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)

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).

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.

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)

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 ...

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)

"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)

Cognitive neuroscientists are turning to an increasingly rich array of neurodynamical systems to explain mental phenomena. In these explanations, cognitive capacities are decomposed into a set of functions, each of which is described mathematically, and then these descriptions are mapped on to corresponding mathematical descriptions of the dynamics of neural systems. In this paper, I outline a novel explanatory schema based on these explanations. I then argue that these explanations present a novel type of dynamicism for the philosophy of mind (...) and neuroscience, componential dynamicism, that focuses on the parts of cognitive systems that fill certain functional roles in producing cognitive phenomena. (shrink)

The dynamical hypothesis states that cognitive systems are dynamical systems. While dynamical systems play an important role in many cognitive phenomena, the dynamical hypothesis as stated applies to every system and so fails both to specify what makes cognitive systems distinct and to distinguish between proposals regarding the nature of cognitive systems. To avoid this problem, I distinguish several different types of dynamical systems, outlining four dimensions along which dynamical systems can vary: total-state versus partial-state, internal versus external, macroscopic versus (...) microscopic, and systemic versus componential, and illustrate these with examples. I conclude with two illustrations of partial-state, internal, microscopic, componential dynamicism. (shrink)

Dynamical systems play a central role in explanations in cognitive neuroscience. The grounds for these explanations are hotly debated and generally fall under two approaches: non-mechanistic and mechanistic. In this paper, I first outline a neurodynamical explanatory schema that highlights the role of dynamical systems in cognitive phenomena. I next explore the mechanistic status of such neurodynamical explanations. I argue that these explanations satisfy only some of the constraints on mechanistic explanation and should be considered pseudomechanistic explanations. I defend this (...) argument against three alternative interpretations of the neurodynamical explanatory schema. The independent interpretation holds that neurodynamical explanations and mechanisms are independent. The constitutive interpretation holds that neurodynamical explanations are constitutive but otherwise non-mechanistic. Both the independent and constitutive interpretations fail to account for all the features of neurodynamical explanations. The partial interpretation assumes that the targets of dynamical systems models are mechanisms and so holds that neurodynamical explanations are incomplete because they lack mechanistic details. I contend instead that the targets of those models are dynamical systems distinct from mechanisms and defend this claim against several objections. I conclude with a defense of the pseudomechanistic interpretation and a discussion of the source of their explanatory power in relation to a causal-mechanical description of the world. (shrink)

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

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)

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)

The mass media promotes terrorism by stressing fear and an uncertain future. Major changes in US foreign and domestic policy essentially went unreported and unchallenged by the dominant news organizations. Notwithstanding the long relationship in the United States between fear and crime, the role of the mass media in promoting fear has become more pronounced since the United States `discovered' international terrorism on 11 September 2001. Extensive qualitative media analysis shows that political decision-makers quickly adjusted propaganda passages, prepared as part (...) of the Project for the New American Century, to emphasize domestic support for the new US role in leading the world. These messages were folded into the previous crime-related discourse of fear, which may be defined as the pervasive communication, symbolic awareness, and expectation that danger and risk are a central feature of everyday life. Politicians marshaled critical symbols and icons joining terrorism with Iraq, the Muslim faith, and a vast number of non-western nations to strategically promote fear and use of audience beliefs and assumptions about danger, risk and fear in order to achieve certain goals, including expanding domestic social control. (shrink)

When there have been substantial failures by institutional leadership in their oversight responsibility to protect research integrity, the public should demand that these be recognized and addressed by the institution itself, or the funding bodies. This commentary discusses a case of research failures in developing genomic predictors for cancer risk assessment and treatment at a leading university. In its review of this case, the Office of Research Integrity, an agency within the US Department of Health and Human Services, focused their (...) report entirely on one individual faculty member and made no comment on the institution’s responsibility and its failure to provide adequate oversight and investigation. These actions missed an important opportunity to emphasize the institution’s critical responsibilities in oversight of research integrity and the importance of institutional transparency and accountability. (shrink)

Failure to recognize the "realistic" motivations for Putnam's commitment to internal realism has led to a widely shared misunderstanding of Putnam's arguments against metaphysical realism. Realist critics of these arguments frequently offer rebuttals that fail to confront his arguments. Simply put, Putnam's arguments --the brains in a vat argument as well as the model-theoretic argument -- are "reductios" that are intended to show that "metaphysical realism itself is not sufficiently realistic". If that claim can be substantiated then Putnam can go (...) on to argue that his own view is, by comparison, more realistic than metaphysical realism. (shrink)

When do organizations decide to ‘adopt’ a given social issue such that they come to acknowledge it in their patterns of action and communication? Traditional answers to this question have focused either on the characteristics of the issue itself, or on the traits of the focal organization. In many cases, however, a firm’s decision to adopt or ignore an issue is not a straightforward function of firm or issue characteristics. Instead, we view issue adoption as a socially constructed process of (...) information exchange between parties that are involved in the emergence and evolution of the issue, mediated by third-party organizations. We refer to this process as the infomediary process and these latter organizations as ‘infomediaries,’ after the information mediation and brokerage roles they play in the social processes linking social issues to organizational impact. We present a concise theoretical model of how infomediaries establish credible linkages between focal organizations and social issues. The thrust of the model is that the infomediation process, rather than the issue or firm characteristics, is what really drives firm-level issue adoption decisions. (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)

The hearers of the Apocalypse of John are set in another world in which lambs conquer and suffering rules, where victims have become the victors.

Theories in cognitive science, and especially cognitive neuroscience, often claim that parts of cognitive systems are reused for different cognitive functions. Philosophical analysis of this concept, however, is rare. Here, I first provide a set of criteria for an analysis of reuse, and then I analyse reuse in terms of the functions of subsystems. I also discuss how cognitive systems execute cognitive functions, the relation between learning and reuse, and how to differentiate reuse from related concepts like multi-use, redundancy, and (...) duplication of parts. Finally, I illustrate how my account captures the reuse of dynamical subsystems as unveiled by recent research in cognitive neurobiology. This recent research suggests two different evolutionary justifications for reuse claims. _1_ Introduction _2_ Criteria for Analyses of Reuse _3_ Use and Reuse _4_ The Reuse of Dynamical Systems in Cognitive Systems _5_ Conclusion. (shrink)