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)

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.

This chapter contains sections titled: Serial Killers, Real and Imagined Dexter Gacy Are Serial Killers Morally Responsible? Moral Responsibility: Emotions and Cognitive Frames.

Paralogismen betreffs der Leibnizschen Prädikatlehre werden aufgezeigt und widerlegt. Enthaltensein heißt die Inverse von Ableitung; den zwei Arten von Ableitung, die Leibniz kennt, entsprechen zwei Arten von Enthaltensein. Die beiden Arten von Enthaltensein bieten Leibniz die Möglichkeit zu der logischen und irreduziblen Unterscheidung zwischen notwendigen und bedingten Wahrheiten. Die Unterscheidung zwischen einem Individuum und einer Eigenschaft wird mit mengentheoretischen Methoden und auch mit Hilfe von epistemologischen Begriffen untersucht. Die besondere kategorische Form des Aussagesatzes impliziert, daß es für alle Aussagesätze nur (...) eine einzige Tiefen-Grammatik gibt, welche wesentlich verschiedene Ausdruckweisen von kategorischen Aussagen umfaßt. (shrink)

The foundation of the Christian counselling movement -- Christian counselling in the UK -- The aims of Christian counselling -- Integrating psychological and biblical truth -- Sigmund Freud--the founding father of psychotherapy -- The individual psychology of Alfred Adler -- Abraham Maslow--the man with new age tendencies -- Carl Rogers--a man who believed in himself -- Albert Ellis--the aggressive atheist -- The Bible's verdict on psychological 'truth' -- The case against Larry Crabb -- Self-esteem: the secular foundation -- Self-esteem and (...) the Christian counselling movement -- Self-esteem dogma in the light of scripture. (shrink)

"Aristotle was a systematic writer who often cross-referred to the definitions of terms given elsewhere in his work. Book 5 of the Metaphysics is important because it consists of definitions of the main uses of key terms in Aristotle's philosophy, and it is extremely valuable to have a commentary on this important text by Alexander of Aphrodisias, the leading commentator of his school. Alexander provides a detailed commentary on all of the thirty terms analysed in Book 5, weighing alternative interpretations (...) of what Aristotle says one against another, defending Peripatetic views against actual and possible criticisms, and attempting to integrate what is said in Book 5 into the context of the Metaphysics as a whole."--Bloomsbury Publishing. (shrink)

1 Non-reductive physicalists deny that there is any explanation of mentality in purely physical terms, but do not deny that the mental is entirely determined by and constituted out of underlying physical structures. There are important issues about the stability of such a view which teeters on the edge of explanatory reductionism on the one side and dualism on the other (see Kim 1998). 2 Save perhaps for eliminative materialism (see Churchland 1981 for a classic exposition). In fact, however, while.

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)

In an essay entitled “Public Policy and Philosophical Critique: The William James and Theodore Roosevelt Dialogue on Strenuousness” Patrick Dooley examines the public discourse concerning the ebb and flow of moral energy that took place in America during twilight years of the nineteenth century. In it, he discusses how a diverse “community of investigators,” James and Roosevelt prominent among them, articulated a “common agenda of problems” in a cultural conversation concerning the benefits, moral as well as political, of (...) the strenuous life of energetic moral exertion.1This problem of moral energy rose to prominence in the waning decades of nineteenth century. This post-Civil War era proved to be an “especially... (shrink)

It is often assumed that when we see common opaque objects in standard light this is in virtue of seeing their facing surfaces. Here I argue that we should reject that claim. Either we don't see objects' facing surfaces, or—if we hold on to the claim that we do see such things—it is at least not in virtue of seeing them that we see common opaque objects. I end by showing how this conclusion squares both with our intuitions and with (...) the facts of vision science. (shrink)

What the Church teaches and why on issues of euthanasia, invitro fertilization, genetic counseling, assisted suicide, living wills, persistent vegetative state, organ transplants, and more.

Offers a vivid, nuanced, and chronological account of Buddhistreligion in Japan -- from its emergence in the sixth centuryright through to the present day.

In this foundational work in contemporary political theory, William Connolly makes a distinctive contribution to our understanding of the relationship between ...

We can know some things about each others' mental lives. The view that some of this knowledge is genuinely perceptual is getting traction. But the idea that we can see any of each others' mental states themselves - the Simple Perceptual Hypothesis - remains unpopular. Very often the view that we can perceptually know, for example, that James is angry, is thought to depend either on our awareness of James' expression or on the way James appears - versions of what (...) I call the Expressive Hypothesis. The Expressive Hypothesis is intuitive. But in this chapter I argue that it does not allow us to do away with the thought that we sometimes perceive people's mental states. I take my arguments to provide some tentative support for the Simple Perceptual Hypothesis. (shrink)

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)

There has been recent interest in the hypothesis that we can directly perceive some of each other’s mental features. One popular strategy for defending that hypothesis is to claim that some mental features are embodied in a way that makes them available to perception. Here I argue that this view would imply a particular limit on the kinds of mental feature that would be perceptible (§2). I sketch reasons for thinking that the view is not yet well-motivated (§3). And I (...) present an alternative, epistemological strategy (§4). The epistemological strategy is to discern which features of our environment are perceptible by reflection on our capacity to identify them. If the epistemological strategy is accepted it becomes plausible that we sometimes directly perceive some of each other’s mental features. But it becomes implausible to suppose that our perceptual access is limited in the way the embodied view would imply. I end by sketching reasons to think that we sometimes directly perceive each other’s desires (§5). (shrink)

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

Our knowledge of each others’ mental features is sometimes epistemically basic or non-inferential. The alternative to this claim is Inferentialism, the view that such knowledge is always epistemically inferential. Here, I argue that Inferentialism is not plausible. My argument takes the form of an inference to the best explanation. Given the nature of the task involved in recognizing what mental features others have on particular occasions, and our capacity to perform that task, we should not expect always to find good (...) inferential explanations of our knowledge. This conclusion is an epistemological one. The motivation for it is independent of metaphysical concerns about functionalism or about the best way to model the cognitive architecture which produces our knowledge of others’ minds. Given this it is compatible both with the truth of functionalism and theory–theory construed as a cognitive model. (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 ...

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)

William Connolly presents a lucid and concise defense of the thesis of "essentially contested concepts" that can well be read as a general introduction to political theory, as well as for its challenge to the prevailing understanding of political discourse. In Connolly's view, the language of politics is not a neutral medium that conveys ideas independently formed but an institutionalized structure of meanings that channels political thought and action in certain directions. In the new preface he pursues the implications (...) of this perspective for a distinctive conception of ethics and democracy. (shrink)

In The City of God , XI, 10, St Augustine claims that the divine nature is simple because ‘it is what it has’ . We may take this as a slogan for the Doctrine of Divine Simplicity , a doctrine which finds its way into orthodox medieval Christian theological speculation. Like the doctrine of God's timeless eternality, the DDS has seemed obvious and pious to many, and incoherent, misguided, and repugnant to others. Unlike the doctrine of God's timeless eternality, the (...) DDS has received very little critical attention. The DDS did not originate with Augustine, but I am not primarily concerned with its pedigree. Nor am I concerned to ask how the doctrine interacts with trinitarian speculation. I will have my hands full as it is. In Section I of this paper I shall provide a rough characterization of the DDS, indicate its complexity, and focus on a particular aspect of the doctrine which will exercise us in the remainder of the paper, namely, the thesis that the divine attributes are all identical with each other and with God. In section n I shall discuss Alvin Plantinga's recent objections to Aquinas' version of the DDS. I shall then offer a more detailed presentation of what I take to be Aquinas' version , and recast it in terms of a theory of attributes which is significantly different from Plantinga's . Although the recasting of the doctrine will enable me to rebut Plantinga's objections , it by no means solves all the problems of the DDS. In section vi I shall discuss the chief lingering problem facing a defender of the DDS. (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 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)

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)

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)