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)

From Shakespeare to Beckett, the contradictory figure of the fool who possesses unexpected wisdom has been a popular and effective literary trope and rhetorical figure for centuries. Philosophy needs idiots too, argues Keston Sutherland in _Stupefaction_. This is a book about how idiots are created, how they are used, and the types of truth that depend on them. Sutherland examines how speculative and satirical descriptions of stupidity function in art and in argument. His examples include Alexander Pope’s (...) dunce, Adorno’s philistine, Wordsworth’s mechanical adopter of poetic diction, and phenomenologist Michel Henry’s drunkard who rides an escalator to nothingness. Sutherland also provides an important new account of the figure of the bourgeois in Marx and a powerfully original interpretation of commodity fetishism as a satire against bourgeois objectivity. This unusual analysis of the trope of the idiot will appeal to scholars of literature and philosophy alike. (shrink)

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)

Whether or not quantum physics can account for molecular structure is a matter of considerable controversy. Three of the problems raised in this regard are the problems of molecular structure. We argue that these problems are just special cases of the measurement problem of quantum mechanics: insofar as the measurement problem is solved, the problems of molecular structure are resolved as well. In addition, we explore one consequence of our argument: that claims about the reduction or emergence of molecular structure (...) cannot be settled independently of the choice of a particular resolution to the measurement problem. Specifically, we consider how three standard putative solutions to the measurement problem inform our under- standing of a molecule in isolation, as well as of chemistry’s relation to quantum physics. (shrink)

While it might seem prima facie plausible that divine foreknowledge is all that is needed for prophecy, this seems incorrect. To issue a prophecy, God hasto know not just how someone will act, but how someone would act were the prophecy issued. This makes some think that Middle Knowledge is required.I argue that Thomas Flint’s two Middle Knowledge based accounts of prophecy are unsatisfactory, but one of them can be repaired. However the resources needed for repair also yield a sketch (...) of a foreknowledge-only account of prophecy. (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)

The present study investigated whether individual differences between psychologists in thinking styles are associated with accuracy in diagnostic classification. We asked novice and experienced clinicians to classify two clinical cases of clients with two co-occurring psychological disorders. No significant difference in diagnostic accuracy was found between the two groups, but when combining the data from novices and experienced psychologists accuracy was found to be negatively associated with certain decision making strategies and with a higher self-assessed ability and preference for a (...) rational thinking style. Our results underscore the idea that it might be fruitful to look for explanations of differences in the accuracy of diagnostic judgments in individual differences between psychologists (such as in thinking styles or decision making strategies used), rather than in experience level. (shrink)

Professional philosophers and advanced students working in metaphysics and the philosophy of science will find this book both provocative and stimulating.

For a novice this book is a mathematically-oriented introduction to modal logic, the discipline within mathematical logic studying mathematical models of reasoning which involve various kinds of modal operators. It starts with very fundamental concepts and gradually proceeds to the front line of current research, introducing in full details the modern semantic and algebraic apparatus and covering practically all classical results in the field. It contains both numerous exercises and open problems, and presupposes only minimal knowledge in mathematics. A specialist (...) can use the book as a source of references. Results and methods of many directions in propositional modal logic, from completeness and duality to algorithmic problems, are collected and systematically presented in one volume. (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...

Thomas Samuel Kuhn (1922–1996) is one of the most influential philosophers of science of the twentieth century, perhaps the most influential. His 1962 book The Structure of Scientific Revolutions is one of the most cited academic books of all time. Kuhn’s contribution to the philosophy of science marked not only a break with several key positivist doctrines, but also inaugurated a new style of philosophy of science that brought it closer to the history of science. His account of the development (...) of science held that science enjoys periods of stable growth punctuated by revisionary revolutions. To this thesis, Kuhn added the controversial ‘incommensurability thesis’, that theories from differing periods suffer from certain deep kinds of failure of comparability. (shrink)

This Is A New Release Of The Original 1868 Edition.

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

This book provides an accessible, critical introduction to the three main approaches that dominated work in the philosophy of mathematics during the twentieth century: logicism, intuitionism and formalism.

Thomas Kuhn transformed the philosophy of science. His seminal 1962 work "The Structure of Scientific Revolutions" introduced the term 'paradigm shift' into the vernacular and remains a fundamental text in the study of the history and philosophy of science. This introduction to Kuhn's ideas covers the breadth of his philosophical work, situating "The Structure of Scientific Revolutions" within Kuhn's wider thought and drawing attention to the development of his ideas over time. Kuhn's work is assessed within the context of other (...) philosophies of science notably logical empiricism and recent developments in naturalized epistemology. The author argues that Kuhn's thinking betrays a residual commitment to many theses characteristic of the empiricists he set out to challenge. Kuhn's influence on the history and philosophy of science is assessed and where the field may be heading in the wake of Kuhn's ideas is explored. (shrink)

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)

This volume contains the Arabic translations of a lost treatise by Alexander of Aphrodisias "On the Principles of the Universe" with English translation, introduction and commentary. It also includes an Arabic and Syriac glossary. The introduction and commentary deal in detail with the manuscripts, the translators and the exegetical tendencies of the text, as well as with its reception in Arabic philosophy. The main theme of the work is the motion of the heavenly bodies and their influence on the (...) physical world. (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 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.

' But, although such a being (a purely intellectual being) might perhaps be conceived to exist, and although, in studying our internal frame, ...

Common errors on the mind.--Errors of suppressed correlatives.--The civil service examinations.--The classical controversy.--Metaphysics and debating societies.--The university ideal, past and present.--The art of study.--Religious tests and subscriptions.--Procedure of deliberative bodies.

Achieving space domain awareness requires the identification, characterization, and tracking of space objects. Storing and leveraging associated space object data for purposes such as hostile threat assessment, object identification, and collision prediction and avoidance present further challenges. Space objects are characterized according to a variety of parameters including their identifiers, design specifications, components, subsystems, capabilities, vulnerabilities, origins, missions, orbital elements, patterns of life, processes, operational statuses, and associated persons, organizations, or nations. The Space Object Ontology provides a consensus-based realist framework (...) for formulating such characterizations in a computable fashion. Space object data are aligned with classes and relations in the Space Object Ontology and stored in a dynamically updated Resource Description Framework triple store, which can be queried to support space domain awareness and the needs of spacecraft operators. This paper presents the core of the Space Object Ontology, discusses its advantages over other approaches to space object classification, and demonstrates its ability to combine diverse sets of data from multiple sources within an expandable framework. Finally, we show how the ontology provides benefits for enhancing and maintaining longterm space domain awareness. (shrink)

Unlike some other reproductions of classic texts (1) We have not used OCR(Optical Character Recognition), as this leads to bad quality books with introduced typos. (2) In books where there are images such as portraits, maps, sketches etc We have endeavoured to keep the quality of these images, so they represent accurately the original artefact. Although occasionally there may be certain imperfections with these old texts, we feel they deserve to be made available for future generations to enjoy.

George Berkeley (1685-1753) is the superstar of Irish Philosophy. He entered Trinity College, Dublin, in 1700 and became a fellow in 1707. In 1724 he resigned his Fellowship to become Dean of Derry, and in 1734 he was made Bishop of Cloyne. He settled in Oxford in 1752 and died the following year. The work of George Berkeley is marked by its diversity and range. His writings take in such topics as mathematics, psychology, politics, health, economics, deism and education, as (...) well as that with which he is most associated - philosophy. Whatever topic he dealt with, his grasp of the subject matter was always impressive and his criticisms of his contemporaries often acute. Among the most noteable of the British Empiricists, he took his starting point from Locke's new 'way of ideas', but he rejected abstract ideas and the possibility of real existence outside perception. It is for this doctrine that he is most known - that there is no such thing as matter, and that things are collections of ideas which can exist only in our minds and only for so long as they are perceived. This philosophy, summed up in his phrase 'to be is to be perceived', he termed 'immaterialism'. A.C. Fraser's collection includes a series of what were previously unpublished notes by Berkeley on all the main topics of his philosophy. This, the 1901 edition, was the first complete edition of his works. (shrink)

In the late Middle Ages the philosopher and mystic Meister Eckhart preached that to know the truth you must be the truth. But how to be the truth? Eckhart's answer comes in the form of an imperative: release yourself, let be. Only then will you be able to understand that the deepest meaning of being is releasement. Only then will you become who you truly are. This book interprets Eckhart's Latin and Middle High German writings under the banner of an (...) imperative of releasement, and then shows how the twentieth-century thinker Martin Heidegger creatively appropriates this idea at several stages of his career. Heidegger had a lifelong fascination with Eckhart, referring to him as "the old master of letters and life." Drawing on archival material and Heidegger's marginalia in his personal copies of Eckhart's writings, Moore argues that Eckhart was one of the most important figures in Heidegger's philosophy. This book also contains previously unpublished documents by Heidegger on Eckhart, as well as the first English translation of Nishitani Keiji's essay "Nietzsche's Zarathustra and Meister Eckhart," which he initially gave as a presentation in one of Heidegger's classes in 1938. (shrink)

Many introductions to this field start with the problem of justifying scientific knowledge but Alexander Bird begins by examining the subject matter, or metaphysics, of science. Using topical scientific debates he vividly elucidates what it is for the world to be governed by laws of nature. This idea provides the basis for explanations and causes and leads to a discussion of natural kinds and theoretical entities. With this foundation in place he goes on to consider the epistemological issues of (...) how science arrives at knowledge, favouring a treatment of scientific reasoning based on inference to the best explanation. Drawing on contemporary work in epistemology, Bird argues that scepticism about induction should not be a problem for science and examines the consequences of this position for controversies surrounding the ideas of scientific progress and scientific revolution. Bird's insightful treatment makes Philosophy of Science an ideal text for undergraduate courses. The guides to further reading provided in each chapter help the reader pursue interesting topics and facilitate the use of the book in conjunction with primary sources. (shrink)

Scotland has played an immense role in European high culture through the centuries, and among its cultural links none have been greater than those with France. This book shows that the links with France stretch back deep into the Middle Ages, and continue without a break into the 18th century, the Age of Enlightenment.

Hate speech law can be found throughout the world. But it is also the subject of numerous principled arguments, both for and against. These principles invoke a host of morally relevant features and practical considerations . The book develops and then critically examines these various principled arguments. It also attempts to de-homogenize hate speech law into different clusters of laws/regulations/codes that constrain uses of hate speech, so as to facilitate a more nuanced examination of the principled arguments. Finally, it argues (...) that it is morally fitting for judicial and legislative judgments about the overall warrant of hate speech law to reflect principled compromise. Principled compromise is characterized not merely by compromise over matters of principled concern but also by compromise which is itself governed by ideals of moral duty or civic virtue. (shrink)

[opening paragraph]: Our sense of free will depends upon a balance between reliability and flexibility in relation to cause-and-effect. Without the former, all outcomes would be arbitrary; without the latter, all outcomes would be predetermined. In neither case would there be any way of putting one's will into effect. So much is clear, yet establishing that precarious balance has proved so difficult that Kant himself declared ‘freedom of the will’ to be one of only three metaphysical problems which lie beyond (...) the powers of the human intellect . Western debate on this topic reflects a complex ethical and religious inheritance. Insights from Greek philosophy and Hebrew scripture were combined and filtered through Christian and Jewish traditions which developed in late antiquity and through the middle ages. These formed the context for the Enlightenment, whose dominant thinkers in turn provide the backdrop against which today's scholars act and react. (shrink)