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 connectivity via a 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.

The cries of Lamentations are desperate, wailing up from the darkest side of human existence. They will not be silenced. Lament harasses those who oppress and calls all to justice—even God.

In lieu of an abstract, here is a brief excerpt of the content:Journal of the History of Philosophy 41.3 (2003) 426-427 [Access article in PDF] Timothy Smiley, editor. Mathematics and Necessity: Essays in the History of Philosophy. New York: Oxford University Press, 2000. Pp. ix + 166. Cloth, $35.00.Mathematics and Necessity contains essays by M. F. Burnyeat, Ian Hacking, and Jonathan Bennett based on lectures given to the British Academy in 1998. All concern the history of the philosophical treatment of (...) mathematics, necessity, or both, although there is no single thread running through all three essays.Burnyeat focuses on Plato's understanding of mathematics in the Republic, making use of the Timeaus in particular to defend his interpretation. Plato claimed that in the ideal society mathematics should be studied for a full ten years, which many have thought excessive. To explain it, Burnyeat argues that the role of mathematics is pervasive: ethics and politics are mathematical, because in Plato's view mathematics is a constitutive part of ethical understanding. On Burnyeat's interpretation, goodness is part of the objective world, and mathematics is a science of values. The link between mathematics and goodness in the objective world is forged by the concord, harmony, and unity of proportions, which express the goodness of the Divine Craftsman's beneficent design. Proportions are both intrinsically good and the proper study of mathematics.Burnyeat explains why Plato thinks abstract kinematics (the pure non-sensible counterpart to astronomy) and abstract harmonics lead to knowledge of the good. Abstract kinematics concerns the "harmony of the spheres" described in the Republic. Drawing heavily on the Timeaus, Burnyeat argues that the circular motions of the spheres are motions in the intelligence of the world soul and that there are similar motions in human souls. The world soul and human souls are spatial and have circular motions (invisibility and intangibility make them incorporeal). Souls are the most important subject matter of abstract harmonics—the study of good proportions. A soul that understands the various mathematical disciplines and their relations takes on the harmony and hence goodness of the world soul. Such a soul serves as a model for organizing the social world, a model which properly trained rulers can use to shape a community. Burnyeat's well-argued essay is compelling and exciting. [End Page 427]Ian Hacking's views provide a great contrast to Burnyeat's Plato. Hacking conducts a phenomenological inquiry into why some philosophers have become obsessed by mathematics as a source of philosophical inspiration. He holds that mathematics concerns a relatively minor part of human culture and that the influence of mathematics on philosophy is pernicious; he even describes it as an infection.Hacking examines the views of six philosophers: Plato, Leibniz, Mill, Descartes, Lakatos, and Wittgenstein. Hacking's assessment of the six philosophers is at times disputable, but it is also interesting and stimulating, and serves his phenomenological inquiry.Hacking traces philosophy's infection by mathematics to two factors. A mathematical proof can be perspicuous; that is, a proof can be "grasped," which requires seeing directly why something must be true and being able to recapitulate it. A mathematical proof can also anticipate facts about the world. He thinks that these two factors affect us in two ways: they give us the idea of a priori knowledge, and they dazzle us into unreasoned conviction in proofs. One might respond that, setting aside the feeling proofs give us, we are still justified in being impressed by them. Hacking argues that much of what impresses is based on a misunderstanding of their nature, which he attempts to correct.According to Hacking, a mathematical demonstration involves shifts of meaning that analytically bind the proof and the theorem it establishes. They thereby mutually support each other and provide what he calls self-authentication. The correctness of the proof is supported by the "analytified" truth of the theorem and the theorem is considered true because proven.This bootstrapping feature of mathematical proofs supports Hacking's deflationary account of necessity. Hacking suggests that the "must" of logical necessity rests upon our unwillingness to accept empirical counter-examples to the... (shrink)

From religion to philosophy to science, all human systems of definition are formed by human brains. The nature and limits of the human brain are the nature and limits of those systems. This essay shows how the human brain works normally then unusually, and what this reveals about the limits of human knowledge. There are many conditions and instances where the brain processes information unusually, including mental disorders, physical events, and drug use. This essay focuses on the neurological events called (...) mystical experiences. (shrink)

Molecular and biochemical analysis of the biogenesis of peroxisomes has made rapid progress in recent years. Research on the mechanism of targeting of peroxisomal proteins has revealed that many, but not all, peroxisomal proteins have a conserved tripeptide motif in their carboxy‐terminal portions which is required for entry into peroxisomes; the topogenic signal mechanism thus differs in these instances from those employed in mitochondria and endoplasmic reticulum. Other factors involved in peroxisome biogenesis are also coming to light.

This short peer-reviewed text is a concise look at the psychology of how human beings make decisions, including how they form their worldviews and make arguments.

This paper aims to provide two abductive considerations adducing in favor of the thesis of Necessitism in modal ontology. I demonstrate how instances of the Barcan formula can be witnessed, when the modal operators are interpreted 'naturally' -- i.e., as including geometric possibilities -- and the quantifiers in the formula range over a domain of natural, or concrete, entities and their contingently non-concrete analogues. I argue that, because there are considerations within physics and metaphysical inquiry which corroborate modal relationalist claims (...) concerning the possible geometric structures of spacetime, and dispositional properties are actual possible entities, the condition of being grounded in the concrete is consistent with the Barcan formula; and thus -- in the geometric setting -- merits adoption by the Necessitist. (shrink)

The notion that eukaryotes are ancestrally sexual has been gaining attention. This idea comes in part from the discovery of sets of “meiosis‐specific genes” in the genomes of protists. The existence of these genes has persuaded many that these organisms may be engaging in sex, even though this has gone undetected. The involvement of sex in protists is supported by the view that asexual reproduction results in the accumulation of mutations that would inevitably result in the decline and extinction of (...) such lineages. It is argued that this phenomenon can be obviated by polyploidy and that the “meiosis‐specific genes” are used in other processes, including polyploidy control and homologous recombination, independent of meiosis. These phenomena account for the finding that these genes are expressed in cultures devoid of apparent cell fusion events. Hence, it is also proposed that asexual, and not sexual, reproduction is the ancestral condition. (shrink)

Part of the appeal of the biological approach to personal identity is that it does not have to countenance spatially coincident entities. But if the termination thesis is correct and the organism ceases to exist at death, then it appears that the corpse is a dead body that earlier was a living body and distinct from but spatially coincident with the organism. If the organism is identified with the body, then the unwelcome spatial coincidence could perhaps be avoided. It is (...) argued that such an identification would be a mistake. A living organism has a different part/whole relationship and persistence conditions than the alleged body. A case will be made that the concept ‘human body’ is a conceptual mess, vague in an unprincipled manner, and that an eliminativist stance towards dead bodies is the appropriate response. CiteULike Connotea Del.icio.us What's this? (shrink)

Oxford Philosophical Texts Series Editor: John Cottingham The Oxford Philosophical Texts series consists of authoritative teaching editions of canonical texts in the history of philosophy from the ancient world down to modern times. Each volume provides a clear, well laid out text together with a comprehensive introduction by a leading specialist, giving the student detailed critical guidance on the intellectual context of the work and the structure and philosophical importance of the main arguments. Endnotes are supplied which provide further commentary (...) on the arguments and explain unfamiliar references and terminology, and a full bibliography and index are also included. The series aims to build up a definitive corpus of key texts in the Western philosophical tradition, which will form a reliable and enduring resource for students and teachers alike. David Hume's aim in writing An Enquiry concerning Human Understanding was to introduce his philosophy to a European culture in which many educated people read original works of philosophy. He gives an elegant and accessible presentation of strikingly original and challenging views about the limited powers of human understanding, the attractions of scepticism, the compatibility of free will and determinism, and weaknesses in the foundations of religion. Hume's philosophy was highly controversial in the eighteenth century and remains so today. The text printed in this edition is that of the Clarendon critical edition of Hume's works. A substantial introduction by the editor explains the intellectual background to the work and surveys its main themes. The volume also includes detailed explanatory notes on the text, a glossary of terms, a full list of references, and a section of supplementary readings. (shrink)

As a continuation of the work of the third author in [5], we make further observations on the features of Galois cohomology in the general model theoretic context. We make explicit the connection between forms of definable groups and first cohomology sets with coefficients in a suitable automorphism group. We then use a method of twisting cohomology (inspired by Serre’s algebraic twisting) to describe arbitrary fibres in cohomology sequences—yielding a useful “finiteness” result on cohomology sets. Applied to the special case (...) of differential fields and Kolchin’s constrained cohomology, we complete results from [3] by proving that the first constrained cohomology set of a differential algebraic group over a bounded, differentially large, field is countable. (shrink)

This work has been selected by scholars as being culturally important, and is part of the knowledge base of civilization as we know it. This work was reproduced from the original artifact, and remains as true to the original work as possible. Therefore, you will see the original copyright references, library stamps (as most of these works have been housed in our most important libraries around the world), and other notations in the work. This work is in the public domain (...) in the United States of America, and possibly other nations. Within the United States, you may freely copy and distribute this work, as no entity (individual or corporate) has a copyright on the body of the work.As a reproduction of a historical artifact, this work may contain missing or blurred pages, poor pictures, errant marks, etc. Scholars believe, and we concur, that this work is important enough to be preserved, reproduced, and made generally available to the public. We appreciate your support of the preservation process, and thank you for being an important part of keeping this knowledge alive and relevant. (shrink)

Amongst the remarkable variety of motility that cells display, cytokinesis (cell division) is particularly striking. Dramatic changes in cell shape occur before, during and after cytokinesis. Myosin II is implicated in the ‘rounding up’ of cells prior to cytokinesis, and is essential in the formation of the contractile cleavage furrow during cytokinesis. Now it appears that myosin II plays a role in all stages of cytokinesis, as a recent report(1) suggests that myosin II drives post‐mitotic cell spreading. A similar type (...) of motile mechanism operating in cell spreading may occur in other cell types in other situations. (shrink)

It is widely accepted in science that the universe is a closed deterministic system in which everything can, ultimately, be explained by purely physical...

In this classic work David Bohm, writing clearly and without technical jargon, develops a theory of quantum physics which treats the totality of existence as an unbroken whole.

This volume is devoted to Lewis's work in metaphysics and epistemology. Topics covered include properties, ontology, possibility, truthmaking, probability, the mind-body problem, vision, belief, and knowledge. The purpose of this collection, and the volumes that precede and follow it, is to disseminate more widely the work of an eminent and influential contemporary philosopher. The volume will serve as a useful work of reference for teachers and students of philosophy.

"First Published in 1999, Routledge is an imprint of Taylor & Francis, an informa company.".

Religion, science, and naturalism -- Perception and religious experience -- Panexperientialism, freedom, and the mind-body relation -- Naturalistic, dipolar theism -- Natural theology based on naturalistic theism -- Evolution, evil, and eschatology -- The two ultimates and the religions -- Religion, morality, and civilization -- Religious language and truth -- Religious knowledge and common sense.

It is widely accepted in science that the universe is a closed deterministic system in which everything can, ultimately, be explained by purely physical causation. And yet we all experience ourselves as having the freedom to choose between alternatives presented to us — ‘we’ are in the driving seat. The puzzling status of volition is explored in this issue by a distinguished body of scientists and philosophers.

Kensinger (2009) and Mather (2007) both argue that intrinsic features of emotional items are remembered better than intrinsic features of non-emotional items. However, Kensinger attributes these effects to negative valence whereas Mather attributes them to arousal. In this paper, we note several reasons why arousal may be the driving factor even when a study reveals more detailed memory for negative items than for positive items. We also reanalyze previous data (Mather & Nesmith, 2008) to show that although both arousal and (...) negative valence were correlated with memory accuracy, enhanced memory accuracy was accounted for by arousal rather than valence. (shrink)

In this innovative study, Lea David critically investigates the relationship between human rights and memory, suggesting that, instead of understanding human rights in a normative fashion, human rights should be treated as an ideology. Conceptualizing human rights as an ideology gives us useful theoretical and methodological tools to recognize the real impact human rights has on the ground. David traces the rise of the global phenomenon that is the human rights memorialization agenda, termed 'Moral Remembrance', and explores what (...) happens once this agenda becomes implemented. Based on evidence from the Western Balkans and Israel/Palestine, she argues that the human rights memorialization agenda does not lead to a better appreciation of human rights but, contrary to what would be expected, it merely serves to strengthen national sentiments, divisions and animosities along ethnic lines, and leads to the new forms of societal inequalities that are closely connected to different forms of corruptions. (shrink)

Liberal thinkers of the eighteenth and nineteenth centuries were alert to the political costs and human cruelties involved in European colonialism, but they also thought that European expansion held out progressive possibilities. In Progress, Pluralism, and Politics David Williams examines the colonial and anti-colonial arguments of Adam Smith, Immanuel Kant, Jeremy Bentham, and L.T. Hobhouse. Williams locates their ambivalent attitude towards European conquest and colonial rule in a set of tensions between the impact of colonialism on European states, the (...) possibilities of progress in distant and diverse places, and the relationship between universalism and cultural pluralism. In so doing he reveals some of the central ambiguities that characterize the ways that liberal thought has dealt with the reality of an illiberal world. Of particular importance are appeals to various forms of universal history, attempts to mediate between the claims of identity and the reality of difference, and the different ways of thinking about the achievement of liberal goods in other places. Pointing to key elements in still ongoing debates within liberal states about how they should relate to illiberal places, Progress, Pluralism, and Politics enriches the discussion on political thought and the relationship between liberalism and colonialism. (shrink)

"My work has had nothing to do with gay liberation," Michel Foucault reportedly told an admirer in 1975. And indeed there is scarcely more than a passing mention of homosexuality in Foucault's scholarly writings. So why has Foucault, who died of AIDS in 1984, become a powerful source of both personal and political inspiration to an entire generation of gay activists? And why have his political philosophy and his personal life recently come under such withering, normalizing scrutiny by commentators as (...) diverse as Camille Paglia, Richard Mohr, Bruce Bawer, Roger Kimball, and biographer James Miller? David M. Halperin's Saint Foucault is an uncompromising and impassioned defense of the late French philosopher and historian as a galvanizing thinker whose career as a theorist and activist will continue to serve as a model for other gay intellectuals, activists, and scholars. A close reading of both Foucault and the increasing attacks on his life and work, it explains why straight liberals so often find in Foucault only counsels of despair on the subject of politics, whereas gay activists look to him not only for intellectual inspiration but also for a compelling example of political resistance. Halperin rescues Foucault from the endless nature-versus-nurture debate over the origins of homosexuality ("On this question I have absolutely nothing to say," Foucault himself once remarked) and argues that Foucault's decision to treat sexuality not as a biological or psychological drive but as an effect of discourse, as the product of modern systems of knowledge and power, represents a crucial political breakthrough for lesbians and gay men. Halperin explains how Foucault's radical vision of homosexuality as a strategic opportunity for self-transformation anticipated the new anti-assimilationist, anti-essentialist brand of sexual identity politics practiced by contemporary direct-action groups such as ACT UP. Halperin also offers the first synthetic account of Foucault's thinking about gay sex and the future of the lesbian and gay movement, as well as an up-to-the-minute summary of the most recent work in queer theory. "Where there is power, there is resistance," Michel Foucault wrote in The History of Sexuality, Volume I. Erudite, biting, and surprisingly moving, Saint Foucault represents Halperin's own resistance to what he views as the blatant and systematic misrepresentation of a crucial intellectual figure, a misrepresentation he sees as dramatic evidence of the continuing personal, professional, and scholarly vulnerability of all gay activists and intellectuals in the age of AIDS. (shrink)