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)

This book is a defense of modal realism; the thesis that our world is but one of a plurality of worlds, and that the individuals that inhabit our world are only a few out of all the inhabitants of all the worlds. Lewis argues that the philosophical utility of modal realism is a good reason for believing that it is true.

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 article examines the ontology and politics of Peter Sloterdijk's Spheres trilogy, focusing in particular upon the notion of microspherical enclosure explicated in the first volume of this series. Noting Sloterdijk's unusual alignment of his philosophy with media theory, three main contentions are put forward. Firstly, that Sloterdijk's reconfiguration of Heidegger's fundamental ontology represents a largely unacknowledged renunciation of the primacy of Being-towards-death in the authentic existence of Dasein, foregrounding instead an originary co-belonging between mother and child. Secondly, that Sloterdijk (...) borrows from media theory a concern regarding the facticity of all communication, grounding philosophical discourse in the determinate locality of its origin, but does so while exalting a pre-natal communicative immediacy that would seem to disparage the everydayness of Dasein. Finally, that Sloterdijk's oft-justified scepticism regarding globalization often retreats into an anti-cosmopolitanism that, in its nostalgia for the comfort, security and immediacy of the matrixial co-belonging, evinces a covert but potentially noxious politics of exclusion. (shrink)

In the Garden of Eden, we had unmediated contact with the world. We were directly acquainted with objects in the world and with their properties. Objects were simply presented to us without causal mediation, and properties were revealed to us in their true intrinsic glory.

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)

What happens when machines become more intelligent than humans? One view is that this event will be followed by an explosion to ever-greater levels of intelligence, as each generation of machines creates more intelligent machines in turn. This intelligence explosion is now often known as the “singularity”. The basic argument here was set out by the statistician I.J. Good in his 1965 article “Speculations Concerning the First Ultraintelligent Machine”: Let an ultraintelligent machine be defined as a machine that can far (...) surpass all the intellectual activities of any man however clever. Since the design of machines is one of these intellectual activities, an ultraintelligent machine could design even better machines; there would then unquestionably be an “intelligence explosion”, and the intelligence of man would be left far behind. Thus the first ultraintelligent machine is the last invention that man need ever make. The key idea is that a machine that is more intelligent than humans will be better than humans at designing machines. So it will be capable of designing a machine more intelligent than the most intelligent machine that humans can design. So if it is itself designed by humans, it will be capable of designing a machine more intelligent than itself. By similar reasoning, this next machine will also be capable of designing a machine more intelligent than itself. If every machine in turn does what it is capable of, we should expect a sequence of ever more intelligent machines. This intelligence explosion is sometimes combined with another idea, which we might call the “speed explosion”. The argument for a speed explosion starts from the familiar observation that computer processing speed doubles at regular intervals. Suppose that speed doubles every two years and will do so indefinitely. Now suppose that we have human-level artificial intelligence 1 designing new processors. Then faster processing will lead to faster designers and an ever-faster design cycle, leading to a limit point soon afterwards. The argument for a speed explosion was set out by the artificial intelligence researcher Ray Solomonoff in his 1985 article “The Time Scale of Artificial Intelligence”.1 Eliezer Yudkowsky gives a succinct version of the argument in his 1996 article “Staring at the Singularity”: “Computing speed doubles every two subjective years of work.. (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...

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.

Unpopular in its day, David Hume's sprawling, three-volume A Treatise of Human Nature (1739-40) has withstood the test of time and had enormous impact on subsequent philosophical thought. Hume's comprehensive effort to form an observationally grounded study of human nature employs John Locke's empiric principles to construct a theory of knowledge from which to evaluate metaphysical ideas. A key to modern studies of eighteenth-century Western philosophy, the Treatise considers numerous classic philosophical issues, including causation, existence, freedom and necessity, and (...) morality. Unabridged republication of the edition originally published by Oxford at the Clarendon Press, London, 1888. Index. Appendix. (shrink)

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.

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