The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Çağımızın seçkin kültür ve düşünce tarihçilerinden Frank Turner’ın Yale Üniversite’sinde verdiği derslerden oluşan Rousseau’dan Nietzsche’ye Avrupa Düşünce Tarihi, Aydınlanma döneminden yirminci yüzyılın başına dek Avrupa’da yaşanan radikal değişimi fikir akımları ve öncü figürler üzerinden anlatıyor. Oxford Today’in editörü Richard Lofthouse tarafından derlenen bu dersler, farklı disiplinleri ustaca bir araya getirerek döneme dair kapsamlı bir bakış açısı sunuyor. Yale’in en sevilen hocalarından Turner’ın açık, akıcı ve öğretici üslubu sayesinde düşünce tarihinin zorlu dönemeçlerinde kolaylıkla yol alacak, dersler bittikten sonra (...) kitabın sonundaki okuma listesini takip ederek daha fazlasını öğrenmek isteyeceksiniz. (shrink)

Richard Tieszen presents an analysis, development, and defense of a number of central ideas in Kurt Gödel's writings on the philosophy and foundations of mathematics and logic. Tieszen structures the argument around Gödel's three philosophical heroes - Plato, Leibniz, and Husserl - and his engagement with Kant, and supplements close readings of Gödel's texts on foundations with materials from Gödel's Nachlass and from Hao Wang's discussions with Gödel. He provides discussions of Gödel's views, and develops a new type of (...) platonic rationalism that requires rational intuition, called 'constituted platonism'. (shrink)

In a number of essays published over the last decade or so, W. V. Quine has made some interesting suggestions concerning the ontology of theories. If I understand him correctly, one of his principal objects has been to formulate a criterion by means of which one can correctly decide what are the ontological commitments of any given theory. My aim in this paper is to reveal what I think are inadequacies in Quine's criterion and to indicate the direction in which (...) a proper formulation lies. (shrink)

This book draws upon philosophical arguments, criminological evidence, and legal literature on prisoners' rights and sentencing to explore the restrictions and deprivations that can be legitimately imposed on serious offenders in the name of punishment.

Offering a collection of fifteen essays that deal with issues at the intersection of phenomenology, logic, and the philosophy of mathematics, this 2005 book is divided into three parts. Part I contains a general essay on Husserl's conception of science and logic, an essay of mathematics and transcendental phenomenology, and an essay on phenomenology and modern pure geometry. Part II is focused on Kurt Godel's interest in phenomenology. It explores Godel's ideas and also some work of Quine, Penelope Maddy and (...) Roger Penrose. Part III deals with elementary, constructive areas of mathematics. These are areas of mathematics that are closer to their origins in simple cognitive activities and in everyday experience. This part of the book contains essays on intuitionism, Hermann Weyl, the notion of constructive proof, Poincaré and Frege. (shrink)

Nature, God and Humanity clarifies the task of forming an ethics of nature, thereby empowering readers to develop their own critical, faith-based ethics. Calling on original, thought-provoking analyses and arguments, Richard L. Fern frames a philosophical ethics of nature, assesses it scientifically, finds support for it in traditional biblical theism, and situates it culturally. Though defending the moral value of beliefs affirming the radical Otherness of God and human uniqueness, this book aims not to compel the adoption of any (...) particular ethic but rather illumine the contribution diverse forms of inquiry make to an ethics of nature. How does philosophy clarify moral conviction? What does science tell us about nature? Why does religious faith matter? Rejecting the illusion of a single, rationally-compelling ethics, Fern answers these questions in a way that fosters both agreement and disagreement, allowing those holding conflicting ethics of nature to work together for the common good. (shrink)

Theories of Truth provides a clear, critical introduction to one of the most difficult areas of philosophy. It surveys all of the major philosophical theories of truth, presenting the crux of the issues involved at a level accessible to nonexperts yet in a manner sufficiently detailed and original to be of value to professional scholars. Kirkham's systematic treatment and meticulous explanations of terminology ensure that readers will come away from this book with a comprehensive general understanding of one of philosophy's (...) thorniest set of topics. -/- Included are discussions of the correspondence, coherence, pragmatic, semantic, performative, redundancy, appraisal, and truth-as-justification theories. There are also chapters or sections of chapters on the liar paradox, three-valued logic, Field's critique of Tarski, Davidson's program, Dummett's theory of linguistic competence, satisfaction, recursion, the extension/intension distinction, and an explanation of how theories of justification, properly understood, differ from theories of truth. -/- A persistent theme is that philosophers have too often failed to recognize that not all theories of truth are intended to answer the same question. When the various questions are made distinct, it is apparent that many of the "debates" in this field are really cases of philosophers talking past one another. There is much less disagreement within the field than has commonly been thought. (shrink)

This analysis of Frege's views on language and metaphysics in On Sense and Reference, arguably one of the most important philosophical essays of the past hundred years, provides a thorough introduction to the function/argument analysis and applies Frege's technique to the central notions of predication, identity, existence and truth. Of particular interest is the analysis of the Paradox of Identity and a discussion of three solutions: the little-known Begriffsschrift solution, the sense/reference solution, and Russell's 'On Denoting' solution. Russell's views wend (...) their way through the work, serving as a foil to Frege. Appendices give the proofs of the first 68 propositions of Begriffsschrift in modern notation. This book will be of interest to students and professionals in philosophy and linguistics. (shrink)

In _Freedom and the End of Reason_, Richard L. Velkley offers an influential interpretation of the central issue of Kant’s philosophy and an evaluation of its position within modern philosophy’s larger history. He persuasively argues that the whole of Kantianism—not merely the Second Critique—focuses on a “critique of practical reason” and is a response to a problem that Kant saw as intrinsic to reason itself: the teleological problem of its goodness. Reconstructing the influence of Rousseau on Kant’s thought, Velkley (...) demonstrates that the relationship between speculative philosophy and practical philosophy in Kant is far more intimate than generally has been perceived. By stressing a Rousseau-inspired notion of reason as a provider of practical ends, he is able to offer an unusually complete account of Kant’s idea of moral culture. (shrink)

The mere exposure phenomenon (repeated exposure to a stimulus is sufficient to improve attitudes toward that stimulus) is one of the most inspiring phenomena associated with Robert Zajonc’s long and productive career in social psychology. In the first part of this article, Richard Moreland (who was trained by Zajonc in graduate school) describes his own work on exposure and learning, and on the relationships among familiarity, similarity, and attraction in person perception. In the second part, Sascha Topolinski (a recent (...) graduate who never met Zajonc, but found his ideas inspirational) describes his own work concerning embodiment and fluency in the mere exposure effect. Also, several avenues for future research on the mere exposure phenomenon are identified, further demonstrating its continuing relevance to the field. (shrink)

This book grew out of my confusion. If logic is objective how can there be so many logics? Is there one right logic, or many right ones? Is there some underlying unity that connects them? What is the significance of the mathematical theorems about logic which I've learned if they have no connection to our everyday reasoning? The answers I propose revolve around the perception that what one pays attention to in reasoning determines which logic is appropriate. The act of (...) abstracting from our reasoning in our usual language is the stepping stone from reasoned argument to logic. We cannot take this step alone, for we reason together: logic is reasoning which has some objective value. For you to understand my answers, or perhaps better, conjectures, I have retraced my steps: from the concrete to the abstract, from examples, to general theory, to further confirming examples, to reflections on the significance of the work. (shrink)

Comparative case studies of lawyer deviance and discipline offer a unique perspective on how and why lawyers misbehave, how regulatory bodies respond, and the efficacy of those responses. Such studies also provide valuable pedagogic tools, opening the eyes of law students to the ways in which they, too, could transgress ethical rules. This special issue builds on my two books on misbehaving lawyers in New York and California by presenting vivid accounts of such lawyers in the UK, Canada, Australia, New (...) Zealand, and the Netherlands. (shrink)

We propose a framework for including information‐processing bounds in rational analyses. It is an application of bounded optimality (Russell & Subramanian, 1995) to the challenges of developing theories of mechanism and behavior. The framework is based on the idea that behaviors are generated by cognitive mechanisms that are adapted to the structure of not only the environment but also the mind and brain itself. We call the framework computational rationality to emphasize the incorporation of computational mechanism into the definition of (...) rational action. Theories are specified as optimal program problems, defined by an adaptation environment, a bounded machine, and a utility function. Such theories yield different classes of explanation, depending on the extent to which they emphasize adaptation to bounds, and adaptation to some ecology that differs from the immediate local environment. We illustrate this variation with examples from three domains: visual attention in a linguistic task, manual response ordering, and reasoning. We explore the relation of this framework to existing “levels” approaches to explanation, and to other optimality‐based modeling approaches. (shrink)

Several theoretical perspectives have generated research on grandparental investment, notably socialization and evolutionary psychological perspectives. Using data collected from more than 200 older adults (mean age 67 years), we test three hypotheses derived from socialization and evolutionary perspectives about grandparents’ relationships with and investment in grandchildren. Results indicate that (1) emotional closeness with both children and children-in-law is positively related to reports of emotional closeness with grandchildren; (2) maternal grandmothers invest more in grandchildren than do other grandparents; and (3) grandparents (...) invest more in daughters’ children than in sons’ children. Discussion addresses limitations of self-report methodology in this context and situates the current findings within the body of research indicating the existence of psychological mechanisms designed to guide differential nepotism. (shrink)

Here is an in-depth look at the role myth, mortality, and religion play in J. R. R. Tolkien's works such as The Hobbit, The Lord of the Rings, and The Silmarillion -- including Tolkien's private letters and revealing opinions of his own work. Richard L. Purtill brilliantly argues that Tolkien's extraordinary ability to touch his readers' lives through his storytelling -- so unlike much modern literature -- accounts for his enormous literary success. This book demonstrates the moral depth in (...) Tolkien's work and cuts through current subjectivism and cynicism about morality. A careful reader will find a subtle religious dimension to Tolkien's work -- all the more potent because it is below the surface. Purtill reveals that the author's fantasy stories creatively incorporate profound religious and ethical ideas. For example, Purtill shows us how hobbits reflect both the pettiness of unimaginative parochial humanity and the unexpected heroism of ordinary people in crisis. Purtill effectively addresses larger issues of the place of myth, the relation of religion and morality to literature, the relation of Tolkien's work to traditional mythology, modern fantasy and science fiction, and the lessons Tolkien's work teaches that are applicable to our own lives. Book jacket. (shrink)

Numerous retributivists hold that deserved punishment has intrinsic value. A number of puzzles regarding that claim are identified and discussed. An alternative, more Kantian account of intrinsic value is then identified and the ways in which legal punishment might be understood to cohere with it are explored. That account focuses on the various ways in which legal punishment might be persons-respecting. It is then argued that this Kantian account enables us to solve or evade the puzzles generated by the other (...) intrinsic value account. (shrink)

This volume is about searching for fundamental theory in physics which has become somewhat elusive in recent decades. Like a group of blind men investigating an elephant, one physicist postulates the trunk as a hose, another a leg as a tree, the body a wall or barrier, the tail a rope and the ears as a fan. The organizers of the Vigier series symposia strongly believe cross polination by exploring many avenues of seemingly disparate research is key to breakthrough discovery (...) and solicited papers on all areas of physics deemed pertinent in Astrophysics, Cosmology, nuclear physics, quantum theory, electromagnetism, thermodynamics, vacuum field theory and topology. (shrink)

The contributions in the book examine the historical and contemporary manifestations of organized crime, the symbiotic relationship between legitimate and ...

Arguing against most scholars of business ethics who have articulated a set of moral principles and applied them to problems faced by business people, Richard Lippke steers away from offering moral directives. In Radical Business Ethics, he develops a more comprehensive perspective on business issues that is tied to larger questions of social justice. Analyzing a select group of timely issues such as advertising, employee privacy, and insider trading in the context of debates about the nature of the just (...) society, Lippke argues that the most plausible theory of justice is one whose implications are highly critical of many features of advanced capitalist societies. Radical Business Ethics will be an eye-opening book for students and scholars of ethics, and anyone interested in the role business plays in a just society. (shrink)

In 1821 the French Académie Royale des Sciences sponsored a prize competition on the causes of animal heat. Carefully designing the contest to serve several interests, the Académie (especially Cuvier and Berthollet) sought to defend Lavoisier's theory and method for studying animal heat and to restore a pre-1789 ideal of non-utilitarian scientific practice. Changing standards of precision in physical research, however, sabotaged these intentions. Even with improved experimental apparatus and techniques, the chief contestants could not quantitatively confirm Lavoisier's theory. Unpublished (...) documents reveal anonymous entrants who refused to accept the Académie's definition of the question. The 1821 competition, then, rendered Lavoisier's theory more dubious than ever in the eyes of contemporary physiological writers. (shrink)

In Being after Rousseau, Richard L. Velkley presents Jean-Jacques Rousseau as the founder of a modern European tradition of reflection on the relation of philosophy to culture—a reflection that calls both into question.

The first of my preliminary arguments which Mr. Wild feels to be erroneous is that in which possibility is held to involve both being and non-being. In defending this thesis I return to the original problem to which it attempted a preliminary solution. The pervasiveness of contingency and change in human experience was first asserted, together with the demand that metaphysics explain, as best it might, all such data; with this much I understand Mr. Wild to agree in the opening (...) paragraph of his critique. Further it was affirmed that through awareness of contingency and change, the understanding comes to possess the concepts of being and nonbeing, and can see that both contingency and change must involve these two concepts. With Mr. Wild I agree that "There is a gulf between being and non-being." To bridge this gulf, then, to mediate these terms, is the very function of possibility. It was this gulf that demanded an intermediate conception, and the characteristics attributed to this mediator were, at the outset, simply those which its function seemed to require. My whole preliminary account of the possible, then, was constructed strictly with this function in mind. Upon careful re-consideration of the matter, I find myself still holding that the bridging of this chasm between the simple non-being of an entity and the simple being of that same entity requires intermediation of precisely the sort that I first offered. How else can we proceed, either in thought or existence, from the non-being of X to the being of X, except by means of that which exceeds but has its basis in the former, and tends toward but falls short of the latter? (shrink)

Although any generalization in matters of such scope is risky, the central issue involved would seem to be this: Can man achieve, and know that he has achieved, a true and adequate philosophy? The Jesuit tendency is to stress the developmental aspects of philosophy and theology, identifying them more closely with the natural sciences. The Dominicans, on the other hand, see in this tendency great dangers, with theological pluralism as perhaps the gravest, short of outright skepticism.

The physical and relational structure of the biologic continuum (both internal and external to the organism) creates the information signature that is the basis for the origination of meaning in the living system. A meaning metric can be grounded in the significance of that information to the stability of the system during the process of adaptive reconciliation of divergences from the steady state condition. From this perspective, an information-theoretic formulation of the process for translating incident information into adaptive action is (...) proposed that can be practically used in defining and quantifying the meaning of that information for the living system. (shrink)