These essays on the way medieval Arabic philosophy was first introduced into European universities explain their formal working and provide fascinating accounts of the hardy souls who first ventured, literally, into hitherto unknown terrain.

These essays on the way medieval Arabic philosophy was first introduced into European universities explain their formal working and provide fascinating accounts of the hardy souls who first ventured, literally, into hitherto unknown terrain.

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified forms. Because (...) proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Many of our ideological, political, moral, religious, aesthetic, scientific beliefs, as well as those concerning everyday life, are controversial; other people do not share them. As a rule, that does not bother us much: we tend to retain our contestable beliefs even if we ascribe no less skill and well-informedness to those who represent other points of view than to ourselves. But is that really reasonable? Shouldn't we often admit that we might be as wrong as others? And if we (...) do, shouldn't this consequently lead us to give up many of our beliefs in favor of agnostic attitudes? Marc Andree Weber argues that in the face of disagreement with equally competent and well-informed interlocutors we should almost always refrain from insisting on our controversial beliefs – with the few exceptions being all the more remarkable. (shrink)

Transparency and openness are broadly endorsed in energy and environmental modelling and analysis, but too little attention is given to the transparency of value-laden assumptions. Current practices for transparency focus on making model source code and data available, documenting key equations and parameter values, and ensuring replicability of results. We argue that, even when followed, these guidelines are insufficient for achieving deep transparency, in the sense that results often remain driven by implicit value-laden assumptions that are opaque to other modellers (...) and researchers, and that may not be understood by wider audiences to be controversial. This paper identifies additional best practices for achieving transparency by highlighting issues where disagreement over value judgements will persist for the foreseeable future. Recommendations for deepening transparency are developed by learning from successes and ongoing challenges represented in three case studies. We provide recommendations to accelerate the adoption of additional best practices for deepening transparency of energy and environmental modelling in policy-relevant domains, increasing stakeholder participation with non-modellers, and encouraging interdisciplinary dialogue. (shrink)

The purpose of this anthology is to bring together in one volume some of the texts published in the series "Werkprofile", which focus on Kant’s relationship to his philosophical contemporaries and predecessors, and to make them accessible to a wider audience in English. In doing so, the volume is aimed at those who have an interest in better understanding the premises of Kant's philosophy, its historical context, and the development of many of Kant’s fundamental ideas. As it is often hard (...) to glean philosophical motivation directly from reading Kant’s texts, understanding Kant’s commitment to answering certain questions and his silence on others, requires a historical approach. This broader purview will also be helpful for grasping deeper systematic questions at work throughout Kant’s philosophy. The anthology thus aims at inviting a more wide-angled view of Kant’s philosophy by focusing on overlooked references and historical figures. Scholarship on these references is still at an early stage, even though important steps have been taken in this direction in recent years. The aim of our volume is to build on this development and to supplement and expand the content of existing research. (shrink)

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Recognizing the importance of health‐promoting relationships in engaging people who are experiencing homelessness in care, most research on health clinics for homeless persons has involved some recognition of client–provider relationships. However, what has been lacking is the inclusion of a critical analysis of the policy context in which relationships are enacted. In this paper, we question how client–provider relationships are enacted within the culture of community care with people who are experiencing homelessness and how clinic‐level and broader social and health (...) policies shape relationships in this context. We explore these questions within a critical theoretical perspective utilizing a critical ethnographic methodology. Data were collected using multiple methods of document review, participant observation, in‐depth interviews and focus groups. The participants include both clients at a community health clinic, and all clinic service providers. We explore how clients and providers characterized each other as ‘good’ or ‘bad’. For providers, this served as a means by which they policed behaviours and enforced social norms. The means by which both providers’ and clients’ negotiated relationships are explored, but this is couched within both local and system‐level policies. This study highlights the importance of healthcare providers and clients being involved in broader policy and systemic change. (shrink)

Contemporary scholarship interprets Sergej Bulgakov’s sophiology as an engagement of Orthodox theology with the modern world and as being on its way to becoming a political theology. In this paper I undertake a re-evaluation of the kind of engagement sophiology was and was intended to be, and of the kind of world it was destined for. It will be argued that sophiology was not so much a political-theological engagement with the world concentrating on the relation of religion and politics or (...) state and church, but rather an economic-theological engagement in the tradition of oikonomia theology that tried to understand the world in its relation to and as part of divine oikonomia. Furthermore, the world sophiology promotes engagement with is not only the real contemporary world, or the sociological ideal type of modernity, but primarily the world as such, this secular and human world over and against the divine and transcendent world. (shrink)

Under the impact of cultural, economic and legislative forces the traditional role of the university health center is changing. The academic health center is rapidly evolving from a relatively undifferentiated general hospital, primarily responsible for the education of undergraduate students of medicine, into a center of clinical research, caring for very specialized mixes of patients, and having as its primary educational mission the training of subspecialists. The nature of the forces responsible for this change are analyzed, and some of its (...) possible consequences for the definition of quality health care, for the shape of medical practice and medical education, and for the allocation of resources for health care are explored. This exploration suggests that the functional separation of the medical school from the highly technical, clinical research center is inevitable. This in turn may exacerbate tensions within medicine between the physician as scientist and as healer, between curative and preventive practice and between personal and public health. Although the effects of this separation on medical education remain obscure, it has already occasioned the most comprehensive review of the medical curriculum since the time of Flexner. Out of this is likely to develop a more generalist view of the education of future physicians. (shrink)

What is the nature of truth? Blake Hestir offers an investigation into Plato's developing metaphysical views, and examines Plato's conception of being, meaning, and truth in the Sophist, as well as passages from several other later dialogues including the Cratylus, Parmenides, and Theaetetus, where Plato begins to focus more directly on semantics rather than only on metaphysical and epistemological puzzles. Hestir's interpretation challenges both classical and contemporary interpretations of Plato's metaphysics and conception of truth, and highlights new parallels between (...) Plato and Aristotle, as well as clarifying issues surrounding Plato's approach to semantics and thought. This book will be of interest to scholars and students of ancient Greek philosophy, metaphysics, contemporary truth theory, linguistics, and philosophy of language. (shrink)

This paper examines the development of the modern concept of substance from Leibniz to Hegel. I will focus primarily on the problem of the inner and outer nature of substance. I will show that if one considers Hegel’s discussion of substance against the background of the controversy between Leibniz and Kant about the inner and outer nature of substance, it becomes clear that for Hegel both Leibniz and Kant grasped the whole concept of substance only partially and in its abstract (...) moments. This is because they both concentrate on one aspect of substance and absolutize it. Hegel, on the other hand, not only overcomes the fundamental difference between the inner and outer of substance, but also develops the connection between the different moments of substance, causality and interaction from the rationalist concept of substance itself. (shrink)

Doxastic involuntarists have paid insufficient attention to two debates in contemporary epistemology: the permissivism debate and the debate over norms of assertion and belief. In combination, these debates highlight a conception of belief on which, if you find yourself in what I will call an ‘equipollent case’ with respect to some proposition p, there will be no reason why you can’t believe p at will. While doxastic involuntarism is virtually epistemological orthodoxy, nothing in the entire stock of objections to belief (...) at will blocks this route to doxastic voluntarism. Against the backdrop of the permissivism debate and the literature on norms of belief and assertion, doxastic involuntarism emerges as an article of faith, not the obvious truth it’s usually purported to be. (shrink)

Call generalism about children’s and adults’ wellbeing the thesis that the same theory of wellbeing applies to both children and adults. Our goal is to examine whether generalism is true. While this question has not received much attention in the past, it has recently been suggested that generalism is likely to be false and that we need to elaborate different theories of children’s and adults’ wellbeing. In this paper, we defend generalism against the main objections it faces and make a (...) positive case for it. (shrink)

Does knowledge depend in any interesting way on our practical interests? This is the central question in the pragmatic encroachment debate. Pragmatists defend the affirmative answer to this question while purists defend the negative answer. The literature contains two kinds of arguments for pragmatism: principle-based arguments and case-based arguments. Principle-based arguments derive pragmatism from principles that connect knowledge to practical interests. Case-based arguments rely on intuitions about cases that differ with respect to practical interests. I argue that there are insurmountable (...) problems for both kinds of arguments, and that it is therefore unclear what motivates pragmatism. (shrink)

Dance anthropologists and ethnomusicologists are trained to treat the labels ‘dance’ and ‘music’ with caution, because the terms carry preconceptions that may mask significant aspects of the structured movement/sound systems they study. Yet many talk about ‘the body’ – the medium through which these systems come into being – as something given and ‘true’, without investigating its emic conceptualizations or looking into the implications these may have in terms of how music and dance are experienced. The article investigates the dancing (...) bodies of western ballet dancers and of Tiwi dancers of northern Australia. The latter have an extensive vocabulary for body parts, but no word for ‘body’ as a bounded entity, comparable to the ‘body’ conceptualized by ballet dancers. The article argues that for the Tiwi landscape and human bodies are unavoidably tied together and that the dancers incarnate both land and cosmology. While specific parts have a concrete practical existence, the whole body expands into the landscape so that the landscape becomes flesh. Through the aesthetic transformation of dancing, dancers and land become one, and life is sustained and the land revitalized. (shrink)

Pacifism is the view that necessarily, the nonconsensual harming of pro tanto rights-bearers is all-things-considered morally impermissible. Critics of pacifism frequently point to common moral intuitions about self-defenders and other-defenders as evidence that pacifism is false and that self- and other-defense are often morally justified. I call this the Justification View and defend its rival, the Excuse View. According to the latter, a robust view of moral excuse adequately explains the common moral intuitions invoked against pacifism and is compatible with (...) pacifism. The paper proceeds in five steps. First, I identify ten intuitive data points that require explanation. Second, I introduce the justification/excuse distinction. Third, I demonstrate the Excuse View’s equal explanatory power with respect to the intuitive data. Fourth, I defend the Fair Use Principle: When evaluating the plausibility of rival theories J and E, the use of datum d’s full intuitive force against E and for J is epistemically permissible only if (i) d is better explained by J than E and (ii) no intuitive components of d are equally well-explained by E. Finally, I conclude that the conjunction of pacifism and the Excuse View renders the intuitive defense of the Justification View largely moot, and that this is a substantial victory for pacifism. (shrink)

During the past 25 years, the words “theory of action” and “agency theory” have become key-terms in a new branch of philosophy. The themes appear to gain a centrality and influence such that one is led to think that they should cover most of philosophy, including the foundation for all of the human sciences. The number of treatises on human action and on philosophical and special-scientific theories of action is staggering. For the most part inspired by analytic philosophy, the new (...) approach threatens to take over that school’s central place on the stage of international philosophical concern. Having ousted theory of science from that position with an avalanche of analytic studies, analytic philosophy, in turn, is now being overrun by philosophy of action as supposedly suitable basis for the sciences. (shrink)

With their landmark architectures, exhibitions and museums of science and technology partake in the spatial inscription of science in twentieth century landscapes. Unlike other beacons of progress, exhibitions and museums of science and technology double up, inside, as material arrangements of objects, visuals and texts aiming to confer meaning onto the modern world. They both embody and seek to order the spectacle of modernity while often being deployed with the aim of promoting particular visions of social and material progress. An (...) approach sensitive to the material, spatial, and experiential dimensions of displaying science and technology suggests that exhibitions and museums were in the twentieth century crucial sites for reflecting upon and promoting particular futures. (shrink)

Andrée-Anne Cormier and Harry Brighouse explore the question of whether there are good reasons for schools to try and produce citizens disposed to use, and practiced in, civil discourse and behavior, and if so, what this implies for schools. First, the authors propose an account of the value (and disvalue) of civility, drawing on Cheshire Calhoun’s conception. They argue that civility is good in many circumstances, but not always. In some circumstances, it is neither beneficial nor morally required. Second, (...) they elucidate the reasons for teaching civility in schools and what they think that doing so would involve, what demands it would make on teachers, and how the aim of promoting civility would shape the structure of schools. Finally, they identify some reasons for pessimism that schools can be very successful in promoting civility. They do not think that these are conclusive reasons against teaching civility in schools, but they suggest that civility can only be taught well if educators are clear-eyed about the hurdles they will have to overcome. (shrink)

Robert Rosen has proposed several characteristics to distinguish “simple” physical systems (or “mechanisms”) from “complex” systems, such as living systems, which he calls “organisms”. The Memory Evolutive Systems (MES) introduced by the authors in preceding papers are shown to provide a mathematical model, based on category theory, which satisfies his characteristics of organisms, in particular the merger of the Aristotelian causes. Moreover they identify the condition for the emergence of objects and systems of increasing complexity. As an application, the cognitive (...) system of an animal is modeled by the “MES of cat-neurons” obtained by successive complexifications of his neural system, in which the emergence of higher order cognitive processes gives support to Mario Bunge’s “emergentist monism.”. (shrink)

In this paper we argue that God and the Good Life, a prominent philosophy as a way of life (PWOL) undergraduate course, serves the needs of novices in philosophy classrooms, whether they plan to continue in the study of philosophy or not. We draw from both philosophy and educational psychology in making our case and highlight four distinctive components of God and the Good Life pedagogy at the University of Notre Dame: 1) transformative learning goals, 2) immersive experiences, 3) deep (...) personal connections to students’ everyday lives, and 4) cooperative relationships of mutual support in a community of dialogue. We end with a coda on even wider relevance for PWOL pedagogies in bringing about the pluralistic society we hope for, even in our deeply polarized societal moment. (shrink)

Socrates op de markt, Filosofie in bedrijf was first published in the Netherlands in 1997 and reprinted in 1999.1 It was translated into German and published in Germany in late 2000. The book covers the need today for Socratic dialogue, its methods, its uses and related concepts. These include elenchus (the refutation of what one thought one knew); maieutics (Socratic midwifery making latent knowledge conscious); the relationship of knowledge to feeling, virtue and the formation of personality; and the distinction between (...) three types of knowledge: scientific (episteme), professional (techne) and practical wisdom (phronesis). Our extracts — the first in English — set out Kessels’ arguments for using Socratic dialogue today, his account of its unique role in organisational learning, and a case history: a dialogue with a top management team in which elenchus plays a signal part as they seek to define a policy for handling redundancies. (shrink)

According to what I will call ‘the disanalogy thesis,’ beliefs differ from actions in at least the following important way: while cognitively healthy people often exhibit direct control over their actions, there is no possible scenario where a cognitively healthy person exhibits direct control over her beliefs. Recent arguments against the disanalogy thesis maintain that, if you find yourself in what I will call a ‘permissive situation’ with respect to p, then you can have direct control over whether you believe (...) p, and you can do so without manifesting any cognitive defect. These arguments focus primarily on the idea that we can have direct doxastic control in permissive situations, but they provide insufficient reason for thinking that permissive situations are actually possible, since they pay inadequate attention to the following worries: permissive situations seem inconsistent with the uniqueness thesis, permissive situations seem inconsistent with natural thoughts about epistemic akrasia, and vagueness threatens even if we push these worries aside. In this paper I argue that, on the understanding of permissive situations that is most useful for evaluating the disanalogy thesis, permissive situations clearly are possible. (shrink)

Kant is well known for his criticism of knowledge claims of traditional metaphysics. The concept of substance must be considered one of the most important notions in ontology. Kant transforms traditional ontology into an analytic of pure understanding. Accordingly, the concept of substance has become a category of pure understanding. The application of this category in the First Analogy of Experience faces some particular problems, which are highlighted in the current debate. This paper seeks to furnish a coherent reading of (...) the First Analogy by considering which purpose the category of substance is meant to serve in transcendental idealism. (shrink)