Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

The meeting focused on uses of ontologies, with a special focus on spatial ontologies, in addressing the ever increasing needs faced by biology and medicine to cope with ever expanding quantities of data. To provide effective solutions computers need to integrate data deriving from myriad heterogeneous sources by bringing the data together within a single framework. The meeting brought together leaders in the field of what are called "top-level ontologies" to address this issue, and to establish strategies among leaders in (...) the field of biomedical ontology for the creation of interoperable biomedical ontologies which will serve the goal of useful data integration. (shrink)

In 2005, IOS Press published the first issue of applied Ontology. At the time, we argued that, at the core of the journal, there was “a desire to understand the nature of reality and how people construe their world”. We declared that ontology was both “fundamental to human thought” and “to translating our thoughts into computational artifacts” (Guarino & Musen,2005). With an editorial board of distinguished scholars representing the fields of computer science, informatics, information science, philosophy, linguistics, psychology, and (...) social science, we had the firm belief that applied Ontologywould fulfill an important academic niche, becoming an essential forum for discussion on topics such as ontological analysis, conceptual modeling, and the role of domain models in building and managing information systems. The facts now show that we were correct. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science has (...) always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

Semantic interoperability requires the use of standards, not only for Electronic Health Record (EHR) data to be transferred and structurally mapped into a receiving repository, but also for the clinical content of the EHR to be interpreted in conformity with the original meanings intended by its authors. Accurate and complete clinical documentation, faithful to the patient’s situation, and interoperability between systems, require widespread and dependable access to published and maintained collections of coherent and quality-assured semantic resources, including models such as (...) archetypes and templates that would (1) provide clinical context, (2) be mapped to interoperability standards for EHR data, (3) be linked to well specified, multi-lingual terminology value sets, and (4) be derived from high quality ontologies. Wide-scale engagement with professional bodies, globally, is needed to develop these clinical information standards. (shrink)

Each annual Ontology Summit initiative makes a statement appropriate to each Summit’s theme as part of our general advocacy designed to bring ontology science and engineering into the mainstream. The theme this year is "Towards an Open Ontology Repository". This communiqué represents the joint position of those who were engaged in the year's summit discourse on an Open Ontology Repository (OOR) and of those who endorse below. In this discussion, we have agreed that an "ontology repository is a facility where (...) ontologies and related information artifacts can be stored, retrieved and managed." -/- We believe in the promise of semantic technologies based on logic, databases and the Semantic Web, a Web of exposed data and of interpretations of that data (i.e., of semantics), using common standards. Such technologies enable distinguishable, computable, reusable, and sharable meaning of Web and other artifacts, including data, documents, and services. We also believe that making that vision a reality requires additional supporting resources and these resources should be open, extensible, and provide common services over the ontologies. (shrink)

This is a short editorial to introduce the double issue of Applied Ontology that celebrates the journal's tenth anniversary. At a time when information technology of all kinds depends on the use of explicit ontologies, our journal addresses the modeling issues that underlie the next generation of computational systems. As the editors of Applied Ontology, we are excited by how far we have come in the past decade and by the opportunities that await our research community.

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content.

On the basis of careful textual exegesis and philosophical analysis, and contrary to the received view, Mark R. Wheeler demonstrates that Aristotle presents and systematically explicates his definition of the essence of the truth in the Metaphysics. Aristotle states the nominal definitions of the terms "truth" and "falsehood" as part of his arguments in defense of the logical axioms. These nominal definitions express conceptions of truth and falsehood his philosophical opponents would have recognized and accepted in the context of (...) dialectical argument. On the basis of these nominal definitions, Aristotle develops his definitions of the essences of truth and falsehood--his "real" definitions of truth and falsehood. Aristotle's methodical exposition of his essential definitions of truth and falsehood in the Metaphysics serves as a well-developed example of how his philosophical inquiry starts with nominal definitions and ends with real definitions. Wheeler also argues for the novel claim that Aristotle defines the most fundamental kind of truth in terms of accurate measurement. Aristotle's metrical conception of truth serves as the theoretical basis for specifying the truth conditions of various assertions, for identifying the sorts of beings implicated in these truth conditions, and for explaining the nature of approximate truth and falsehood. Far from offering us a minimal account of truth, Wheeler shows how Aristotle offers us a sophisticated and metrical theory of truth. (shrink)

Current sociological theories appear to have lost their general persuasiveness in part because, unlike the theories of the ‘classical era’, they fail to maintain an integrated stance toward society, and the practical role that sociology plays in society. The authors explore various facets of this failure and possibilities for reconstructing sociological theories as integrated wholes capable of conveying a moral and political immediacy. They discuss the evolution of several concepts (for example, the social, structure, and self) and address the significant (...) disputes (for example, structuralism versus humanism, and individual versus society) that have dominated twentieth-century sociological thought. Their ideas and analyses are directed towards an audience of students and theorists who are coming to terms with the project of sociological theory, and its relationship with moral discourses and political practice. The authors of these essays are sociological theorists from the United States, the United Kingdom and Canada. They are all established, but not ‘establishment’ authors. The book contains no orthodoxies, and no answers. However, the essays do contribute to identifying the range of issues that will constitute the agenda for the next generation of sociological theorists. (shrink)

Let us begin with the simple observation that applied mathematics can be very tough! It is a common occurrence that basic physical principle instructs us to construct some syntactically simple set of differential equations, but it then proves almost impossible to extract salient information from them. As Charles Peirce once remarked, you can’t get a set of such equations to divulge their secrets by simply tilting at them like Don Quixote. As a consequence, applied mathematicians are often forced to pursue (...) roundabout and shakily rationalized expedients if any useful progress is to be made. Often these provisional and quasi-empirical procedures within applied mathematics loom large in motivating the “anti-realist” or “anti-unificationist” conclusions of Nancy Cartwright and allied authors. (shrink)

Freud’s famous essay “The ‘Uncanny’” is often poorly understood. In this paper, I clear up the popular misconception that Freud identifies all uncanny phenomena with the return of repressed infantile complexes by showing that he offers not one but two theories of the uncanny: “return of the repressed,” and another explanation that has to do with the apparent confirmation of “surmounted primitive beliefs.” Of the two, I argue that it is the latter, more often overlooked theory that faces fewer serious (...) objections and carries greater explanatory power in respect of the uncanny. (shrink)

This is one of those cases to which Dr. 8 oodhouse's remark applies with all its force, that a method which leads to true results must have its logic — H.S Smith (" On Some of the Methods at Present in Use in Pure Geometry," p. 6) A goodly amount of modern metaphysics has concerned itself, in one form or another, with the question: what attitude should we take in regard to a language whose semantic underpinnings seem less than certain? (...) Since much of standard English is surely of this type, many philosophers have felt driven to extreme and unpalatable resolutions — wholesale rejection of attractive logical rules, radical "antirealism", "minimalism" about truth, and so forth, Scientists, however, have long dealt with analogous foundational insecurities and, under the duress of practicality, have framed a set of shifting attitudes towards language and reasoning that seem far more commonsensical than the extreme positions to which pure philosophy has often been led. Following this lead, this essay will recommend a more nuanced approach to linguistic insecurity that is neither naively optimistic nor mired in the gloomy sloughs of antirealism. (shrink)

Stereological techniques allow biologists to create quantitative, three-dimensional descriptions of biological structures from two- dimensional images of tissue viewed under the microscope. For example, they can accurately estimate the size of a particular organelle, the total length of a mass of capillaries, or the number of neurons or synapses in a particular region of the brain. This book provides a practical guide to designing and critically evaluating stereological studies of the nervous system and other tissues. It explains the basic concepts (...) behind design-based stereology and how to get started. Also included are detailed descriptions of how to prepare tissue appropriately, perform pilot studies and decide on the appropriate sampling strategy, and account for phenomena such as tissue shrinkage. Numerous examples of applications of stereological methods that are applicable to studies of the central system and a wide variety of other tissues are explained. The book is therefore essential reading for neurobiologists and cell biologists interested in generating accurate representations of cell and tissue architecture. (shrink)

Together again for the first time, Marx and Durkheim join forces in the pages of Disintegration: Bad Love, Collective Suicide, and the Idols of Imperial Twilight for a dialectical exploration of the moral economy of neoliberalism, animated, as it is not only by the capitalist chase for surplus value, but also by an immortal vortex of sacred powers. Classical sociology and psychoanalysis are reconstituted within Hegelian social ontology and dialectical method that differentiates between the ephemeral and free and the eternal (...) and fixed aspects of modern life. (shrink)

In ancient China, a revered Taoist sage named Zhuangzi told many parables. In Existential Psychology and the Way of the Tao, a selection of these parables will be featured. Following each parable, an eminent existential psychologist will share a personal and scholarly reflection on the meaning and relevance of the parable for psychotherapy and contemporary life. The major tenets of Zhuangzi's philosophy are featured. Taoist concepts of emptiness, stillness, Wu Wei (i.e. intentional non-intentionality), epistemology, dreams and the nature of reality, (...) character building in the midst of pain, meaning and the centrality of relationships, authenticity, self-care, the freedom that can come from one's willingness to confront death, spiritual freedom, and gradations of therapeutic care are topics highlighted in this book. (shrink)

There is considerable likelihood that Gottlob Frege began writing his Foundations of Arithmetic with the expectation that he could introduce his numbers, not with sets, but through some algebraic techniques borrowed from earlier writers of the Gottingen school. These rewriting techniques, had they worked, would have required strong philosophical justification provided by Frege's celebrated "context principle," which otherwise serves little evident purpose in the published Foundations.

Artificial intelligence, the "science and engineering of intelligent machines", still has yet to create even a simple "Advice Taker" [McCarthy, 1959]. We have previously argued [Waser, 2011] that this is because researchers are focused on problem-solving or the rigorous analysis of intelligence (or arguments about consciousness) rather than the creation of a "self" that can "learn" to be intelligent. Therefore, following expert advice on the nature of self [Llinas, 2001; Hofstadter, 2007; Damasio, 2010], we embarked upon an effort to design (...) and implement a self-understanding, self-improving loop as the totality of a (seed) AI. As part of that, we decided to follow up on Richard Dawkins' [1976] speculation that "perhaps consciousness arises when the brain's simulation of the world becomes so complete that it must include a model of itself" by defining a number of axioms and following them through to their logical conclusions. The results combined with an enactive approach yielded many surprising and useful implications for further understanding consciousness, self, and "free-will" that continue to pave the way towards the creation of safe/moral autopoiesis. (shrink)

There are three major weaknesses with Glenberg 's theory. The first is that his theory makes assumptions about internal representations that cannot be adequately tested. The second is that he tries to accommodate data from three disparate domains: mental models, linguistics, and memory. The third is that he makes light of advances in cognitive neuroscience.

What can we learn about the nature of technology by studying practices of maintenance and repair? This volume addresses this question by bringing together scholarship from philosophers of technology working at the forefront of this emerging and exciting topic. -/- The chapters in this volume explore how attending to maintenance and repair can challenge and complement existing ways of thinking about technology focused on use and design and introduce new philosophical perspectives on the relationship between technology, time and human practice. (...) They examine the significance of maintenance and repair practices at different scales in relation to a diverse range of philosophical traditions and a wide variety of technologies, from urban infrastructure such as bridges and buildings to data technologies such as servers and software systems. Together, the contributions highlight common themes in the philosophical study of maintenance, including the role of skill, the significance of social values and the potential of these practices to transform the technologies to which they are applied. By reflecting on the different ways in which we keep technologies going, from the devices we use in our homes to the large technical systems which surround us, this volume reveals the philosophical significance of practices of maintenance, not only as a source of new insights but also as a resource for enriching our understanding of a variety of existing topics in philosophy. -/- Maintenance and Philosophy of Technology will appeal to scholars and advanced students working in philosophy of technology, philosophy of engineering and science & technology studies. (shrink)

This article draws attention to the origins, forms, and implications of “toxic discourse” as a genre central to the understanding of the public sphere in business in society.RachelCarson'sSilentSpringis used as a pivotal cultural document establishing “toxic discourse” as an ongoing form of moral narrative rooted in the rationality of counterpublics. Toxic discourse is framed within a center/periphery model in which toxic discourse gains salience in periods of economic dislocation and uncertainty. In these periods, toxic discourse draws together those on the (...) periphery or counterpublics who otherwise would not unite in their opposition to the center. The article critically examines how stakeholder theory, despite making sense of the public sphere for agents of organizations, glosses counterpublics and relegates toxic discourse, as evident in the “Occupy Movement,” to the ephemeral role of temporary, disruptive protest groups with very little of substance to communicate. (shrink)

This chapter addresses some basic ethical questions about psychological operations. It defines PSYOP, then compares and contrasts it with both conventional military activities and contemporary information warfare. Then it briefly clarifies emerging public policy problems, outlines relevant legal particularities, and offers general policy considerations with regard to ethical considerations in its employment.

It is time to bring the rich resources of these traditions into the contemporary debate about the nature of self. This volume is the first of its kind.

I argue that beliefs are a special sort of feeling about the truth-value of statements. Once that conclusion is drawn, beliefs can be seen to have little to do with what is really of import in epistemology — the formation of shared meanings. I then argue that doxastic involuntarism suggests that we must examine something else — attentional voluntarism — if we are to understand how agents change behaviors, and that once we examine attentional voluntarism, we are thrust into the (...) social realm, and into social epistemology. Throughout, I will be discussing Alcoholics Anonymous, an organization whose use of symbolic language and social support has been demonstrated to create a social epistemology for its members which has an empirical effect upon their behavior. By so doing, I hope to suggest a sort of praxis by which we might ‘ground’ social epistemology, which I regard as a grand theory in the Mertonian sense. (shrink)

Taylor focuses on the dramatic presentation of time and self at each state of Kierkegaard's dialectic of the stages of existence.

In his groundbreaking book, Thin Objects, Linnebo (2018) argues for an account of neo-Fregean abstraction principles and thin existence that does not rely on analyticity or conceptual rules. It instead relies on a metaphysical notion he calls “sufficiency”. In this short discussion, I defend the analytic or conceptual rule account of thin existence.

Prospective developments in computer and nanotechnology suggest that there is some possibility—perhaps as early as this century—that we will have the technological means to attempt to duplicate people. For example, it has been speculated that the psychology of individuals might be emulated on a computer platform to create a personality duplicate—an “upload.” Physical duplicates might be created by advanced nanobots tasked with creating molecule-for-molecule copies of individuals. Such possibilities are discussed in the philosophical literature as (putative) cases of “fission”: one (...) person “splitting” into two. Many philosophers, perhaps most, reject the idea of fission, appealing to some form of a “no-branching” condition to rule out such possibilities. I argue, to the contrary, that there are good moral reasons to think that any account of personal identity that does not permit fission is deeply problematic, especially in connection with theorizing about criminal punishment. I discuss and reject David Lewis’ famous account of personal identity that invokes “multiple occupancy” to allow for branching. In contrast, I offer an account of personal identity that permits branching using the type/token distinction to help with such puzzling cases. (shrink)

I hope to show that each of 1, 2, and 3 are plausible, yet we can derive 4: 1. It is epistemically permissible to believe that our preferred views in multi-proposition disputes are true, or at least more likely true than not. 2. If it is epistemically permissible to believe that our preferred views in multi-proposition disputes are true, or at least more likely true than not, then it is epistemically permissible for us to believe that we are über epistemic (...) superiors to our disagreeing colleagues in multi-proposition disputes. 3. It is not epistemically permissible to believe that we are über epistemic superiors to our disagreeing colleagues in multi-proposition disputes. 4. At least one of 1, 2, or 3, is false. (shrink)

This chapter puts to rest for all of eternity the self-undermining charge against conciliationism.

Quietist Moral Realists accept that there are moral facts and properties, while aiming to avoid many of the explanatory burdens thought to fall on traditional moral realists. This chapter examines the forms that Quietist Moral Realism has taken and the challenges it has faced, in order to better assess its prospects. The best hope, this chapter argues, lies in a pragmatist approach that distinguishes the different functions of diverse areas of discourse. This paves the way for a form of Quietism (...) that does not simply remain quiet about the explanatory demands of metaethics, but rather is able to diagnose where they go wrong. By combining a neopragmatic analysis of the discourse with an easy approach to ontology, , we can develop a form of Quietist Moral Realism that is far stronger than critics of quietism have appreciated. (shrink)

In a vivid re-creation of late sixteenth-century Flemish intellectual life, Mark Morford explores the intertwined careers of one of the period's most influential thinkers and one of its most original artists: Justus Lipsius and Peter Paul Rubens. He investigates the scholarship of Lipsius (1547-1606), whose revival of Roman Stoicism guided his contemporaries during the revolt of the Netherlands from the rule of Spain and whose teaching prepared future leaders in church and state. Maintaining that Lipsius' thought reached Peter Paul (...) Rubens through his brother, Philip Rubens, Morford analyzes the artist's use of Stoic philosophical and political allegory, beginning with his painting The Four Philosophers. This book discusses the revival of Stoicism in northern Europe, focusing on Lipsius' editions of Tacitus and Seneca, his widely read handbooks on constancy and politics, and his interaction with leading scholars and public figures. As his letters reveal, Lipsius was inconsistent in his life and unsuccessful in reconciling Stoicism with Catholic doctrine; Rubens, although at first sympathetic to the doctrines of Lipsius, is shown to have later transcended their limitations. (shrink)

Using path-breaking discoveries of cognitive science, Mark Johnson argues that humans are fundamentally imaginative moral animals, challenging the view that morality is simply a system of universal laws dictated by reason. According to the Western moral tradition, we make ethical decisions by applying universal laws to concrete situations. But Johnson shows how research in cognitive science undermines this view and reveals that imagination has an essential role in ethical deliberation. Expanding his innovative studies of human reason in Metaphors We (...) Live By and The Body in the Mind, Johnson provides the tools for more practical, realistic, and constructive moral reflection. (shrink)

In recent years the ways in which humans treat animals has come to hold a central place in contemporary ethics, encapsulating, as it does, our increasingly strained relationship with our environment as well as overlapping with other global issues such as overpopulation and hunger. Animal Rights: All That Matters is a compelling account of some of the often bitterly contentious debates surrounding animal ethics. Starting from the key argument that - ethically speaking - there is far less difference between humans (...) and animals than has conventionally been allowed, Mark Rowlands goes on to explore and illuminate a host of contemporary issues - from farming and animal experimentation to hunting and the preservation of endangered species. This accessible and readable book will appeal to both students and general readers, giving a fascinating introduction to animal rights - and what matters most about them -- P. 4 of cover. (shrink)

According to noncognitivists, when we say that stealing is wrong, what we are doing is more like venting our feelings about stealing or encouraging one another not to steal, than like stating facts about morality. These ideas challenge the core not only of much thinking about morality and metaethics, but also of much philosophical thought about language and meaning. _Noncognitivism in Ethics_ is an outstanding introduction to these theories, ranging from their early history through the latest contemporary developments. Beginning with (...) a general introduction to metaethics, Mark Schroeder introduces and assesses three principal kinds of noncognitivist theory: the speech-act theories of Ayer, Stevenson, and Hare, the expressivist theories of Blackburn and Gibbard, and hybrid theories. He pays particular attention both to the philosophical problems about what moral facts could be about or how they could matter which noncognitivism seeks to solve, and to the deep problems that it faces, including the task of explaining both the nature of moral thought and the complexity of moral attitudes, and the ‘Frege-Geach’ problem. Schroeder makes even the most difficult material accessible by offering crucial background along the way. Also included are exercises at the end of each chapter, chapter summaries, and a glossary of technical terms - making _Noncognitivism in Ethics_ essential reading for all students of ethics and metaethics. (shrink)

Friedrich Nietzsche was a troublesome genius, a figure outside the mainstream philosophical tradition whose very apartness has made him central to contemporary philosophy. Nietzsche and Political Thought reclaims the political implications of Nietzsche's work: it shows how his philosophy of power addresses key issues in modern political thought especially those having to do with the historical and cultural nature of human agency.In this thought-provoking study, Mark Warren claims entirely new ground. He develops a "postmetaphysical" political philosophy that provides a (...) link between Nietzsche's work and the later philosophies of the Frankfurt School and Michel Foucault.Warren comes to terms with Nietszche's views on power, freedom, domination, equality, ideology - topics that recent interpretations have neglected in favor of a focus on the literary and philosophical aspects of his work, but that in fact make these literary and philosophical concerns relevant to social and political thought. Importantly, Warren draws a distinction between the implications of Nietzsche's theories concerning power and agency for contemporary political thought and Nietzsche's own politics. He demonstrates how Nietzsche's actual political views did not reflect - and in large part falsified - his own philosophical insights which taken by themselves point toward a pluralistic society in which egalitarianism underscores individuality. But his politics, Warren argues, derived too heavily from a deficient understanding of modern social and political organization.Mark Warren is Visiting Assistant Professor of Political Science at Northwestern University. Nietzsche and Political Thought is included in the series Studies in Contemporary German Social Thought, edited by Thomas McCarthy. (shrink)

I argue that the technology to attempt to create posthumans is much closer than many realize and that the right to become posthuman is much more complicated than it might first appear.