Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

When the U.S. conducts warfare, elements of a force are drawn from different services and work together as a single team to accomplish an assigned mission. To achieve such unified action, it is necessary that the doctrines governing the actions of members of specific services be both consistent with and subservient to joint Doctrine. Because warfighting today increasingly involves not only live forces but also automated systems, unified action requires that information technology that is used in joint warfare must be (...) aligned with joint doctrine. It requires also that the separate information systems used by the different elements of a joint force must be interoperable, in the sense that data and information that is generated by each element must be usable (understandable, processable) by all the other elements that need them. Currently, such interoperability is impeded by multiple inconsistencies among the different data and software standards used by warfighters. We describe here the on-going project of creating a Joint Doctrine Ontology (JDO), which uses joint doctrine to provide shared computer-accessible content valid for any field of military endeavor, organization, and information system. JDO addresses the two previously mentioned requirements of unified action by providing a widely applicable benchmark for use by developers of information systems that will both guarantee alignment with joint doctrine and support interoperability. (shrink)

This essay is my brief review of Nicholas Phillipson’s biography of Adam Smith. I discuss the highlights of his treatment of Smith’s fascinating life. Phillipson does a beautiful job of surveying Smith’s academic career. Especially useful is Phillipson’s discussion of the influence David Hume had on Smith’s thought, as well as the influences of Montesquieu, Samuel Johnson, Voltaire, Rousseau, and others.

This essay is my review of economist Mark Skousen’s book, The Big Three in Economics. In it, he discusses the economic work of Adam Smith, Karl Marx, and John Maynard Keynes. He gives even-handed treatments of the major contributions of each, for example, Smith’s reputation refutation of mercantilist policies and Smith’s crucial insight into the role that division of labor plays in economic growth. My only complaint is that Skousen doesn’t adequately explain his choice of Marx as (...) a great economist. What enduring contributions did he make to the field? Why name him rather than (say) David Ricardo? (shrink)

I argue that trends of diagnosing anti-Muslim attitudes and activism as “Islamophobia” in European and the U.S. contexts may actually aid and abet more subtle varieties of the very stigmatization and exclusion that the “phobia” moniker aims to isolate and oppose. My comparative purpose is to draw into relief—to make explicit and subject to critical analysis— features of normative public discourse in these two sociopolitical contexts broadly perceived to be peaceful, prosperous, liberal-democratic. The features I focus on function under the (...) auspices of tolerant and nonexclusionary forms of “civic nationalism” that, in effect, fuel the conflict in question. (shrink)

Remarkably, the theological discourse surrounding Hans Frei and postliberal theology has continued for nearly thirty years since Frei's death. This is due not only to the complex and provocative character of Frei's work, nor only to his influence upon an array of thinkers who went on to shape the theological field in their own right. It is just as indebted to the critical responses that his thinking continues to inspire. One recurrent point of criticism takes aim at Frei's use of (...) Ludwig Wittgenstein's later work for theological ends. In his recent book Liberalism versus Postliberalism: The Great Divide in Twentieth Century Theology, John Allan Knight challenges what he sees as Frei's dependence on problematic Wittgensteinian assumptions. This article raises a few concerns about Knight's charges against Frei. Specifically, I argue that Knight's account tends to conflate the work of Wittgenstein and Frei. It does this by undervaluing two determinative features of Frei's work: (1) its basic Christological orientation; and (2) its Christologically motivated use of ad hoc apologetics. I argue that the Wittgensteinian view that Knight attributes to Frei is not Frei's view at all, and is, moreover, a problematic account of Wittgenstein on its own terms. Finally, Knight's claim that Frei's work “depends upon” and “is suffused” with the understanding of Wittgenstein that Knight attributes to him is based upon an account of Frei's treatment of the sensus literalis that is not entirely accurate. Without question, Knight does remarkable service to Frei's legacy by keeping important debates over his work alive. In what follows, I propose several points where I think Knight's account might be further enriched. The result, I hope, will be a more nuanced understanding of the ways that Frei actually appropriated and deployed Wittgenstein's thought. I will contextualize my account of Frei with reference both to Wittgenstein's writings and the literature surrounding his writings. Setting forth these accounts in tandem should help make further available Wittgenstein's work for subsequent work by postliberal theologians. (shrink)

Despite their purported demographic and institutional decline, White evangelical voters were instrumental in the election of Donald Trump in 2016, and even more so in his 2020 loss. The story of Trump’s electoral successes among Christian voters in the last two elections is in large part the story of religious nationalism—and White Christian nationalism in particular—because Trump personifies the convergence of nationalism-infused forms of messianism and apocalypticism intrinsic to White evangelicalism, which culminate in QAnon cultic ideology. However, these same ethnoreligious/nationalist (...) patterns and logics extend much further back than Trump’s insurgent candidacy. This chapter traces the recurring, resurgent patterns of “zombie nationalism” among White evangelical Christians in the United States over the last half century that emerged in response to periods of significant societal change and certain recurring sociopolitical issues. In particular, alongside established elective affinities around ethnicity (whiteness) and religion (Christianity), this chapter makes the case for incorporating gender and sexual politics as key factors in the articulation and legitimation of religious nationalism in the United States. White Christian nationalism tends to reemerge as a salient political force during periods of rapid social change and diversification, driven by racialized religious grievances symptomatic of Nietzsche’s concept of ressentiment, or the paradoxical internalization and reprojection of a person’s or group’s perceived endangerment, victimhood, and/or suffering, in order to gain power. Drawing on examples of marriage equality and reproductive rights, this chapter demonstrates how an understanding of sexual politics is key to both apprehending and breaking the cyclical reanimation of White Christian nationalism. Escaping the nihilistic impulses driving these cycles will require White evangelicals to develop new hermeneutical tools capable of transforming the exclusionary patterns of racism, ethnocentrism, heteronormativity, and patriarchy that fuel the engine of ressentiment animating zombie nationalism. (shrink)

This essay explores the possibility that religiously motivated intolerance and conflict can be reframed and positively utilized for constructive social-political purposes. After reviewing efforts by political philosophers over the past two decades to accommodate religious voices in political discourse, I scrutinize Charles Taylor’s attempt to improve upon the limits of “accommodationist” approaches to religious intolerance and conflict. I argue that both accommodationist and Taylor’s recognition-based approaches to religiously motivated conflict take the gravity of such conflict with insufficient seriousness. I then (...) explore the potential goods of intentional conflict by examining Chantal Mouffe’s account of agonistic pluralism as a proposal for thinking beyond tolerance as an orienting value for resolving intransigent conflict. While I argue that Mouffe’s account finally suffers from certain of the same misgivings as the accommodationist and recognition-based approaches, I conclude that agonistic pluralism’s aim to conceptually reframe (rather than eliminate) intolerance and conflict moves in an important and promising direction. (shrink)

US citizens perceive their society to be one of the most diverse and religiously tolerant in the world today. Yet seemingly intractable religious intolerance and moral conflict abound throughout contemporary US public life - from abortion law battles, same-sex marriage, post-9/11 Islamophobia, public school curriculum controversies, to moral and religious dimensions of the Black Lives Matter and Occupy Wall Street movements, and Tea Party populism. Healthy Conflict in Contemporary American Society develops an approach to democratic discourse and coalition-building across deep (...) moral and religious divisions. Drawing on conflict transformation in peace studies, recent American pragmatist thought, and models of agonistic democracy, Jason Springs argues that, in circumstances riven with conflict between strong religious identities and deep moral and political commitments, productive engagement may depend on thinking creatively about how to constructively utilize conflict and intolerance. The result is an approach oriented by the recognition of conflict as a constituent and life-giving feature of social and political relationships. (shrink)

This article makes a case for the capacity of "social practice" accounts of agency and freedom to criticize, resist, and transform systemic forms of power and domination from within the context of religious and political practices and institutions. I first examine criticisms that Michel Foucault's analysis of systemic power results in normative aimlessness, and then I contrast that account with the description of agency and innovative practice that pragmatist philosopher Robert Brandom identifies as "expressive freedom." I argue that Brandom can (...) provide a normative trajectory for Foucault's diagnoses of power and domination, helping to resolve its apparent lack of ethical direction. I demonstrate that Foucault, in turn, presents Brandom with insights that might overcome the charges of abstraction and conservatism that his pragmatic inferentialism frequently encounters. The result is a vindication of social practice as an analytical lens for social criticism that is at once both immanent and radical. (shrink)

Hans Frei, one of the most influential American theologians of the twentieth century, is generally considered a founder of postliberal theology. Frei never set forth his thinking systematically, and he has been criticized for being inconsistent, contradictory, and insufficiently rigorous. Jason Springs seeks here to offer a re-evaluation of Frei's work. Arguing that Hans Frei's theology cannot be understood without a meticulous consideration of the complex equilibrium of his theological and philosophical interests and influences, Springs vindicates Frei's christologically motivated (...) engagement with Ludwig Wittgenstein, Clifford Geertz, and Erich Auerbach, as well as his use of ordinary language philosophy and non-foundational philosophical insights, while illuminating his indebtedness to Karl Barth's theology. Moreover, by placing Frei's work in critical conversation with developments in pragmatist thought and cultural theory since his death, this re-reading aims to resolve many of the misunderstandings that vex his theological legacy. What emerges from Toward a Generous Orthodoxy is a sharpened account of the christologically anchored, interdisciplinary, and conversational character of Frei's theology, one he came to describe as a "generous orthodoxy"--modeling a way for academic theological voices to take seriously both their vocation to the Christian church and their roles as interlocutors in academic discourse. (shrink)

Amid the debates over the meaning and usefulness of the word “culture” during the 1980s and 90s, practice theory emerged as a framework for analysis and criticism in cultural anthropology. While theorists have gradually begun to explore practice-oriented frameworks as promising vistas in cultural anthropology and the study of religion, these remain relatively recent developments that stand to be historically explicated and conceptually refined. This article assesses several ways that practice theory has been articulated by some of its chief expositors (...) and critics, and places these developments in conversation with comparable accounts of “social practices” by recent pragmatist philosophers. My aim in generating such a conversation is to illuminate the ways that Ludwig Wittgenstein’s later work provides important resources for cultural analysis that are already implicit in practice theory, yet either frequently overlooked or dismissed by practice theorists. To demonstrate its relevance for cultural theorists in the study of religion, I show how such a Wittgensteinian understanding of practice theory coheres with, and illuminates, Clifford Geertz’s account of meaning, thick description and religious practices. (shrink)

This essay responds to four critical essays by Rosemary Kellison, Ebrahim Moosa, Joseph Winters, and Martin Kavka on the author’s recent book, Healthy Conflict in Contemporary American Society: From Enemy to Adversary (Cambridge, 2018). Parts I and II work in tandem to further develop my accounts of strategic empathy and agonistic political friendship. I defend against criticisms that my argument for moral imagination obligates oppressed people to empathize with their oppressors. I argue, further, that healthy conflict can be motivated by (...) a kind of “secular” love. This enables my position to immanently criticize and mediate the claims that one must either love (agapically) one’s opponent in order to engage them in “healthy conflict,” on one hand, or that one must vanquish, exclude, or “cancel” one’s opponent, on the other. In Part III, I demonstrate how my account mediates the challenge of an alleged standing opposition between moral imagination and socio-theoretical critique. I defend a methodologically pragmatist account of immanent prophetic criticism, resistance, and conflict transformation. Finally, I respond to one critic’s vindication of a strong enemy/adversary opposition that takes up the case of white supremacist violence in the U.S. I argue that the time horizon for healthy conflict must be simultaneously immediate and also long-term, provided that such engagements remain socio-critically self-reflexive and seek to cultivate transformational responses. (shrink)

This essay clarifies and defends the methodological multidimensionality and improvisational character of Clifford Geertz’s account of interpretation and explanation. In contrast to accounts of power analysis offered by Michel Foucault and Talal Asad, I argue that Geertz’s work can simultaneously attend to meaning, power, identity, and experience in understanding and assessing religious practices and cultural formations.

Is the institutionalization of religious freedom through human rights jurisprudence simply a means by which the modern nation-state manufactures and regulates “religion”? Is the discourse of religious freedom principally a technology of state governance? These questions challenge the ways that scholars conceptualize the relation between states, nationalism, human rights, and religious freedom. This article forwards an approach to human rights and methodological nationalism that both counters and explores alternatives to the prevailing conceptions of human rights, nationalism, and state sovereignty in (...) the discourse on the putative impossibility—and, by some accounts, insidiousness—of religious freedom. I first explicate the interpretive and contestatory dimensions of human rights discourse concerning religious freedom. I then explore cross-cutting ambivalences within the nationalisms that states need and cultivate in effort to transmute their monopoly upon coercive force (i.e. power) into legitimated authority. I argue that these provide two dimensions in and through which state sovereignty may be opposed, criticized, held accountable, and subject to change. (shrink)

This paper explores the difference it makes to incorporate the multi-focal conception of violence that has emerged in peace studies over recent decades into the discourse of non-violent direct action (Galtung 1969, 1990; Uvin 2003; Springs 2015b). I argue that non-violent action can and should incorporate and deploy the distinctions between direct, cultural, and structural forms of violence. On one hand, these analytical distinctions can facilitate forms of self-reflexive critical analysis that guard against certain violent conceptual and practical implications of (...) non-violence, however inadvertent those may be. At the same time, these lenses help reconceptualise non-violent action in ways that open up an array of strategies and tools not previously prevalent among activists committed to non-violence. Non-violent action may itself be either complicit in, or might be enabled to illuminate and cut against, forms of violence that infuse social, political, and economic structures (i.e. structural violence). Appeals to non-violence and the actions with which they interweave may be complicit in, or might be enabled to illuminate and cut against, religious, ideological, aesthetic, and even scientific understandings and conceptual frames that underpin and support structural violence (i.e. cultural violence). In each case, non- violence must be critically examined with all these possibilities in mind. I first define and contextualize a multidimensional account of violence in terms of direct, structural, and cultural violence. I then consider two examples of how it challenges thinking about non-violence. (shrink)

Religious nationalism is a complex topic fraught with sensitive questions. Does religion cause violence? Is nationalism a quasi-religion? Are the constant conflicts around the world really about religion, or is religion merely a form of false consciousness? Is religious nationalism primarily a powerful tool that political elites use to manipulate the masses? -/- Religious Nationalism: A Reference Handbook challenges dominant scholarly works on religious nationalism by identifying the preconceptions that skew analysis of the phenomenon dubbed “religious nationalism.” The book utilizes (...) a multidisciplinary approach that draws insight from theories of nationalism, religious studies, peace research, and political theory, and reframes the questions of religious nationalism within the perspectives of secularism, modernity, and Orientalism. In doing so, the authors enable readers to uncover their own presumptions regarding the role of religion in public life. The work also outlines connections between the analysis of the role of religion in conflict to thoughts regarding how religion may relate to processes of peacebuilding and conflict transformation, and further connects the discussion of religious nationalism to broader conversations on the so-called resurgence of religion. (shrink)

In this paper I critically explore the possibility that the hope for engaging in democratic discourse and coalition-building across deep— potentially irreconcilable— moral, religious divisions in current U.S. public life depends less upon further calls for “more tolerance,” and instead in thinking creatively and transformatively about how to democratize and constructively utilize conflict and intolerance. Is it possible to distinguish between constructive and destructive forms of intolerance? If so, what are the prospects for re-orienting analysis of democratic practices and processes (...) so that what typically appear as forms of simple intolerance (and thus, as candidates for marginalization or exclusion from political processes) might be reconceived and re-directed for the purposes of constructively transforming those practices and processes? Further, what would an analytical framework that aimed to distinguish and cultivate “healthy conflict” in contrast to degenerative or destructive conflict look like? How would such an approach facilitate efforts on the ground to recognize, understand and transform religiously-motivated conflict? I pose answers to these questions by bringing strands from the “religion in public life” debates that have unfolded over recent decades among ethicists and political philosophers into conversation with conflict transformation literature in peace studies. Bridging these resources will help to re-conceptualize basic assumptions about tolerance and conflict as a pivotal first step in constructively transforming conflicts motivated by, or identified with, moral commitments and religious identities. (shrink)

This article provides an exposition of restorative justice ethics, briefly explaining how and why its relational constitution enables it to comprise a theory of justice. I then describe how that relational constitution permits it to overlap, and work in tandem, with a wide range of religious and philosophical traditions. Numerous writings in religion and peacebuilding explore the roles that restorative justice has played in transitional justice contexts (Tutu 2000, Abu-Nimer 2001, de Gruchy 2002, Biggar 2003, Walker 2004, Villa-Vicencio 2009). Less (...) examined are cases in which restorative justice aims to provide a sustainable alternative to justice institutions and systems that generate substantial systemic injustices—what peace studies scholars describe as the inter-lacing of structural, cultural, and direct forms of violence (Springs 2015). In part two, then, I make the case that intervening in, and countering, structural and cultural violence, and systemic injustices, is conceptually intrinsic to restorative justice. Moreover, this opens possibilities for restorative justice to present sustainable alternatives to—and work to transform— structural violence occurring in retributive justice systems. Restorative justice can uniquely intervene in these ways, I argue, because of the form of moral and spiritual association its relational constitution engenders. As a test case, I briefly examine its capacity to intervene in the justice system that perhaps leads the world in the levels of structural and cultural violence—the United States. (shrink)

Just as Quine and others have argued for a deflationism about the property of truth, Sinan Dogramaci has argued for a deflationism about rationality. Specifically, Dogramaci claims that we have no reason to think that the basic, deductive, epistemic rules we call “rational” have any sort of “unifying property.” A “unifying property” is a property that is necessary, sufficient, and explanatorily illuminating. My goal in this paper is to undermine Dogramaci’s argument for this radical position. I do this by first (...) outlining Dogramaci’s distinctive view on the function of our epistemically evaluative terms. This view, called epistemic communism, has it that the function of terms like “rational” is to support the coordination of our community on a single set of epistemic rules. I offer a reconstruction of Dogramaci’s argument from epistemic communism to deflationism about rationality. I next raise an objection to Dogramaci’s argument: different sets of epistemic rules do not equally support the coordinative function. Dogramaci has a response to this objection, but I argue that this response is less than satisfactory. I illustrate that this response is unsatisfactory by employing work by David Enoch and Joshua Schechter. After pushing my objection to Dogramaci’s argument, I develop, on Dogramaci’s behalf, an objection to my non-deflationary attempt to undermine his argument. In the final section of the paper, I reply to this objection offered on Dogramaci’s behalf and conclude that whether we are epistemic communists or not, we need not accept deflationism. (shrink)

This paper explores the “cultural-linguistic” dimensions of Hans Frei’s theology. I make the case that several of the pragmatic and sociological concerns usually identified as distinctive marks of Frei’s later theology of the 1980s are, in fact, central to his work as far back as the early 1960s. Moreover, I demonstrate that such “cultural-linguistic” insights present important continuous threads in the development of his theology from early to late. Attending to this dimension illuminates the trajectory of Frei’s thinking as consistently (...) Wittgensteinian in sensibility, and deeply indebted to his career-long conversation with Karl Barth’s theology. If successful, this reading should clarify the ways in which Frei’s early work is more innovative, and his later work less derivative, than is often recognized. (shrink)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

In his 1993 article George Bealer offers three separate arguments that are directed against the internal coherence of empiricism, specifically against Quine’s version of empiricism. One of these arguments is the starting points argument (SPA) and it is supposed to show that Quinean empiricism is incoherent. We argue here that this argument is deeply flawed, and we demonstrate how a Quinean may successfully defend his views against Bealer’s SPA. Our defense of Quinean empiricism against the SPA depends on showing (1) (...) that Bealer is, in an important sense, a foundationalist, and (2) that Quine is, in an important sense, a coherentist. Having established these two contentions we show that Bealer’s SPA begs the question against Quinean empiricists. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (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)

A key source of support for the view that challenging people’s beliefs about free will may undermine moral behavior is two classic studies by Vohs and Schooler (2008). These authors reported that exposure to certain prompts suggesting that free will is an illusion increased cheating behavior. In the present paper, we report several attempts to replicate this influential and widely cited work. Over a series of five studies (sample sizes of N = 162, N = 283, N = 268, N (...) = 804, N = 982) (four preregistered) we tested the relationship between (1) anti-free-will prompts and free will beliefs and (2) free will beliefs and immoral behavior. Our primary task was to closely replicate the findings from Vohs and Schooler (2008) using the same or highly similar manipulations and measurements as the ones used in their original studies. Our efforts were largely unsuccessful. We suggest that manipulating free will beliefs in a robust way is more difficult than has been implied by prior work, and that the proposed link with immoral behavior may not be as consistent as previous work suggests. (shrink)

Changes in an upper level ontology have obvious conse-quences for the domain ontologies that use it at lower levels. It is therefore crucial to document the changes made between successive versions of ontologies of this kind. We describe and apply a method for tracking, explaining and measuring changes between successive versions of upper level ontologies such as the Basic Formal Ontology (BFO). The proposed change-tracking method extends earlier work on Realism-Based Ontology Versioning (RBOV) and Evolutionary Terminology Auditing (ETA). We describe (...) here the application of this evaluation method to changes between BFO 1.0, BFO 1.1, and BFO 2.0. We discuss the issues raised by this application and describe the extensions which we added to the original evaluation schema in order to account for changes in an ontology of this type. Our results show that BFO has undergone eight types of changes that can be systematically explained by the extended evaluation schema. Finally, we discuss problematic cases, possible pitfalls and certain limits of our study that we propose to address in future work. (shrink)

Objective: Compassion has been associated with eudaimonia and prosocial behavior, and has been regarded as a virtue, both historically and cross-culturally. However, the psychological study of compassion has been limited to laboratory settings and/or standard survey assessments. Here, we use an experience sampling method (ESM) to compare naturalistic assessments of compassion with standard assessments, and to examine compassion, its variability, and associations with eudaimonia and prosocial behavior. -/- Methods: Participants took a survey which included standard assessments of compassion and eudaimonia. (...) Then, over four days, they were repeatedly asked about their level of compassion, eudaimonia, and situational factors within the moments of daily life. Finally, prosocial behavior was tested using the Dual Gamble Task and an opportunity to donate task winnings. -/- Results: Analyses revealed within-person associations between ESM compassion and eudaimonia. ESM compassion also predicted eudaimonia at the next ESM time point. While not impervious to situational factors, considerable consistency was observed in ESM compassion in comparison with eudaimonia. Further, ESM compassion along with eudaimonia predicted donating behavior. Standard assessments did not. -/- Conclusion: Consistent with virtue theory, some individual’s reports displayed a probabilistic tendency toward compassion, and ESM compassion predicted ESM eudaimonia and prosocial behavior toward those in need. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

In this paper we examine to what extent the lengths of the links in an animated articulated figure can be changed without the viewer being aware of the change. This is investigated in terms of a framework that emphasizes the role of attention in visual perception. We conducted a set of five experiments to establish bounds for the sen-sitivity to changes in length as a function of several parameters and the amount of attention available. We found that while length changes (...) of 3% can be perceived when the relevant links are given full attention, changes of over 20% can go unnoticed when attention is not focused in this way. These results provide general guidelines for algorithms that produce or process character motion data and also bring to light some of the potential gains that stand to be achieved with attention-based algorithms. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

This paper describes an AFOSR-supported basic research program that focuses on developing a new framework for combining hard with soft data in order to improve space situational awareness. The goal is to provide, in an automatic and near real-time fashion, a ranking of possible threats to blue assets (assets trying to be protected) from red assets (assets with hostile intentions). The approach is based on Conceptual Spaces models, which combine features from traditional associative and symbolic cognitive models. While Conceptual Spaces (...) are revolutionary, they lack an underlying mathematical framework. Several such frameworks have attempted to represent Conceptual Spaces, but by far the most robust is the model developed by Holender. His model utilizes integer linear programming in order to obtain an overall similarity value between observations and concepts that support the formation of hypotheses. This paper will describe a method for building Conceptual Spaces models for threats that utilizes ontologies as a means to provide a clear semantic foundation for this inferencing process; in particular threat ontologies and space domain ontologies are developed and employed in this approach. A space situational awareness use-case is presented involving a kinetic kill scenario and results are shown to assess the performance of this fusion-based inferencing framework. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

Induced by intake of the psychedelic substances LSD, psilocybin, DMT and mescaline, psychedelic experiences have been extensively described by subjects as entailing a most unusual increase in the scope and quality of their consciousness. Accordingly, psychedelic experiences have been widely characterised as an “expansion of consciousness.” This article poses the following question, as yet unaddressed in contemporary philosophy and the tradition of phenomenology: to what exactly does “expansion of consciousness” refer as a general characterisation of psychedelic experiences, and what role (...) might attention play therein? On the basis of Aron Gurwitsch’s phenomenology of attention, the following thesis is presented: (a) “expansion of consciousness” refers to a particular restructuration of consciousness in psychedelic experiences. (b) This occurs by means of certain extreme transformations in direction, scope, mode and degree of attention. In order to explicate this thesis, the characteristic features of psychedelic experiences that pertain to expansion of consciousness and attention are first systematically identified from a survey of subject reports. Second, it is demonstrated that the few previous attempts to understand expansion of consciousness in terms of attention as a filter/reducing-valve, spotlight or zoom-lens each fail to explain how consciousness is structured in psychedelic experiences. Third, it is argued that psychedelic expansion of consciousness is a general restructuration of consciousness by means of extreme attentional transformations. In conclusion, brief consideration is given to the question of whether psychedelic expansion of consciousness can have epistemic and ethical value for life. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

Doing Practical Ethics supports the deliberate practice of philosophical skills relevant to understanding, evaluating, and developing arguments in forms commonly used in the field of practical ethics. Each chapter includes an explanation of a specific moral reasoning skill, demonstration exercises with sample solutions that offer students immediate feedback on their initial practice attempts, and extensive sets of practice exercises. It is suitable for any ethics course that centrally features argument from principle, argument from analogy, or inference to the best explanation. (...) It may be used as a standalone text in a debate-focused course. Paired with an anthology in a readings-focused course, it will help students develop the skills they need to understand and evaluate the arguments in the assigned readings. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

Given the significance of Nicholas of Cusa’s ecclesiastical career, it is no surprise that a good deal of academic attention on Nicholas has focused on his role in the history of the church. Nevertheless, it would also be fair to say that a good deal of the attention that is focused on the life and thought of Nicholas of Cusa is the legacy of prior generations of scholars who saw in his theoretical work an opportunity to define the most salient (...) features of transformations in the habits of thinking leading from the Middle Ages into the epoch of modernity. Thus, although contemporary scholars have not been able to achieve any clear consensus on the question of whether Nicholas belongs to the Middle Ages or to modernity, the field of Cusanus studies has become much more attentive to the possibility that the uniqueness and significance of Nicholas’s vision is a function of his ability to synthesize and redeploy a variety of strands in the Catholic intellectual tradition—strands that are as apt to involve practical matters of canon law and church reform as they are to hinge on a unique and richly developed mystical theology. Given the flourishing of the attention devoted to Nicholas in the late 20th and early 21st centuries, the choices about which texts to include in this article were difficult ones. The rationale for this article’s predominant focus on scholarship of the late 20th and early 21st centuries is that, insofar as the recent studies listed here enter into the debates that have been shaped by their predecessors, the sources mentioned here will point readers to the prior work in the field not acknowledged here. (shrink)

Discussions concerning whether there is a natural right to health care may occur in various forms, resulting in policy recommendations for how to implement any such right in a given society. But health care policies may be judged by international standards including the UN Universal Declaration of Human Rights. The rights enumerated in the UDHR are grounded in traditions of moral theory, a philosophical analysis of which is necessary in order to adjudicate the value of specific policies designed to enshrine (...) rights such as a right to health care. We begin with an overview of the drafting of the UDHR and highlight the primary influence of natural law theory in validating the rights contained therein. We then provide an explication of natural law theory by reference to the writings of Thomas Aquinas, as well as elucidate the complementary “capabilities approach” of Martha Nussbaum. We conclude that a right to health care ought to be guaranteed by the state. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

This paper challenges the common assumption that perceptual episodes are bearers of representational content by developing a naïve realist theory of perception that can account for a number of central perceptual phenomena.