The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium has set in train a strategy to overcome this problem. Existing (...) OBO ontologies, including the Gene Ontology, are undergoing a process of coordinated reform and new ontologies being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable, logically well-formed, and to incorporate accurate representations of biological reality. We describe the OBO Foundry initiative, and provide guidelines for those who might wish to become involved. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these relations (...) and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

The integration of biomedical terminologies is indispensable to the process of information integration. When terminologies are linked merely through the alignment of their leaf terms, however, differences in context and ontological structure are ignored. Making use of the SNAP and SPAN ontologies, we show how three reference domain ontologies can be integrated at a higher level, through what we shall call the OBR framework (for: Ontology of Biomedical Reality). OBR is designed to facilitate inference across the boundaries of domain ontologies (...) in anatomy, physiology and pathology. (shrink)

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena.

The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. (...) It is further distinguished from other maps in that it represents not some specific portion of spatial reality (say: Leeds in 1996), but rather the generalized or idealized spatial reality associated with a generalized or idealized human being at some generalized or idealized instant of time. It will be our concern in what follows to outline the approach to ontology that is represented by the FMA and to argue that it can serve as the basis for a new type of anatomical information science. We also draw some implications for our understanding of spatial reasoning and spatial ontologies in general. (shrink)

Tumors, abscesses, cysts, scars, fractures are familiar types of what we shall call pathological continuant entities. The instances of such types exist always in or on anatomical structures, which thereby become transformed into pathological anatomical structures of corresponding types: a fractured tibia, a blistered thumb, a carcinomatous colon. In previous work on biomedical ontologies we showed how the provision of formal definitions for relations such as is_a, part_of and transformation_of can facilitate the integration of such ontologies in ways which have (...) the potential to support new kinds of automated reasoning. We here extend this approach to the treatment of pathologies, focusing especially on those pathological continuant entities which arise when organs become affected by carcinomas. (shrink)

Original essays by leading philosophers of science explore the question of whether metaphysics can and should be naturalized--conducted as part of natural science.

This paper compares two alternative explanations of pragmatic encroachment on knowledge (i.e., the claim that whether an agent knows that p can depend on pragmatic factors). After reviewing the evidence for such pragmatic encroachment, we ask how it is best explained, assuming it obtains. Several authors have recently argued that the best explanation is provided by a particular account of belief, which we call pragmatic credal reductivism. On this view, what it is for an agent to believe a proposition is (...) for her credence in this proposition to be above a certain threshold, a threshold that varies depending on pragmatic factors. We show that while this account of belief can provide an elegant explanation of pragmatic encroachment on knowledge, it is not alone in doing so, for an alternative account of belief, which we call the reasoning disposition account, can do so as well. And the latter account, we argue, is far more plausible than pragmatic credal reductivism, since it accords far better with a number of claims about belief that are very hard to deny. (shrink)

"Expanding the Palace of Torah" offers a broad philosophical overview of the challenges the women's revolution poses to Orthodox Judaism, and Orthodox Judaism's response to those challenges.

This is the first German volume for more than one century, dealing with the two main subjects that have dominated the present reception of the Spanish philosopher and theologian Francisco Suárez (1548-1617): metaphysics and law theory. The contributors discuss both Suárez as an influential thinker of modern European school metaphysics and as a representant of a global law philosophy and ethics. They also debate on the combination of theory and praxis in the light of the question which commitment a universal (...) First Philosophy could have today. The volume is complimented by an introduction to Suárez's works and vita, an overview and guide to recent primary and secondary literature, as well as a name register.--publlisher's desciption. (shrink)

The divine attributes of immensity and omnipresence have been integral to classical Christian confession regarding the nature of the triune God. Divine immensity and omnipresence are affirmed in doctrinal standards such as the Athanasian Creed (c. 500), the Fourth Lateran Council (1215), the Council of Basel (1431–49), the Second Helvetic Confession (1566), the Westminster Confession of Faith (1647), the Second London Baptist Confession (1689), and the First Vatican Council (1869–70). In the first section of this chapter, I offer a brief (...) historical overview of divine immensity and divine omnipresence in the Christian tradition. I then offer a brief taxonomy of contemporary models of divine omnipresence in the philosophical and theological landscape. In the second, more constructive section, I aim to gesture toward the retrieval of several classical insights regarding immensity and omnipresence that remain unexplored in contemporary analytic work. (shrink)

Ross, Alf Loar, Brian, Editor.Directives and Norms. New York: Humanities Press, [1967]. ix, 188 pp. Reprint available April 2009 by The Lawbook Exchange, Ltd. ISBN-13: 978-1-58477-961-2. ISBN-10: 1-58477-961-6. Cloth with dust jacket. $65.00 * Reprint of the first American edition. One of the most interesting jurists of the post-World War II era, Ross [1899-1979] was a legal and moral philosopher, scholar of international law and the leading representative of Scandinavian Legal Realism. This book and On Law and Justice (1958) are (...) his principal works. In Directives and Norms Ross asks whether imperatives (or, to use his term, 'directives') are subject to logic in the same way as indicatives. He shows the difference between indicative and directive discourse and explains the concepts 'directive' and 'norm' as they function in the social sciences, especially in the study of law. A contemporary essay in the Modern Law Review (32:544), though critical of this work, was still impressed by its "clear and convincing account" of these processes. (shrink)

Redesigning humans -- Engaging with transhumanism -- Living "forever" : transhumanism and mortality -- "Unlimited" intelligence and well-being -- The role of the philosopher in transhumanism -- Transhumanism and Buddhist philosophy : two approaches to suffering -- Conclusion : Contesting and considering.

The understanding of the primary-secondary quality distinction has shifted focus from the mechanical philosophers’ proposal of primary qualities as explanatorily fundamental to current theorists’ proposal of secondary qualities as metaphysically perceiver dependent. The chapter critically examines this shift and current arguments to uphold the primary-secondary quality distinction on the basis of the perceiver dependence of color; one focus of the discussion is the role of qualia in these arguments. It then describes and criticizes reasons for characterizing color, smell, taste, sound, (...) and warmth and color as secondary qualities on the basis of our commonsense divisions among sensory modalities; Grice’s proposal for distinguishing among the sensory modalities is focal here. The general conclusion is that reasons for drawing the primary-secondary quality distinction are unconvincing. (shrink)

The study of social norms sprawls across all of the social sciences but the the concept lacks a unified conception and formal theory. We synthesize an account that can be applied generally, at the social scale of analysis, and can be applied to empirical evidence generated in field and lab experiments. More specifically, we provide new analysis on representing norms for application in empirical political science, and in parts of economics that do not follow the recent trend among some behavioral (...) economists to build models of the cognitive and motivational states of individuals taken “one at a time”. Foundational sources for our project are Bicchieri (2006, 2017), Kuran (1995), and Stirling (2012, 2016). From Bicchieri take that a norm exists in a social structure when a significant networked subset of individuals share descriptive and injunctive expectations that it regulates their interactions. From Kuran we take the insight that prevailing norms may come to be widely disliked by participants in networks but survive because norm suppress public displays of disenchantment. From Stirling we apply conditional game theory (CGT) to provide the technical resources for building our model of a norm-regulated social interaction. The example we use is a multi-player Investment/Trust Game. (shrink)

This chapter examines the spectrum inversion hypothesis as an argument against certain kinds of account of what it’s like to be conscious of color. The hypothesis aims to provide a counterexample to accounts of what it’s like to be conscious of color in non-qualitative terms, as well as to accounts of what it’s like to be conscious of color in terms of the representational content of conscious visual states (which, according to some philosophers, is in turn given an account in (...) non-qualitative terms). I explain the hypothesis’s reasoning in sections 1 and 2. I then take up background issues: since the counterexample provided by the hypothesis is typically given as a possibility rather than an actuality, I briefly discuss the kind of possibility involved in section 3, and the methodologies used to evaluate the plausibility of possibilities in section 4. In section 5, I describe some general considerations that are commonly used against the spectrum inversion hypothesis. I take up attempts to support the hypothesis with findings from color science in section 6. I end with comments skeptical of both the motivation for the spectrum inversion hypothesis and the methodology used to support it. (shrink)

In this paper I analyse the implications of “flattening” the curve for long-term care residents in the Province of Ontario, Canada during the first wave of the SARS-CoV-2/COVID-19 pandemic. I then question what the role of healthcare systems are in the response to public health emergencies and problematize their status as entities in need of protection. The ethical implications of this are discussed in light of potential challenges raised by climate change.

The role of individual factors in behavioral neuroscience is an important, but still neglected, area of research. For example, the Elevated Plus-Maze Test has been one of the most used paradigms to gauge unconditioned aversively motivated behavior in rodents. However, despite a great number of experiments with this test there have been only few efforts to assess systematic individual variations in the elevated plus-maze and related neurobiological functions. The present review aims to give, first, a general overview and introduction about (...) the test, and second, an animal model of anxiety based on natural variance of plus-maze behavior within a given unselected population of rats. Finally, critical aspects of such approaches in animal research are discussed, and suggestions are given as to where to go from here. (shrink)

Heinz Robert Schlettes skeptische Religionsphilosophie - bereits in ihrer Entstehungszeit quer zum Mainstream - hat in besonders intensiver Weise fundamentale Infragestellungen der Religion durch die Moderne einbezogen. Im Stichwort Empörung hat sie den humanen Gehalt der Religions-kritik aufgenommen - und sowohl religions-philosophisch identifiziert als auch für eine heute noch rechtfertigbare religiöse Haltung reklamiert. Schlettes Ansatz heute in die veränderten Konstellationen einer globalisierten Säkularisierungsdynamik und neuen Religionspräsenz wie eine Sonde einzuführen, verspricht erhellend aufklärerische Wirkung. Dies unternehmen die hier versammelten Beiträge im (...) Spektrum aus Philosophie, Theologie und literarischem Essay. (shrink)

In The Man Problem, Ross Honeywill posits that the potential for evil in all men is the social, political, and economic problem of our age. Drawing on the work of social critics and theorists including Zygmunt Bauman, Karl Marx, Hannah Arendt, Simone de Beauvoir, Jean Baudrillard, Slavoj Žižek, and others, the book traces destructive masculinity through cultural texts, social systems, and everyday life practices. Using the lens of social theory, social philosophy, feminist cultural studies, and sociology, The Man Problem explores (...) the legacy of the Enlightenment as a context for a social world constructed by men (in modernity), deconstructed (in postmodernity) and reconstructed (in the liquid present). This book investigates the outlines of the patriarchy and why the men who legitimate it behave the way they do. Despite the troubled and troubling legacy of masculinity, Honeywill reveals an alternative path forward. (shrink)

In this incisive political analysis, Kristin Ross thinks through everyday existence across a range of practices-from philosophy to history, from the visual arts to popular fiction-and across the forms taken by collective political action in contemporary struggles. Ross returns to Henri Lefebvre's powerful intuition that ordinary life is both residue and resource, the site of profound alienation and, by the same token, the origin of all emancipatory initiatives and desires.

Mental fictionalism is not the benign view that we may better understand the mind if we think of mental states as something like useful fictions, but the more radical view that mental states just are useful fictions. This paper argues that, if one were to treat mental states as a kind of fiction, the genre of fiction best suited to this purpose would be fantasy make-believe, in which magic is a central feature. After defending a promising fictionalist account of mental (...) discourse as a kind of prop-oriented make believe against recent criticism, the paper ultimately concludes that mental fictionalism faces further, potentially insurmountable, challenges. Most significantly, there is a problematic disanalogy between folk psychology and fiction: our mental state attributions aim to track truth, and this crucial aspect of our mental discourse cannot be captured if we interpret it as a kind of fictional discourse. For this and other reasons, the cost of adopting mental fictionalism likely outweighs its benefits. Whether or not these problems can be resolved, there is still much to be gained from taking mental fictionalism seriously: in doing so we may illuminate several important features of our own folk psychology that often go unnoticed. (shrink)

This unique study considers the influences of Stoic critics on the evolution of Thomas More's thought. The author argues that More's engaement with Erasmus's work radicalized his understanding of Christianity and shaped the writing of Utopia.

Paul Churchland does not open his latest book,The Engine of Reason, the Seat of the Soul, modestly. He begins by announcing, “This book is about you. And me … More broadly still, it is about every creature that ever swam, or walked, or flew over the face of the Earth” (p. 3). A few sentences later, he says, “Fortunately, recent research into neural networks … has produced the beginnings of a real understanding of how the biological brain works—a real understanding, (...) that is, of howyouwork, and everyone else like you” (p. 3). The implicit identification here of “me and you and everyone” with “the biological brain” might lead an uncharitable reader to view Churchland's book as “Eliminativism for the non-specialist,” that is, as an attempt to popularize the view of the mindbody problem with which, among his professional peers, Churchland has long been identified. However, I think that such a readingwouldbe uncharitable. He is, of course, frequently sceptical about the utility of folk psychology, but in this book he is much less concerned to disparage folk psychology as a failedtheory(by contrast with, for example, the arguments in Churchland 1979) than to urge the more modest view that the more we understand the brain, the better we shall be at helping those whose brains are damaged in ways that interfere seriously with the fulfilment of their lives. Hence, I am inclined to take him at his word when he says in the Preface that “The book is motivated first of all by sheer excitement over the new picture that is now emerging … [and] … also by the idea that this is information that the public needs to know” (p. xi). What excites Churchland so, at least overtly, is not the negative thesis he has defended elsewhere that folk-psychological terms fail to refer; his enthusiasm is mainly reserved for the positive thesis that minds are, essentially, interacting assemblies of recurrent neural networks. It is therefore this positive thesis, and Churchland's defence of it, that I will assess in the following discussion. (shrink)

The idea of an ideological war between science and religion, Thompson argues, is founded on a mistake. But this does not mean that there is nothing at stake. For behind the ill-conceived conflict lie complex issues about the nature of mind, consciousness, experience, subjectivity, quality, value, and the like, all of which need to be disentangled and assessed in their own right. Outgrowing Materialism leads the reader through a sequence of five “Worlds,” each of which offers a distinct way of (...) understanding (or failing to understand) these issues, and where God might belong (or not). Writing accessibly, but with a sharp eye for detail, Thompson sheds new light on the familiar territory of materialism, dualism, and structural realism, and evaluates the growing attraction of the multiverse. He argues that dualism mechanized the material world; then materialism exorcised the mental “ghost” from the machine; and finally, this machine is evaporating into pure mathematics. Outgrowing Materialism is half of Ten Ways to Weave the World: Matter, Mind, and God. The sequel, Embodying Mind, discusses five “Worlds” that precede and follow those discussed here. However, Outgrowing Materialism stands in its own right as a critique of the modern science v. religion dilemma. (shrink)

Guala notes that low-cost punishment is the main mechanism that deters free-riding in small human communities. This mechanism is complemented by unusual human vulnerability to gossip. Defenders of an evolutionary discontinuity supporting human sociality might seize on this as an alternative to enjoyment of moralistic aggression as a special adaptation. However, the more basic adaptation of language likely suffices.

This chapter contains sections titled: Pregnancy and the First Noble Truth: Pain is Inevitable The Second Noble Truth: Pain Arises from Cravings and Attachment The Third Noble Truth: The End of Suffering is Possible, or How to Be a Feminist Buddhist Mommy Mommy Meditations Notes.

This brief, accessible introduction shows that philosophy is valuable, practical, and significant for every aspect of Christian life and ministry.

T. 1. Beim jungen Augustinus.--T. 2. Die antimanichäische Epoche.

A total of 1918 loci, detected by the hybridization of 938 expressed sequence tag unigenes from 26 Triticeae cDNA libraries, were mapped to wheat homoeologous group 4 chromosomes using a set of deletion, ditelosomic, and nulli-tetrasomic lines. The 1918 EST loci were not distributed uniformly among the three group 4 chromosomes; 41, 28, and 31% mapped to chromosomes 4A, 4B, and 4D, respectively. This pattern is in contrast to the cumulative results of EST mapping in all homoeologous groups, as reported (...) elsewhere, that found the highest proportion of loci mapped to the B genome. Sixty-five percent of these 1918 loci mapped to the long arms of homoeologous group 4 chromosomes, while 35% mapped to the short arms. The distal regions of chromosome arms showed higher numbers of loci than the proximal regions, with the exception of 4DL. This study confirmed the complex structure of chromosome 4A that contains two reciprocal translocations and two inversions, previously identified. An additional inversion in the centromeric region of 4A was revealed. A consensus map for homoeologous group 4 was developed from 119 ESTs unique to group 4. Forty-nine percent of these ESTs were found to be homoologous to sequences on rice chromosome 3, 12% had matches with sequences on other rice chromosomes, and 39% had no matches with rice sequences at all. Limited homology was found between wheat ESTs on homoeologous group 4 and the Arabidopsis genome. Forty-two percent of the homoeologous group 4 ESTs could be classified into functional categories on the basis of blastX searches against all protein databases. (shrink)

The Liberating art of philosophy: a foundational anthology provides students with seminal texts and articles that pique their philosophical curiosity, encourage critical thought, and invite questioning.