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)

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)

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.

Since God is a transcendent being, one cannot expect to encounter him in unmediated contact. However, the author argues, there is an analogy between our knowledge of other minds and our knowledge of God. Just as to come to the truth of the former knowledge requires some sophistication, so does the process of discovering the latter truth. Without ever being an apologist, Professor Lewis bases his case upon the uniqueness of religious experience, of which the book as a whole (...) is an analysis. He recognizes a role of reflection in religion and attempts to give some criteria for evaluating religious claims. --J. E. M. (shrink)

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)

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)

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

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.

The study of anarchism as a philosophical, political, and social movement has burgeoned both in the academy and in the global activist community in recent years. Taking advantage of this boom in anarchist scholarship, Nathan J. Jun and Shane Wahl have compiled twenty-six cutting-edge essays on this timely topic in New Perspectives on Anarchism.

Over 40 years of research have shown that traumatic brain injury affects brain volume. However, technical and practical limitations made it difficult to detect brain volume abnormalities in patients suffering from chronic effects of mild or moderate traumatic brain injury. This situation improved in 2006 with the FDA clearance of NeuroQuant®, a commercially available, computer-automated software program for measuring MRI brain volume in human subjects. More recent strides were made with the introduction of NeuroGage®, commercially available software that is based (...) on NeuroQuant® and extends its utility in several ways. Studies using these and similar methods have found that most patients with chronic mild or moderate traumatic brain injury have brain volume abnormalities, and several of these studies found—surprisingly—more abnormal enlargement than atrophy. More generally, 102 peer-reviewed studies have supported the reliability and validity of NeuroQuant® and NeuroGage®. Furthermore, this updated version of a previous review addresses whether NeuroQuant® and NeuroGage® meet the Daubert standard for admissibility in court. It concludes that NeuroQuant® and NeuroGage® meet the Daubert standard based on their reliability, validity, and objectivity. Due to the improvements in technology over the years, these brain volumetric techniques are practical and readily available for clinical or forensic use, and thus they are important tools for detecting signs of brain injury. (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)

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)

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)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (shrink)

E. J. Lowe; The problems of intrinsic change: rejoinder to Lewis, Analysis, Volume 48, Issue 2, 1 March 1988, Pages 72–77, https://doi.org/10.1093/analys/48.2.7.

I examine recent arguments based on functionalism that claim to show that Bohm's theory fails to solve the measurement problem, or if it does so, it is only because it reduces to a form of the many-worlds theory. While these arguments reveal some interesting features of Bohm's theory, I contend that they do not undermine the distinctive Bohmian solution to the measurement problem. ‡I would like to thank Harvey Brown, Martin Thomson-Jones, and David Wallace for helpful discussions. †To contact the (...) author, please write to: Department of Philosophy, University of Miami, P.O. Box 248054, Coral Gables, FL 33124–4670; e-mail: [email protected]. (shrink)

The traditional college student of today is part of the Net Generation who has been raised in an era of instant access. Their communication and learning is complemented by the Internet, a major influence on this cohort. The regular method of contact is text messaging, instant messaging and cell phones. Learning methods for the Net Generation include Internet tools such as Web-CT, Blackboard, online courses, online journals and i-pod downloads. Are they ready to also change from print textbooks to Internet (...) based textbooks? This paper describes the attitudes of some Net Generation students towards the usage of electronic textbooks. Three case studies were conducted: one class used an online textbook and two other classes used e-chapter supplements. Students were questioned on their perceptions of using and learning with e-textbooks. Their views describe some changing thoughts towards network connected media that is the mantra of this generation. (shrink)

The main problem with the many‐worlds theory is that it is not clear how the notion of probability should be understood in a theory in which every possible outcome of a measurement actually occurs. In this paper, I argue for the following theses concerning the many‐worlds theory: If probability can be applied at all to measurement outcomes, it must function as a measure of an agent’s self‐location uncertainty. Such probabilities typically violate reflection. Many‐worlds branching does not have sufficient structure to (...) admit self‐location probabilities. Decision‐theoretic arguments do not solve this problem. †To contact the author, please write to: Department of Philosophy, University of Miami, P.O. Box 248054, Coral Gables, FL 33124‐4670; e‐mail: [email protected]. (shrink)

E. J. Lowe; Wright versus Lewis on the transitivity of counterfactuals, Analysis, Volume 44, Issue 4, 1 October 1984, Pages 180–183, https://doi.org/10.1093/ana.

In lieu of an abstract, here is a brief excerpt of the content:PARODY AND THE ARGUMENT FROM PROBABILITY IN THE APOLOGY by Thomas J. Lewis Over a century ago James Riddell pointed out that Socrates' defense speech in die Apology closely followed the standard form of Athenian forensic rhetoric. He called the Apology "artistic to the core," and he identified parts of "the subde rhetoric of this defense."1 Since then many scholars have explicated the rhetorical elements in Socrates' defense.2 (...) Their work has led in turn to recent attempts to integrate the rhetorical form into an overall understanding of the meaning and significance of the Apology? The puzzle to be solved is what to make of the fact that Socrates disclaims the ability and the intention to use rhetoric in a speech which is itself a rhetorical masterpiece. R. E. Allen raises the possibility thatby using the techniques ofrhetoric and at the same time denying that he is using them Socrates is dissembling or lying. However, Allen rejects this possibility and interprets Socrates' falsehood as only a surface or apparent falsehood. According to Allen it is ironic parody of a disreputable rhetoric which seeks to convince without concern for the truth.4 For Allen the object of the parody is base rhetoric in general, the type of rhetoric denounced by Socrates in the Gorgias as "rhetoric aiming at gratification and pleasure, and indifferent to truth and the good of the soul."5 Two subsequent articles, one by Kenneth Seeskin, the other by Douglas Feaver andJohn Hare, support the view that Socrates is parodying the debased form of rhetoric. However, they place somewhat different emphasis on the exact object of the parody. They argue that the object of Socrates' rhetorical parody is Gorgias' Pahmedes, rather than pandering rhetoric in general.6 After summarizing the many rhetorical similarities between Gorgias' Palamedes and Socrates' defense speech, Seeskin concludes that "Gorgias' Philosophy and Literature, © 1990, 14: 359-366 360Philosophy and Literature Palamedes is not a masterpiece of world literature; it is a collection of topoi—tried and true devices for winning acquittal... [whereas] despite his disclaimer, Socrates' speech is no amateur performance. On the contrary, he knew all the tricks of the trade and employed them with consummate skill" (p. 97). Seeskin uses Plato's Gorgias to explain how Socrates' rhetoric fits within an overall understanding of the Apology. He notes the two types ofrhetoric presented in the Gorgias: base rhetoric, a species of flattery which aims at gratification; and philosophic or true rhetoric which aims at improving the soul. Then Seeskin makes a crucial point. He insists it is not enough to distinguish between base rhetoric and philosophic rhetoric; there must be a way to identify a given instance of rhetoric as either base rhetoric or as philosophic rhetoric. Moreover, he cautions that distinguishing the one from the other is no easy task. "It is impossible to tell them apart on the basis of technique alone. Base rhetoric is no less polished for its baseness.... Nor can one tell them apart on the basis of their stated goals. Flattery succeeds only to the extent that it can pass itself off as something better" (p. 98). Thus, if Socrates and Palamedes employ the same rhetorical devices, Seeskin wonders how we can tell which type ofrhetoric is in the Apology. "Somewhere in the Apology of Socrates there ought to be a clue which allows one to distinguish his defense from the 'standard' defense composed by Gorgias" (p. 99). Seeskin finds the clue in the exordium, where Socrates denies that he is a skillful speaker: "Unless, of course, by a skillful speaker they mean one who speaks the truth. If that is what they mean, I would agree that I am an orator, though not after their pattern" (17b). Although Palamedes makes a comparable claim, Seeskin argues that Palamedes was concerned with appearance rather than truth, and that the key to appearance is the use of the argument from probability. According to Seeskin, Socrates does not rely on the argument from probability, whereas this argument permeates the Palamedes. "Again and again, the speaker tries to show that it would be implausible to suppose that anyone in his position did what he is accused of doing. How... (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)