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)

Let me offer an early disclaimer. I know exactly who the Founders were. I know exactly the crimes against humanity that they were responsible for and those they inherited and were not responsible for. I do not spend time extolling the virtues of Mr. Jefferson, Mr. Adams, Mr. Franklin, and Mr. Madison. Nothing in this work or in my experiment (my life's work) can change the fact or alter the history of the debasement of humanity that preceded the Declaration of (...) Independence (1776), the Constitution (1787), and the Bill of Rights (1791) they were a part of and the obvious fact that the major accomplishment of the Founders' theories about self-government did not apply to African Americans and Native Americans, women, and specifically Black women in their thinking. Still, there exists in their theological imagination infinite hope for their experiment. This work seeks to identify the evidence that shows and suggests that some of them were aware of a grand architectural experiment and design for the nation and its future. Every cracked, broken, and imperfect vessel can be used to bring forward hope. I am a personal witness to this fact of human existence. (shrink)

This volume is the product of an important recent conference, convened by His Holiness the Dalai Lama, focusing on the intellectual legacy of the Tibetan philosopher, yogi, and saint Tsongkhapa (1357-1419). Entitled "Jé Tsongkhapa: Life, Thought, and Legacy," the conference commemorated the sixth hundredth anniversary of Tsongkhapa's passing and was held on December 21-23, 2019, at Ganden Monastery in Mundgod, India. Part 1 concerns Madhyamaka, a natural reflection of the very important and well-known contributions Tsongkhapa made to the study of (...) Indian philosophical thought. The first essay, Guy Newland's "Start Making Sense: Finding Tsongkhapa's Middle Way," provides a straightforward and clear introduction to Tsongkhapa's interpretation of Madhyamaka philosophy, showing how Tsongkhapa played an essential role in clarifying Candrakīrti's contributions to Madhyamaka thought. The second essay, "Celebrating Jé Tsongkhapa: The Twofold Object of the Identity View" by Dr. Dechen Rochard explores Tsongkhapa's understanding of Candrakīrti's negation of individual identity. The essay neatly demonstrates the centrality of the practitioner's view of self to the path to spiritual awakening. In the third chapter, "Thinking Beyond Thought: Tsongkhapa and Mipham on the Conceptualized Ultimate," Jay L. Garfield explores Tsongkhapa's views on the nature of ultimate reality, specifically Tsongkhapa's argument that this entails a movement from inferential to direct awareness of emptiness. The essay explores the need for accurate philosophical analysis in the context of meditation practice so as to directly realize the truths about the nature of self and reality that are the objects of the practice. It thus nicely points to the integration of Buddhist theory and practice. The second section of this volume is dedicated to Tsongkhapa's writings on the tantras. In the first chapter in this section, "Tsongkhapa's Masterful Exegesis of Cakrasaṃvara Tantra," I elucidate Tsongkhapa's approach to the study of tantric literature with a focus on his commentary on the Cakrasaṃvara Tantra. Chapter 6 is Gavin Kilty's contribution, "A Lamp to Illuminate the Five Stages: Tsongkhapa's Reformatory Work on Guhyasamāja Tantra." Kilty first surveys the Guhyasamāja tradition and its transmission to Tibet and the two main Indian exegetical traditions, the Ārya and J.ānapāda schools. Outlining Tsongkhapa's approach to the Guhyasamāja Tantra, he then focuses on how the tradition conceptualizes the generation-stage and completion-stage practices. Chapter 7, "The Shadow of Heshang: Tsongkhapa on Chan, Dzokchen, and Mahāmudrā" by Roger R. Jackson. Jackson explores the claim that Tsongkhapa received and secretly transmitted esoteric instructions on advanced meditation practices to realize the nature of mind and awakening. The volume concludes with a section entitled "Moving Minds," which explores Tsongkhapa's legacy and impact both in Tibet and beyond. It opens with "Jé Tsongkhapa's Contribution to Buddhist Hermeneutics" by Geshé Ngawang Samten. Buddhist hermeneutics, as understood here, is a response to the challenge posed by scriptures that appear to contradict one another. Chapter 9, "Tsongkhapa's Hermeneutics and the Perfection of Wisdom," contributed by Gareth Sparham, takes a more focused look at the interpretation of the Perfection of Wisdom literature in both India and Tibet. The tenth chapter is "Jé Tsongkhapa's Teachings and Translations in Mongolian" by Bataa Mishig-Ish, who surveys the dissemination of Tsongkhapa's oeuvre to Mongolia. The final chapter is BhikṣuṇīThubten Chodron's "Learning, Living, and Teaching Bodhicitta: Jé Tsongkhapa's Contribution to Spreading Compassion in the World." Venerable Chodron argues that Tsongkhapa's approach to teaching compassion is particularly suited for the modern, Western context. While this volume does not come close to exhausting the limits of what might be said concerning the impact of Tsongkhapa's work in Tibet and beyond, it does reunite contributions to this study that briefly converged in Preface xi Mundgod, India, just before the global pandemic ushered in a new awareness of our profound human interdependence. Hopefully these essays will advance the appreciation of Tsongkhapa's intellectual legacy in the wider English-speaking world, where he remains a little understood figure of Asian religious history, unlike in the Tibetan-speaking world, where his impact is justly celebrated. (shrink)

Considered the most original thinker in the Italian philosophical tradition, Giambattista Vico has been the object of much scholarly attention but little consensus. In this new interpretation, David L. Marshall examines the entirety of Vico's oeuvre and situates him in the political context of early modern Naples. He demonstrates Vico's significance as a theorist who adapted the discipline of rhetoric to modern conditions. Marshall presents Vico's work as an effort to resolve a contradiction. As a professor of rhetoric at (...) the University of Naples, Vico had a deep investment in the explanatory power of classical rhetorical thought, especially that of Aristotle, Cicero, and Quintilian. Yet as a historian of the failure of Naples as a self-determining political community, he had no illusions about the possibility or worth of democratic and republican systems of government in the post-classical world. As Marshall demonstrates, by jettisoning the assumption that rhetoric only illuminates direct, face-to-face interactions between orator and auditor, Vico reinvented rhetoric for a modern world in which the Greek polis and the Roman res publica are no longer paradigmatic for political thought. (shrink)

Is conceptual analysis required for reductive explanation? If there is no a priori entailment from microphysical truths to phenomenal truths, does reductive explanation of the phenomenal fail? We say yes . Ned Block and Robert Stalnaker say no.

This article critically evaluates the Medicines and Healthcare products Regulatory Agency’s announcement, in March 2008, that GlaxoSmithKline would not face prosecution for deliberately withholding trial data, which revealed not only that Seroxat was ineffective at treating childhood depression but also that it increased the risk of suicidal behaviour in this patient group. The decision not to prosecute followed a four and a half year investigation and was taken on the grounds that the law at the relevant time was insufficiently clear. (...) This article assesses the existence of significant gaps in the duty of candour which had been assumed to exist between drugs companies and the regulator, and reflects upon what this episode tells us about the robustness, or otherwise, of the UK’s regulation of medicines. (shrink)

Definitions of pragmatism increasingly turn on understanding and relating the philosophies of Richard Rorty and John Dewey. Rorty is often the first and most important lens through which many encounter pragmatism or Dewey; thus, it is crucial to know where “Rorty” ends and where “Dewey” begins. To find that line, this chapter answers the question: What did Rorty believe Dewey contributed to pragmatism, to philosophy, and to humanity? After reviewing how Rorty's personal and academic beginnings intertwined with Dewey, preliminary context (...) is provided by reviewing Rorty's view of pragmatism and neopragmatism and his general interpretive approach to Dewey. These preliminaries yield to analytical descriptions of the main areas in Dewey's work which Rorty was concerned to present: experience; objectivity and truth; inquiry and scientific method; ethics, politics, and democracy; and, finally, the general purpose of philosophy. (shrink)

Goicoechea presents his third volume in a series on agape. In this book he shows in four ways how the agape of Jesus fulfills the ahava and hesed of the Hebrew Bible. First, he shows existentially how he learned and lived this for six years in a Benedictine Minor Seminary and then for three years in a Sulpician Major Seminary. Second, he demonstrates how ahava or our love for God and neighbor and hesed or God's love for us develop through (...) the Hebrew Bible. Goicoechea argues that St. Matthew's Gospel explains the fulfilment of ahava and hesed with Jesus' agape. He concludes by drawing attention to how Levinas and Derrida, two Jewish postmodern philosophers, treat Jewish and Christian love. (shrink)

As sociologists deepen their examinations of human rights in their teaching, research, and thinking, it is essential that such work is conducted in a manner that is both mindful and critical of the knowledge we are building upon in sociology and human rights. As the authors of this volume reveal, creating sociological knowledge that examines human rights for the expansion of human rights is something that sociologists are well equipped to undertake, whether through the use of mathematics, comparative-historical analysis, the (...) study of emotions, conversations, or social psychology. In these chapters you will find the roots of the study of human rights deep within sociological research and thinking as well as emerging techniques that will push the discipline as it seeks to expand understanding of human rights together with so many other aspects of the social condition. (shrink)

This book seeks to elucidate the concept of justice, not so much as it is expressed in law courts (retributive and procedural justice) or in state budgets (distributive justice), but as primary justice - what it means and how it can be grounded in the inalienable rights that each human being possesses qua human being. It draws inspiration from two recent works of philosopher Nicolas Wolterstorff, but also from the groundbreaking Islamic initiative of 2007, the Common Word Letter addressed by (...) 138 eminent Muslim scholars and clerics to the pope and all Christian leaders. This document affirmed that the two highest commandments in both Judaism and Christianity are also at the heart of the Islamic tradition - love of God and love of neighbor. In a style that lends itself to the classroom and beyond, the book's six chapters all begin with a case study of justice, so as to emphasize that justice must also be embodied in righteous social, political and economic practices. Along the way, leading contemporary scholars and activists from both traditions urge the reader - Muslim, Christian, or whatever - to look afresh at an age-old conundrum: how do justice and love interact so as to create a world in which everyone finds his or her rightful place? (shrink)

"Legend is overdue for replacement, and an adequate replacement must attend to the process of science as carefully as Hull has done. I share his vision of a serious account of the social and intellectual dynamics of science that will avoid both the rosy blur of Legend and the facile charms of relativism.... Because of [Hull's] deep concern with the ways in which research is actually done, Science as a Process begins an important project in the study of science. It (...) is one of a distinguished series of books, which Hull himself edits."—Philip Kitcher, Nature "In Science as a Process, [David Hull] argues that the tension between cooperation and competition is exactly what makes science so successful.... Hull takes an unusual approach to his subject. He applies the rules of evolution in nature to the evolution of science, arguing that the same kinds of forces responsible for shaping the rise and demise of species also act on the development of scientific ideas."—Natalie Angier, New York Times Book Review "By far the most professional and thorough case in favour of an evolutionary philosophy of science ever to have been made. It contains excellent short histories of evolutionary biology and of systematics (the science of classifying living things); an important and original account of modern systematic controversy; a counter-attack against the philosophical critics of evolutionary philosophy; social-psychological evidence, collected by Hull himself, to show that science does have the character demanded by his philosophy; and a philosophical analysis of evolution which is general enough to apply to both biological and historical change."—Mark Ridley, Times Literary Supplement "Hull is primarily interested in how social interactions within the scientific community can help or hinder the process by which new theories and techniques get accepted.... The claim that science is a process for selecting out the best new ideas is not a new one, but Hull tells us exactly how scientists go about it, and he is prepared to accept that at least to some extent, the social activities of the scientists promoting a new idea can affect its chances of being accepted."—Peter J. Bowler, Archives of Natural History "I have been doing philosophy of science now for twenty-five years, and whilst I would never have claimed that I knew everything, I felt that I had a really good handle on the nature of science, Again and again, Hull was able to show me just how incomplete my understanding was.... Moreover, [Science as a Process] is one of the most compulsively readable books that I have ever encountered."—Michael Ruse, Biology and Philosophy. (shrink)

What makes us persons? Is it our bodies, our minds, or our consciousness? For centuries, philosophers have sought to answer these questions. While some believe humans are physical or biological, others claim we have an immaterial soul. This book proposes a new alternative. Selves were formed in evolution through connections and commitments to others when early hominins lived in tribal groups and developed languages. As humans learned to fulfill these commitments, they not only cultivated relationships but also created their personal (...) identities. Their habits of responsibility established their characters and therefore their reputations within their communities. This naturalistic approach proposes that a self is defined by the history of its commitments to cultural and personal norms. While brain processes are required, the self is not some internal, private mind but primarily a role within its community. As technology advances, selfhood could in the future be enabled by electronic, quantum, or other non-biological means. So if a self is formed through norms, could artificial intelligence evolve to have self-identity? (shrink)

Martin traces the genealogies of what he considers three of the most distinct and historically immediate fields of modern visual culture: the collection, the body, and the mapping of spaces.

Martin traces the genealogies of what he considers three of the most distinct and historically immediate fields of modern visual culture: the collection, the ...

Drawing on work of the past decade, this volume brings together articles from the philosophy, history, and sociology of science, and many other branches of the biological sciences. The volume delves into the latest theoretical controversies as well as burning questions of contemporary social importance. The issues considered include the nature of evolutionary theory, biology and ethics, the challenge from religion, and the social implications of biology today (in particular the Human Genome Project).

Compares classic and contemporary theories of genetics and evolution and explores the role of teleological thought in biology.

Response to wrongdoing is modeled as a decision process in an organizational context. The model is grounded in theory of risk, ambiguity, and informational influences on decision making. Time pressure, inadequate information and coworker influences are addressed. Along the way, a handful of propositions are provided which emphasize influences on the actual choice between response options.

Biological species have been treated traditionally as spatiotemporally unrestricted classes. If they are to perform the function which they do in the evolutionary process, they must be spatiotemporally localized individuals, historical entities. Reinterpreting biological species as historical entities solves several important anomalies in biology, in philosophy of biology, and within philosophy itself. It also has important implications for any attempt to present an "evolutionary" analysis of science and for sciences such as anthropology which are devoted to the study of single (...) species. (shrink)

Individuals with autistic spectrum disorder (ASD) display diverse deficits in social, cognitive and behavioral functioning. To date, there has been mixed findings on the profile of executive function deficits for high-functioning adults (IQ >70) with ASD. A conceptual distinction is commonly made between “cold” and “hot” executive functions. Cold executive functions refer to mechanistic higher-order cognitive operations (e.g., working memory), whereas hot executive functions entail cognitive abilities supported by emotional awareness and social perception (e.g., social cognition). This study aimed to (...) determine the independence of deficits in hot and cold executive functions for high-functioning adults with ASD. Forty-two adults with ASD (64% male, aged 18-66 years) and 40 age and gender matched controls were administered The Awareness of Social Inference Test (TASIT; emotion recognition and social inference), Letter Number Sequencing (working memory) and Hayling Sentence Completion Test (response initiation and suppression). Between-group analyses identified that the ASD group performed significantly worse than matched controls on all measures of cold and hot executive functions (d =.54-1.5). Hierarchical multiple regression analyses revealed that the ASD sample performed more poorly on emotion recognition and social inference tasks than matched controls after controlling for cold executive functions and employment status. The findings also indicated that the ability to recognise emotions and make social inferences was supported by working memory and response initiation and suppression processes. Overall, this study supports the distinction between hot and cold executive function impairments for adults with ASD. Moreover, it advances understanding of higher-order impairments underlying social interaction difficulties for this population which, in turn, may assist with diagnosis and inform intervention programs. (shrink)

In Christ the Light, Whidden argues that illumination is a critical systematic motif in Aquinas' theology, one that involves the nature of truth, knowledge, and God; at the root, Aquinas' theology of light, or illumination, is Christological, grounding human knowledge of God and eschatological beatitude. This volume establishes the theological network formed by the crucial motif of light/illumination in Aquinas, from how theology operates to the systematic, sacramental, and moral coordinates in Aquinas' theology.

Extreme variation in the meaning of the term “species” throughout the history of biology has often frustrated attempts of historians, philosophers and biologists to communicate with one another about the transition in biological thinking from the static species concept to the modern notion of evolving species. The most important change which has underlain all the other fluctuations in the meaning of the word “species” is the change from it denoting such metaphysical entities as essences, Forms or Natures to denoting classes (...) of individual organisms. Several authors have taken notice of the role of metaphysics in the work of particular biologists. An attempt will be made in this paper to present a systematic investigation of the role which metaphysics has played in the work of representative biologists throughout the history of biology, especially as it relates to their species concepts. (shrink)

Examines the issues of self (including gender), truth, and transcendence in classical Chinese and Western philosophy.

One way to understand science is as a selection process. David Hull, one of the dominant figures in contemporary philosophy of science, sets out in this 2001 volume a general analysis of this selection process that applies equally to biological evolution, the reaction of the immune system to antigens, operant learning, and social and conceptual change in science. Hull aims to distinguish between those characteristics that are contingent features of selection and those that are essential. Science and Selection brings (...) together many of David Hull's most important essays on selection in one accessible volume. (shrink)

If species are the things that evolve at least in large part through the action of natural selection, then both genetic and phenotypic variability are essential to biological species. If all species are variable, then Homo sapiens must be variable. Hence, it is very unlikely that the human species as a biological species can be characterized by a set of invariable traits. It might be the case that at this moment in evolutionary history, all human beings happen to possess a (...) particular set of traits, but if so, this will be in large part an evolutionary accident. As a result, anyone who proposes to base anything, including ethics, on human nature is basing it on historical happenstance. (shrink)

A central subject is the main strand around which the fabric of an historical narrative is woven. Such a subject must possess both spatial and temporal continuity. It is integrated into an historical entity through the relationship between those properties which make it an individual, and their interaction with the historical event. Scientific theory is useful in the reconstruction of past events and the definition of the central subject. Ideas used as central subjects present the problem of finding internal principles (...) of integration which will make the idea continuous over time. The purpose of narratives is to explain an event by integrating it into an organized whole. (shrink)