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)

In lieu of an abstract, here is a brief excerpt of the content:"And They Sang A New Song":Reading John's Revelation From The Position Of The LambJ.A. Jackson (bio) and Allen H. Redmon (bio)Then one of the elders said to me, "Do not weep. See, the Lion of the tribe of Judah, the Root of David, has conquered, so that he can open the scroll and the seven seals." Then I saw between the throne and the four living creatures and (...) among the elders a Lamb standing as if it had been slaughtered.—Revelation 5:5–6In an interview with Markus Müller, René Girard asserts the importance of taking into account the apocalypticism of Christianity. Apocalypse, Girard reminds us, "means revelation: apocalypto means to open up and to show the truth. But it also means absolute violence, so the apocalypse is a violent revelation and a revelation of violence" (Girard 1996). That the Revelation is a violent revelation has been well established. Despite textual evidence that would beg those who approach the text to do just the opposite, readers have fixated on the violence of the Revelation since its inception, finding in it God's final retribution against those who persecute the Church.1 Commentators such as Dennis E. Johnson, William Hendricksen, and George Elden Ladd have produced recent, full-length commentaries that champion the appearance of a Christ in Revelation ready to establish himself as a military champion and exact his revenge on those who persecute him (see, for example, Johnson 2001; Hendricksen 1998; and Ladd 1993). These accounts, and those that follow suit, are blinded by the violent revelation of John's apocalyptic narrative and fail to see the poem's revelation of violence—the other, prophetic half of what Girard rightly contends exists in Christian apocalypse.This error is understandable to some extent. Read in its own light and apart from the Gospel revelation as understood by those familiar with mimetic [End Page 99] theory, one has no hermeneutical principle for recognizing the end to which John is writing. The victims of the text can be ignored in the precise way that all victims are disregarded when the scapegoat mechanism functions properly. Such should not be the case in the Revelation, though, a text in which the scapegoat mechanism is exposed and pushed to its logical conclusions. John offers his reader a glimpse into the way this mechanism will function when all that is left is wall-to-wall violence, when one is left with only two alternatives: succumb to the mechanism and reciprocate its violence, or extricate oneself through nonreciprocation (and potentially die).In the margins of the violent revelation in John's apocalyptic vision, a revelation of violence emerges that can expose humankind's potential to annihilate itself and the mechanism with which it will do so. When read through the lens of mimetic theory, one discovers that John's narrative delivers a revelation of violence, an explicit naming and unmasking of the sacrificial mechanism that can capture for the reader not only the machinations of the sacrificial apparatus but one's own potential participation in it as well. As such, the poem can posit itself as a commandment (a Thou-shall-not-murder) that ultimately refuses the temptation to respond to violence in violence.The fact that John uses the apocalyptic to present this directive should not be surprising. Girard writes: "Only through the mediation of the scapegoat mechanism can violence become its own remedy, and the victimage mechanism can only be triggered by the frenetic paroxysm of the 'crisis.' This means that the violence, having lost its vitality and bite, will paradoxically be more terrible than before its decline. As the whole of humanity makes the vain effort to reinstate its reconciliatory and sacrificial virtues, this violence will without doubt tend to multiply its victims, just as happened in the time of the prophets" (Girard 1978, 195–96). While Girard's commentary on biblical eschatology and apocalypse refers mainly to the scapegoat mechanism as it applies to and is revealed in the Gospel texts, we see the immediacy and the frenzy of the apocalyptic and the ubiquitous violent mimetic appropriations also performed in John's Revelation.2 John captures... (shrink)

Empirical studies have suggested that language-capable robots have the persuasive power to shape the shared moral norms based on how they respond to human norm violations. This persuasive power presents cause for concern, but also the opportunity to persuade humans to cultivate their own moral development. We argue that a truly socially integrated and morally competent robot must be willing to communicate its objection to humans’ proposed violations of shared norms by using strategies such as blame-laden rebukes, even if doing (...) so may violate other standing norms, such as politeness. By drawing on Confucian ethics, we argue that a robot’s ability to employ blame-laden moral rebukes to respond to unethical human requests is crucial for cultivating a flourishing “moral ecology” of human–robot interaction. Such positive moral ecology allows human teammates to develop their own moral reflection skills and grow their own virtues. Furthermore, this ability can and should be considered as one criterion for assessing artificial moral agency. Finally, this paper discusses potential implications of the Confucian theories for designing socially integrated and morally competent robots. (shrink)

William Whewell is considered one of the most important nineteenth-century British philosophers of science and a contributor to modern philosophical thought, particularly regarding the problem of induction and the logic of discovery. In this volume, Robert E. Butts offers selections from Whewell's most important writings, and analysis of counter-claims to his philosophy.

In _Facing the Planetary_ William E. Connolly expands his influential work on the politics of pluralization, capitalism, fragility, and secularism to address the complexities of climate change and to complicate notions of the Anthropocene. Focusing on planetary processes—including the ocean conveyor, glacier flows, tectonic plates, and species evolution—he combines a critical understanding of capitalism with an appreciation of how such nonhuman systems periodically change on their own. Drawing upon scientists and intellectuals such as Lynn Margulis, Michael Benton, Alfred North (...) Whitehead, Anna Tsing, Mahatma Gandhi, Wangari Maathai, Pope Francis, Bruno Latour, and Naomi Klein, Connolly focuses on the gap between those regions creating the most climate change and those suffering most from it. He addresses the creative potential of a "politics of swarming" by which people in different regions and social positions coalesce to reshape dominant priorities. He also explores how those displaying spiritual affinities across differences in creed can energize a militant assemblage that is already underway. (shrink)

But in Why I Am Not a Secularist, distinguished political theorist William E. Connolly argues that secularism, although admirable in its pursuit of freedom and diversity, too often undercuts these goals through its narrow and intolerant ...

Over the past two decades, the renowned political theorist William E. Connolly has developed a powerful theory of pluralism as the basis of a territorial politics. In this concise volume, Connolly launches a new defense of pluralism, contending that it has a renewed relevance in light of pressing global and national concerns, including the war in Iraq, the movement for a Palestinian state, and the fight for gay and lesbian rights. Connolly contends that deep, multidimensional pluralism is the best (...) way to promote justice and inclusion without violence. He advocates a deep pluralism—in contrast to shallow, secular pluralism—that helps to create space for different groups to bring their religious faiths into the public realm. This form of deep pluralism extends far beyond faith, encompassing multiple dimensions of social and personal lives, including household organization and sexuality. Connolly looks at pluralism not only in light of faith but also in relation to evil, ethics, relativism, globalization, and sovereignty. In the process, he engages many writers and theorists—among them, Spinoza, William James, Henri Bergson, Marcel Proust, Gilles Deleuze, Giorgio Agamben, Talal Asad, Michael Hardt, and Antonio Negri. _Pluralism_ is the first book in which Connolly explains the relationship between pluralism and the experience of time, and he offers readings of several films that address how time is understood, including _Time Code_, _Far from Heaven_, _Waking Life_, and _The Maltese Falcon_. In this necessary book Connolly brings a compelling, accessible philosophical critique together with his personal commitment to an inclusive political agenda to suggest how we might—and why we must—cultivate pluralism within both society and ourselves. (shrink)

Macphail’s “null hypothesis,” that there are no differences in intelligence, qualitative, or quantitative, between non-human vertebrates has been controversial. This controversy can be useful if it encourages interest in acquiring a detailed understanding of how non-human animals express flexible problem-solving capacity (“intelligence”), but limiting the discussion to vertebrates is too arbitrary. As an example, we focus here on Portia, a spider with an especially intricate predatory strategy and a preference for other spiders as prey. We review research on pre-planned detours, (...) expectancy violation, and a capacity to solve confinement problems where, in each of these three contexts, there is experimental evidence of innate cognitive capacities and reliance on internal representation. These cognitive capacities are related to, but not identical to, intelligence. When discussing intelligence, as when discussing cognition, it is more useful to envisage a continuum instead of something that is simply present or not; in other words, a continuum pertaining to flexible problem-solving capacity for “intelligence” and a continuum pertaining to reliance on internal representation for “cognition.” When envisaging a continuum pertaining to intelligence, Daniel Dennett’s notion of four Creatures (Darwinian, Skinnerian, Popperian, and Gregorian) is of interest, with the distinction between Skinnerian and Popperian Creatures being especially relevant when considering Portia. When we consider these distinctions, a case can be made for Portia being a Popperian Creature. Like Skinnerian Creatures, Popperian Creatures express flexible problem solving capacity, but the manner in which this capacity is expressed by Popperian Creatures is more distinctively cognitive. (shrink)

In _The Fragility of Things_, eminent theorist William E. Connolly focuses on several self-organizing ecologies that help to constitute our world. These interacting geological, biological, and climate systems, some of which harbor creative capacities, are depreciated by that brand of neoliberalism that confines self-organization to economic markets and equates the latter with impersonal rationality. Neoliberal practice thus fails to address the fragilities it exacerbates. Engaging a diverse range of thinkers, from Friedrich Hayek, Michel Foucault, Hesiod, and Immanuel Kant to (...) Voltaire, Terrence Deacon, Friedrich Nietzsche, and Alfred North Whitehead, Connolly brings the sense of fragility alive as he rethinks the idea of freedom. Urging the Left not to abandon the state but to reclaim it, he also explores scales of politics below and beyond the state. The contemporary response to fragility requires a militant pluralist assemblage composed of those sharing affinities of spirituality across differences of creed, class, gender, sexual orientation, and ethnicity. (shrink)

Complexity, agency, and time -- The vicissitudes of experience -- Belief, spirituality, and time -- The human predicament -- Capital flows, sovereign decisions, and world resonance machines -- The theorist and the seer.

A representationalist-friendly introduction to representationalism which covers a number of central problems and objections.

An impressive body of recent literature posits that traditional notions of civil disobedience prevent us from properly considering potentially legitimate types of ‘uncivil’ political lawbreaking. When might uncivil (covert, legally evasive, morally offensive and potentially violent) lawbreaking prove normatively acceptable? If justifiable, what conditions should its practitioners be reasonably expected to meet? Despite some important insights, defenders of uncivil disobedience rely on a narrow and sometimes misleading view of civil disobedience, as previously practiced and theorized. Notwithstanding legitimate skepticism about Rawlsian (...) notions of civil disobedience, they reproduce its troublesome binary or ‘all-or-nothing’ view of political lawbreaking. Uncivil disobedience’s proponents tend to group a vast array of distinctive types of lawbreaking under one amorphous categorical rubric, impeding the suitably complex, nuanced analysis we need. A superior approach would pay careful attention to uncivil disobedience’s ambivalent historical record, a record suggesting that UD is more likely to reproduce authoritarian populism’s disturbing political logic than counteract it. (shrink)

Does a hard-headed realist approach to international politics necessarily involve scepticism towards progressive foreign policy initiatives and global reform? Should proponents of realism always be seen as morally complacent and politically combative? In this major reconsideration of the main figures of international political theory, Bill Scheuerman challenges conventional wisdom to reveal a neglected tradition of progressive realism with much to contribute to contemporary debates about international policy-making and world government. Far from seeing international reform as well-meaning but potentially irresponsible idealism, (...) progressive realists like E.H. Carr, John Herz, Hans J. Morgenthau, and Reinhold Niebuhr developed forward-looking ideas which offer an indispensable corrective to many presently influential views about global politics. Progressive realism, Scheuerman argues, offers a compelling and provocative vision of radical global change which - when properly interpreted, can help buttress current efforts to address the most pressing international issues. After recovering key subterranean strands in mid-twentieth century realism, Scheuerman underscores their relevance to contemporary international theory. Criticizing more recent realists for abandoning their tradition's best insights, he also demonstrates that reform-minded international theories - including versions of cosmopolitanism, constructivism, the English School, liberalism, and republicanism - could all benefit from taking Progressive Realism seriously. A major contribution both to the history of international relations and contemporary debates in international theory, The Realist Case for Global Reform concludes by considering how progressive realism informs the foreign policies of US President Barack Obama. (shrink)

The media hoop-la about Edward Snowden has obscured a less flashy yet more vital – and philosophically relevant – part of the story, namely the moral and political seriousness with which he acted to make the hitherto covert scope and scale of NSA surveillance public knowledge. Here I argue that we should interpret Snowden’s actions as meeting most of the demanding tests outlined in sophisticated political thinking about civil disobedience. Like Thoreau, Gandhi, King and countless other (forgotten) grass-roots activists, Snowden (...) has in fact articulated a powerful defense of why he was morally obligated to engage in politically motivated law-breaking. He has also undertaken impressive efforts to explain how his actions are distinguishable from ordinary criminality, and why they need not culminate in reckless lawlessness. In fact, his example can perhaps help us advance liberal and democratic ideas about civil disobedience. First, it highlights sound reasons why, pace the orthodox view, the acceptance of punishment by those engaging in civil disobedience should not be seen as a precondition of its legitimacy. Second, Snowden reminds us that ours is an era in which intensified globalization processes directly shape every feature of political existence. Defenders of civil disobedience need to update their reflections accordingly. (shrink)

The ideas of Hans Morgenthau dominated the study of international politics in the United States for many decades. He was the leading representative of Realist international relations theory in the last century and his work remains hugely influential in the field. In this engaging and accessible new study of his work, William E. Scheuerman provides a comprehensive and illuminating introduction to Morgenthau’s ideas, and assesses their significance for political theory and international politics. Scheuerman shows Morgenthau to be an uneasy (...) Realist, uncomfortable with conventional notions of Realism and sometimes unsure whether his reflections should be grouped under its rubric. He was a powerful critic of the existing state system and defended the idea of a world state. By highlighting Morgenthau’s engagement with the leading lights of European political and legal theory, Scheuerman argues that he developed a morally demanding political ethics and an astute diagnosis of the unprecedented perils posed by nuclear weaponry. Believing that the irrationalities of US foreign policy were rooted partly in domestic factors, he sympathized with demands for radical political and social change. Scheuerman illustrates that Morgenthau’s thinking has been widely misunderstood by both disciples and critics and that it offers many challenges to contemporary Realists who discount his normative aspirations. With the advent of the cosmopolitan goal of international reform, Morgenthau’s work serves up an unsettling mix of sympathy and hard-headed skepticism which remains crucially important in the development of the field. Lucidly and persuasively written, this book will be a valuable resource for students and scholars seeking to understand the continued importance of Morgenthau’s thinking. (shrink)

Strawson’s case in favor of panpsychism is at heart an updated version of a venerable form of argument I’ll call the ‘intrinsic nature’ argument. It is an extremely interesting argument which deploys all sorts of high caliber metaphysical weaponry (despite the ‘down home’ appeals to common sense which Strawson frequently makes). The argument is also subtle and intricate. So let’s spend some time trying to articulate its general form.

This study examines the effects of nationality (U.S. vs. China) and personal values on managers’ responses to the Perceived Role of Ethics and Social Responsibility (PRESOR) scale. Evidence that China’s transition to a socialist market economy has led to widespread business corruption, led us to hypothesize that People’s Republic of China (PRC) managers would believe less strongly in the importance of ethical and socially responsible business conduct. We also hypothesized that after controlling for national differences, managers’ personal values (more specifically, (...) self-transcendence values) would have a significant impact on PRESOR responses. The hypotheses were tested using a sample of practicing managers enrolled in part-time MBA programs in the two countries. The results indicate that nationality did not have a consistent impact on PRESOR responses. After controlling for national differences, self-transcendence values had a significant positive impact on two of the three PRESOR dimensions. Conservation values such as conformity and tradition also had a significant association with certain dimensions of the PRESOR scale. (shrink)

"Fractal" is a term coined by mathematician Benoit Mandelbrot to denote the geometry of nature, which traces inherent order in chaotic shapes and processes. Fractal concepts are part of our emerging vocabulary and can be useful in identifying patterns of human behavior, culture, and history, while enhancing our understanding of the nature of consciousness. According to William J. Jackson, the more one studies fractals, the more apparent their connections to the humanities become. In the recursive patterns of religious (...) music, in temple architecture in India, in cathedral structures in Europe and America, in the imagery of religious literature depicting infinity and abundance, and in poetic descriptions of the nature of consciousness, fractal-like configurations are pervasive. Recognition of this structure, which is also found in social organizations and ritual symbolism, requires only that one develop "an eye for fractals" by studying the work of researchers and observing nature. One then begins to see that the separation of humanities and science is convenient oversimplification, not an ultimate fact. Includes a DVD of animated fractals. (shrink)

This is the first full-length study in English of twentieth-century Germany's most influential authoritarian right-wing political theorist, Carl Schmitt, that focuses on the central place of his attack on the liberal rule of law. This is also the first book in any language to devote substantial attention to Schmitt's subterranean influence on some of the most important voices in political thought in the United States after 1945.

The Perceptual Hypothesis is that we sometimes see, and thereby have non-inferential knowledge of, others' mental features. The Perceptual Hypothesis opposes Inferentialism, which is the view that our knowledge of others' mental features is always inferential. The claim that some mental features are embodied is the claim that some mental features are realised by states or processes that extend beyond the brain. The view I discuss here is that the Perceptual Hypothesis is plausible if, but only if, the mental features (...) it claims we see are suitably embodied. Call this Embodied Perception Theory. I argue that Embodied Perception Theory is false. It doesn't follow that the Perceptual Hypothesis is implausible. The considerations which serve to undermine Embodied Perception Theory serve equally to undermine the motivations for assuming that others' mental lives are always imperceptible. (shrink)

Images portraying exercise are commonly used to promote exercise behavior and to measure automatic associations of exercise (e.g., via implicit association tests). The effectiveness of these promotion efforts and the validity of measurement techniques partially rely on the untested assumption that the images being used are perceived by the general public as portrayals of exercise that is pleasant and motivating. The aim of this study was to investigate how content of images impacted people's automatic and reflective evaluations of exercise images. (...) Participants ( N = 90) completed a response time categorization task (similar to the implicit association test) to capture how automatically people perceived each image as relevant to Exercise or Not exercise. Participants also self-reported their evaluations of the images using visual analog scales with the anchors: Exercise / Not exercise, Does not motivate me to exercise / Motivates me to exercise, Pleasant / Unpleasant, and Energizing/Deactivating. People tended to more strongly automatically associate images with exercise if the images were of an outdoor setting, presented sport (as opposed to active labor or gym-based) activities, and included young (as opposed to middle-aged) adults. People tended to reflectively find images of young adults more motivating and relevant to exercise than images of older adults. The content of exercise images is an often overlooked source of systematic variability that may impact measurement validity and intervention effectiveness. (shrink)

This study proposes and tests a model of the relations among corporate accountants’ perceptions of the ethical climate in their organization, the perceived importance of corporate ethics and social responsibility, and earnings management decisions. Based on a field survey of professional accountants employed by private industry in Hong Kong, we found that perceptions of the organizational ethical climate were significantly associated with belief in the importance of corporate ethics and responsibility. Belief in the importance of ethics and social responsibility was (...) also significantly associated with accountants’ ethical judgments and behavioral intentions regarding accounting and operating earnings manipulation. These findings suggest that perceptions of ethical climate, usually presumed to reflect the “tone at the top” in the organization, lead accounting professionals to rationalize earnings management decisions by adjusting their attitudes toward the importance of corporate ethics and social responsibility. This is the first study to document a relationship between organizational ethical climate and professional accountants’ support for corporate ethics and social responsibility, and also the first study to document that industry accountants’ views toward corporate ethics and social responsibility are associated with their willingness to manipulate earnings. The findings have important implications, suggesting that organizational efforts to enhance the ethical climate and emphasize the importance of corporate ethics and social responsibility could reduce the prevalence of earnings manipulation. (shrink)

To be ashamed of one's immorality—that is a step on the staircase at whose end one is also ashamed of one's morality. Friedrich Nietzsche.