretic and discriminative learning paradigms. The synthesis of this tradition outlined in the volume highlights leading ideas about the organization of morphological systems that are shared by word and paradigm approaches, along with strategies that have (...) been developed to formalize these ideas, and ways in which the ideas have been validated by experimental methodologies. An extended comparison of contemporary word and paradigm variants isolates the central assumptions about morphological units and relations that distinguish implicational from realizational models and clarifies the relation of these models to morpheme-based accounts. Designed to be accessible to a wide readership, this book will serve both as an introduction to morphology and morphological theory from the word and paradigm perspective for non-specialists, and for morphologists, as a detailed account of the history of the ideas that underlie these models. (shrink)

Feminism was born in controversy and it continues to flourish in controversy. The distinguished contributors to this volume provide an array of perspectives on issues including: universal values, justice and care, a feminist philosophy of science, and the relationship of biology to social theory.