The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

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)

The past two decades have seen an explosion in the methods and directions of neuroscience research. Along with many others, complexity research has rapidly gained traction as both an independent research field and a valuable subdiscipline in computational neuroscience. In the past decade alone, several studies have suggested that psychiatric disorders affect the spatiotemporal complexity of both global and region-specific brain activity (Liu et al., 2013;Adhikari et al., 2017;Li et al., 2018). However, many of these studies have not accounted for (...) the distributed nature of cognition in either the global or regional complexity estimates, which may lead to erroneous interpretations of both global and region-specific entropy estimates. To alleviate this concern, we propose a novel method for estimating complexity. This method relies upon projecting dynamic functional connectivity into a low-dimensional space which captures the distributed nature of brain activity. Dimension-specific entropy may be estimated within this space, which in turn allows for a rapid estimate of global signal complexity. Testing this method on a recently acquired obsessive-compulsive disorder dataset reveals substantial increases in the complexity of both global and dimension-specific activity versus healthy controls, suggesting that obsessive-compulsive patients may experience increased disorder in cognition. To probe the potential causes of this alteration, we estimate subject-level effective connectivityviaa Hopf oscillator-based model dynamic model, the results of which suggest that obsessive-compulsive patients may experience abnormally high connectivity across a broad network in the cortex. These findings are broadly in line with results from previous studies, suggesting that this method is both robust and sensitive to group-level complexity alterations. (shrink)

1 Evidence-based policy requires researchers to provide the answers to ecological questions that are of interest to policy makers. To find out what those questions are in the UK, representatives from 28 organizations involved in policy, together with scientists from 10 academic institutions, were asked to generate a list of questions from their organizations. 2 During a 2-day workshop the initial list of 1003 questions generated from consulting at least 654 policy makers and academics was used as a basis for (...) generating a short list of 100 questions of significant policy relevance. Short-listing was decided on the basis of the preferences of the representatives from the policy-led organizations. 3 The areas covered included most major issues of environmental concern in the UK, including agriculture, marine fisheries, climate change, ecosystem function and land management. 4 The most striking outcome was the preference for general questions rather than narrow ones. The reason is that policy is driven by broad issues rather than specific ones. In contrast, scientists are frequently best equipped to answer specific questions. This means that it may be necessary to extract the underpinning specific question before researchers can proceed. 5 Synthesis and applications. Greater communication between policy makers and scientists is required in order to ensure that applied ecologists are dealing with issues in a way that can feed into policy. It is particularly important that applied ecologists emphasize the generic value of their work wherever possible. (shrink)

Symposium discussion on Todd Moody's `Conversations with Zombies' , by Owen Flanagan, Thomas Polger, Daniel C. Dennett, Guven Guzeldere, Jaron Lanier, John McCarthy, Selmer Bringsjord, Mary Midgley, Avshalom C. Elitzur, Keith Chandler, David Hodgson and Charles T. Tart, with response from Todd C. Moody.

This third installment in David Breed's intellectual biography of Ralph Wendell Burhoe focuses upon the impact of his thought on the Unitarian Universalist Association and that group's role in Burhoe's career. Dana McLean Greeley, elected president of the American Unitarian Association in 1958, was a key figure in Burhoe's eventual participation in the project, “The Free Church in a Changing World.” Burhoe's emphasis on the need for doctrine that could communicate religious wisdom in terms of science stood in tension (...) with free‐church tradition. Nevertheless, the section of the project's final report, titled “Theology and the Frontiers of Learning,” largely accepted Burhoe's program for a new natural theology based on science. This project brought Burhoe's program to the attention of the denomination and led to the invitation in 1964 from Malcolm Sutherland, on behalf of Meadville/Lombard Theological School in Chicago, of which he was president, for Burhoe to implement his program in the new curriculum of that school. Burhoe accepted. (shrink)

During the Napoleonic Wars there was a shortage of suitable millstones for the British Ordnance gunpowder mills. John MacCulloch spent five summers searching Western Britain for a source of non-siliceous limestones to be used as gunpowder millstones. His search was authorized by the Board of Ordnance, which also paid all his expenses.By 1812 MacCulloch had found suitable limestones in Sutherland, Skye, and at Glen Tilt, but the Board of Ordnance were unable to exploit any of the sources until 1815 (...) when unsuccessful quarries were opened on Skye. After the defeat of Napoleon at Waterloo the British millstone project was abandoned. The military objective of the millstone survey was not achieved, but MacCulloch learned much about the geology of the older rocks of Britain and he built a reputation as an expert geologist through the papers he submitted to the Geological Society of London. (shrink)

In this lengthy book, Daniel Sutherland proposes to rectify our long neglect of Kant's theory of mathematics by means of both historical and systematic analyses. This is a worthy undertaking, since the scope and significance of that theory were lost from view during the twentieth century.

In lieu of an abstract, here is a brief excerpt of the content:Hume's Moral Sentiments and the Structure of the Treatise LOUIS E. LOEB ACCORDING TO NORMAN KEMP SMITH and Thomas Hearn, Hume classified moral sentiments as direct passions.' According to Pb.II A,rdal, Hume classified the basic moral sentiments of approval and disapproval of persons as indirect passions. if either of these interpretations is correct, there is an intimate connection between Books II and 111 of Hume's Treatise. This is because (...) the direct and indirect passions (together with the will) are the subject of Book 11 and moral sentiments are discussed in Book 111. So if moral sentiments are special cases of either direct or indirect passions, the treatment of passions in Book Ii is central to the understanding of Book 111. 1 contend, on the contrary, that Hume's moral sentiments are neither direct nor indirect passions. Consequently, the connection between Books 11 and 111 of the Treatise is much less intimate than A,rdal and Hearn have recently suggested.' i. Hume's Classification of the Impressions of Reflection In the four paragraphs of II, i, I Hume provides an exhaustive "Division of the Subject"--the "subject" being "all the perceptions of the mind. ''4 Nowhere else in the Treatise is a complete "division" to be found. As A,rdal points out, such introductory chapters "are likely to be written after the bulk of the book has been completed, or at least to be carefully revised in the light of the main arguments in the book. ''~ For these reasons, there is a strong presumption that the "division" in!I, i, 1should be taken as canonical. Hume's "division" is straightforward. In the first paragraph, perceptions are divided into ideas and impressions; in the first and second paragraphs, impressions are divided into those of sensation and those of reflection; in the third paragraph, impressions of reflection are divided into the calm and the violent; in the fourth (as I am indebted to Wdham Frankena, Ronald Glossop, and Peter Jones for their most helpful comments. ' Norman Kemp Smith, The Philosophy of David Hume (New York: St. Martm'~ Press, 1966), pp. 167-168; and Thomas K. Hearn, Jr., "Ardal on the Moral Sentiments in Hume's rreattse," Phtlosophy 48 (1973):290. z Passton and Value m Hume's "Treatise" (Edinburgh: Edinburgh University Press, 1966), pp. I 1, 109-133. For a discussion heavily influenced by Ardal, see Stewart R. Sutherland, "Hume on Morality and the Emotions," Phllosophwal Quarterly 26 (1976) : 14-19 especially. ' See Ardal, pp. I-5, 109-133; and Hearn, pp. 288, 292. 9 A Treatise of Human Nature, ed. L. A. Selby-Bigge (Oxford: Clarendon Press, 1888), p. 275; hereafter cited as T followed by page number. 9 Ardal, p. 94. 13951 396 HISTORY OF PHILOSOPHY indicated by the last sentence of the third), the violent impressions of reflection are divided into the direct and the indirect. The structure is of a genus-species sort, and none of the distinctions cut across each other: J calm i sense of beauty and deformity (T, 276), moral sentiments impressions of reflection = emotions (secondary impressions) violent = passions direct indirect desire, aversion, grief, joy, pride, humility, love, hope, fear (T, 277, 439) hatred (T, 276-277) This classification is based upon the only natural reading of paragraph three and the first sentence of paragraph four of II, i, I. I quote this material, adding my own emphasis and deleting Hume's: The reflective impressions may be divided into two kinds, viz. the calm and the violent. Of the first kind is the sense of beauty and deformity in action, composition, and external objects. Of the second are the passions of love and hatred, grief and joy, pride and humility. This division is far from being exact. The raptures of poetry and music frequently rise to the greatest height; while those other impressions, properly called passions, may decay into so soft an emotion, as to become, in a manner, imperceptible. But as in general the passions are more violent than the emotions arising from beauty and deformity, these impressions have been commonly distinguish'd from each other. The subject of the human mind being so copious and various, I shall here take... (shrink)

Figures of Thought looks at how mathematical works can be read as texts and examines their textual strategies. David Reed offers the first sustained and critical attempt to find a consistent argument or narrative thread in mathematical texts. Reed selects mathematicians from a range of historical periods and compares their approaches to organizing and arguing texts, using an extended commentary on Euclid's Elements as a central structuring framework. He develops fascinating interpretations of mathematicians' work throughout history, from Descartes to (...) Hilbert, Kronecker, Dedekind, Weil and Grothendieck. Reed traces the implications of this approach to the understanding of the history and development of mathematics. (shrink)

This book aims to reinvigorate discussions of moral arguments for God's existence.

For this volume David Wiggins has selected and revised eleven of his essays in an area of metaphysics where his work has been particularly influential, and he has added a substantial introduction and one new unpublished essay. Among the subjects treated are substance, identity, persistence, persons, sortals, and artefacts.

Fran Brearton: Robert Graves and The White Goddess Joyce Hill: Authority and Intertextuality in the Works of Ælfric Michael Pennington: Barnardine's Straw: The Devil in Shakespeare's Detail David Womersley: Dulness and Pope Terence Cave: Montaigne Lord Moser: The Future of Our Universities Alexander Murray: The Inquisition and the Renaissance Robert Bagley: The Prehistory of Chinese Music Theory Edwin Cameron: Patents and Public Health: Principle, Politics and Paradox Mervyn King: What Fates Impose: Facing Up to Uncertainty Dominic Lieven: Empire, History (...) and the Contemporary Global Order Joan Oates: Archaeology in Mesopotamia: Digging Deeper at Tell Brak Timothy Besley: The New Political Economy Richard Gray: 'They Worship Death Here': William Faulkner, Sanctuary and Hollywood Lord Sutherland: Nomad's Progress James Piscatori: Imagining Pan-Islam: Religious Activism and Political Utopias. (shrink)

Philosophy Bites brings together the twenty-five best interviews from this hugely successful website.

The important recent book by Schurz ( 2019 ) appreciates that the no-free-lunch theorems (NFL) have major implications for the problem of (meta) induction. Here I review the NFL theorems, emphasizing that they do not only concern the case where there is a uniform prior—they prove that there are “as many priors” (loosely speaking) for which any induction algorithm _A_ out-generalizes some induction algorithm _B_ as vice-versa. Importantly though, in addition to the NFL theorems, there are many _free lunch_ theorems. (...) In particular, the NFL theorems can only be used to compare the expected performance of an induction algorithm _A_, considered in isolation, with the expected performance of an induction algorithm _B_, considered in isolation. There is a rich set of free lunches which instead concern the statistical _correlations_ among the generalization errors of induction algorithms. As I describe, the meta-induction algorithms that Schurz advocates as a “solution to Hume’s problem” are simply examples of such a free lunch based on correlations among the generalization errors of induction algorithms. I end by pointing out that the prior that Schurz advocates, which is uniform over bit frequencies rather than bit patterns, is contradicted by thousands of experiments in statistical physics and by the great success of the maximum entropy procedure in inductive inference. (shrink)

When patients are admitted to the hospital, they are generally expected to remain in or within close proximity to their assigned rooms in order to promote their safety and appropriate medical care. Although there are circumstances when patients may safely leave their hospital room or floor, guidance within the medical literature for the management of patient movement within the hospital are lacking. Excessive restrictions on patient movement may be seen as overly paternalistic, while lax requirements may interfere with high quality (...) care, patient safety and efficient hospital practice. As a result, guidance in the form of institutional policy is warranted. Such policy development should take into consideration the potential clinical, legal, and ethical concerns in balancing the competing values of patients’ preferences and respect for autonomy, while ensuring high quality, safe, and efficacious medical care. This paper will provide a framework for hospitals to create institution-specific patient movement policies that are fair, systematic, and transparent. (shrink)

The question of Voltaire’s belief in (or lack of belief in) God is a vexed one. René Pomeau’s classic study of 1956 argued that Voltaire believed in a God who would punish and reward in the next life. More recently Gerhardt Stenger has shown that, at least after 1764, Voltaire adopted a moderated form of Spinozism. He consistently rejected a materialist atheism on the grounds that the universe showed evidence of intelligent design, and appealed to Spinoza against d’Holbach. This article (...) studies the evolution of Voltaire’s philosophical account of the deity, showing that he moved from a belief in a Newtonian creator God to a Spinozist monopsychism at least by 1756. But, under the influence of Warburton, he had come to reject Bayle’s concept of a society of atheists, and consequently held that the wider public must be encouraged to believe in a providential God, a view he pretended to hold himself. Reading Voltaire after 1756 it is thus essential to understand that he held a double truth theory, so that it is sometimes necessary to ‘read between the lines’ to discover his meaning. (shrink)

I aim to show that standard theories of counterfactuals are mistaken, not in detail, but in principle, and I aim to say what form a tenable theory must take. Standard theories entail a categorical interpretation of counterfactuals, on which to state that, if it were that A, it would be that C is to state something, not relative to any supposition or hypothesis, but categorically. On the rival suppositional interpretation, to state that, if it were that A, it would be (...) that C is to state that it would be that C relative to the supposition that it were that A. The two interpretations make incompatible predictions concerning the correct evaluation of counterfactuals. I argue that the suppositional interpretation makes the correct prediction. (shrink)

The model of clinical ethics consultation (CEC) defended in the ASBH Core Competencies report has gained significant traction among scholars and healthcare providers. On this model, the aim of CEC is to facilitate deliberative reflection and thereby resolve conflicts and clarify value uncertainty by invoking and pursuing a process of consensus building. It is central to the model that the facilitated consensus falls within a range of allowable options, defined by societal values: prevailing legal requirements, widely endorsed organizational policies, and (...) professional standards of practice and codes of conduct. Moreover, the model stipulates that ethics consultants must refrain from giving substantive recommendations regarding how parties to a moral disagreement in the clinic should evaluate their options. We argue that this model of CEC is incomplete, because it wrongly assumes that what counts as the proper set of allowable options among which the parties are to deliberate will itself always be clearly discernible. We illustrate this problem with a recent case on which one of us consulted—a neonate born with trisomy 18 (T18). We try to show that law, policy, and standards of practice reveal no clear answer to the question posed by the case: namely, whether forgoing gastrostomy tube feedings for a baby with T18 is allowable. We suggest there may be other kinds of cases in which it may simply be unsettled whether a given choice falls within the set of allowable options within which consensus is to be facilitated. What should an ethicist do when confronting such unsettled cases? We agree with the facilitation model that an ethicist should remain neutral among the allowable options, when it is clear what the allowable options are. But, in unsettled cases, the role of a consultant should be expanded to include a process of moral inquiry into what the allowable options should be. We end by raising the issue of whether this means an ethicist should share his or her own conclusions or views about the allowability of a given clinical option. (shrink)

Private detectives and deception as official work -- Building believable lies -- Justifying work-related deceptions -- The shadow world of unofficial deception -- Subterranean education and training -- Deception as social currency -- Goofing off and getting along -- The everyday ethics of workplace lies -- Appreciating deception in thinking about organizations.

In his thoughtful defence of very modest moral enhancement, David DeGrazia1 makes the following assumption: ‘Behavioural improvement is highly desirable in the interest of making the world a better place and securing better lives for human beings and other sentient beings’. Later in the paper, he gives a list of some psychological characteristics that ‘all reasonable people can agree … represent moral defects’. I think I am a reasonable person, and I agree that most if not all items on (...) the lists do represent moral defects—I certainly would regard them as such in a close family member or friend. But if I were in the business of ‘making the world a better place and securing better lives for human beings and other sentient beings’, I would hesitate to prescribe moral enhancement for everyone with these acknowledged defects. A lot of good work, from removing tumours to negotiating treaties, may be best done by people with serious moral defects.For a simple consequentialist, a moral defect is just a trait that tends to make the world a worse place. Not being a consequentialist, I think that moral defects should be identified independently of their tendency to produce worse outcomes. For this reason, I think it's necessary to qualify DeGrazia's starting assumption—I think behavioural improvement may sometimes be undesirable if our goal is to make the world a better place. My reasons will be familiar to readers of Bernard Williams.As …. (shrink)

Some modern critics of Kant, like Bernard Williams, argue that his ideal of morality is a form of action which lies beyond any empirical determination. The aim of this article is to show that Kant was not only fully aware of the role of contingent elements in moral action, but that his fundamental conception of practical rationality is itself partly constituted by contingent factors. Practical rationality cannot be separated from its exercise and hence from the necessary empirical conditions of human (...) psychology and historical circumstances. Without a maxim there can be no manifestation of practical reason. Without a human character there is no room for moral virtue. Without achievement no moral action can be complete . Thus, human agency extends beyond the realm of pure motive. These themes reflecting Kant's recognition of the importance of contingency in his general theory of rational action are discussed primarily in the light of the Metaphysics of Morals, which in its structure and program explicitly sets out to tie together the a priori and contingent elements in a unified theory. Legality without morality is blind; morality without legality is vacuous. Einige moderne Kritiker Kants wie Bernard Williams behaupten, Kants Sittlichkeitsideal weise auf eine Handlungsform, die außerhalb alles empirisch Feststellbaren liege. Ziel dieses Beitrags ist es zu zeigen, daß Kant sich der Rolle kontingenter Elemente im moralischen Handeln nicht nur voll bewußt war, sondern daß sein grundlegender Entwurf praktischer Vernunft selbst teilweise auf kontingente Faktoren gegründet ist. Praktische Vernunft kann nicht von ihrer Anwendung getrennt werden und also auch nicht von den notwendig empirischen Bedingungen menschlicher Psychologie und von den historischen Umständen des Handelns. Ohne eine Maxime gibt es keine praktische Vernunft. Ohne einen menschlichen Charakter gibt es keine moralische Tugend. Ohne ein erreichtes Ziel kann keine moralische Handlung vollständig sein. Menschliches Handeln überschreitet die Grenzen des Bereichs bloßer Motive.Die Themen zeigen, daß Kant in seiner allgemeinen Theorie vernünftigen Handelns die Kontingenz ernst nimmt. Sie werden hauptsächlich im Lichte der Metaphysik der Sitten diskutiert, die sich in ihrem Programm und in ihrer Struktur explizit vornimmt, apriorische und kontingente Elemente in einer einheitlichen Theorie zu verbinden. Legalität ohne Moralität ist blind; Moralität ohne Legalität ist leer. (shrink)

This is the first book-length study of the development of civility in Chinese societies. Although some social scientists and political philosophers have discussed civility, none has defined it as an analytical tool to systematically measure attitudes and behavior, and few have applied it to a non-Western society. By comparing the development of civility in mainland China and Taiwan, Civility and Its Development: The Experiences of China and Taiwan analyzes the social conditions needed for civility to become established in a society. (...) Schak argues that the attempts to impose civility top-down from the state are ineffective. Civility appeared in Taiwan only after state efforts to impose it ceased at the end of the 1980s when Taiwan began to democratize, and the PRC government civility campaigns have so far had only limited success. The book concludes with an examination of various differences between Taiwan and the PRC relevant to Taiwan’s having become a society with civility while the PRC still encounters difficulties in doing so. The essential factor in developing civility in Taiwan, Schak contends, was its evolution from a place composed of myriad small, inward-looking communities to a society in which everyone shares a strong identity and civic consciousness, and people consider others as fellow members, not anonymous strangers. “This book represents the most thorough review of what social scientists once called ‘the civilizing process’ in Chinese society. David C. Schak builds on the earlier studies on this issue and goes well beyond the established literature.” —James Watson, Fairbank Professor of Chinese Society and Professor of Anthropology, Emeritus, Harvard University “This is a topic that people talk about all the time, and David C. Schak draws a lot of material together in a systematic and comprehensive way that can stimulate important discussions beyond the academy.” —Thomas Gold, Professor of Sociology, University of California, Berkeley. (shrink)

Tribe, David Review(s) of: A Wealth of insights: Humanist Thought since the Enlightenment, by Bill Cooke Amherst, NY: Prometheus Books, 2011; ISBN 9781591027270.

I am intrigued by the use of the words ‘embedded’ and ‘capacity’ as they appear in what I take to be the strategy of Sovereignty Across Generations where these words are used to make what is evidently implicit within John Rawls’s political liberalism explicit, that is, a normative account of ‘the justice and legitimacy of political orders’. If I am correct about this strategy, my question is quite simple: is something lost in translation in this transition from Rawls’s more historical (...) to this normative orientation? I conclude with a positive comment on the potential that a theory of temporality has for the development of a notion of political self-constitution as it pertains to the transition from ethnos to demos. (shrink)