The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

The Plant Ontology (PO) (http://www.plantontology.org) (Jaiswal et al., 2005; Avraham et al., 2008) was designed to facilitate cross-database querying and to foster consistent use of plant-specific terminology in annotation. As new data are generated from the ever-expanding list of plant genome projects, the need for a consistent, cross-taxon vocabulary has grown. To meet this need, the PO is being expanded to represent all plants. This is the first ontology designed to encompass anatomical structures as well as growth and developmental stages (...) across such a broad taxonomic range. While other ontologies such as the Gene Ontology (GO) (The Gene Ontology Consortium, 2010) or Cell Type Ontology (CL) (Bard et al., 2005) cover all living organisms, they are confined to structures at the cellular level and below. The diversity of growth forms and life histories within plants presents a challenge, but also provides unique opportunities to study developmental and evolutionary homology across organisms. (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 Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)

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)

The Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

While recognising the power and fundamental importance of Wickham’s Framing the Early Middle Ages, this essay explores some of the problems associated with the relative silence within the text about the issue of the forces of production and their development. By contrast, Harman suggests that Wickham’s most important contribution to our understanding of the period, his concept of a peasant-mode of production, is best understood against the backdrop of prior developments of the forces of production. Moreover, the peasant-mode’s temporality is (...) itself best understood against the background of further developments of the forces of production. (shrink)

Sciabarra replies to the seven respondents to his Fall 2002 essay on Rand, Rush, and progressive rock music. He defends the view that Rand's dialectical orientation underlies a fundamentally radical perspective. Rand shared with the counterculture—especially its libertarian progressive rock representatives—a repudiation of authoritarianism, while embracing the "unknown ideal" of capitalism. Her ability to trace the interrelationships among personal, cultural, and structural factors in social analysis and her repudiation of false alternatives is at the heart of that ideal vision, which (...) transcends left and right. (shrink)

In his wide-ranging study of architecture and cultural evolution, Chris Abel argues that, despite progress in sustainable development and design, resistance to changing personal and social identities shaped by a technology-based and energy-hungry culture is impeding efforts to avert drastic climate change. The book traces the roots of that culture to the coevolution of Homo sapiens and technology, from the first use of tools as artificial extensions of the human body to the motorized cities spreading around the world, whose (...) uncontrolled effects are fast changing the planet itself. Advancing a new concept of the meme, called the 'technical meme', as the primary agent of cognitive extension and technical embodiment, Abel proposes a theory of the 'extended self' as a complex and diffuse outcome of that coevolution. Challenging conventional ideas of the self as a separate and autonomous being, the extended self, he explains, encompasses material and spatial as well as psychological and social elements, including the built environment and artifacts, and now reaches out into the virtual world of cyberspace. Drawing upon research into extended cognition and embodied minds from philosophy, psychology and the neurosciences, the book presents a new approach to environmental and cultural studies. N.B. This book was the winner of the International Committee of Architectural Critics 2017 Bruno Zevi Book Award by unanimous decision of the international jury. (shrink)

Expanding his collected essays on architectural theory and criticism, Chris Abel pursues his explorations across disciplinary and regional boundaries in search of a deeper understanding of architecture in the evolution of human culture and identity formation. From his earliest writings predicting the computer-based revolution in customised architectural production, through his novel studies on 'tacit knowing' in design or hybridisation in regional and colonial architecture, to his radical theory of the 'extended self', Abel has been a consistently fresh and provocative (...) thinker, contesting both conventions and intellectual fashions. This revised third edition includes a new introduction and six additional chapters by the author covering a broad range of related topics, up to recent concerns with genetic design methods and virtual selves. Together with the former essays, the book presents a unique global perspective on the changing cultural issues and technologies shaping human identities and the built environment in diverse parts of the world, both East and West (from the book cover). (shrink)

In _The Persistence of the Sacred in Modern Thought,_ Chris L. Firestone, Nathan A. Jacobs, and thirteen other contributors examine the role of God in the thought of major European philosophers from the seventeenth to the nineteenth century. The philosophers considered are, by and large, not orthodox theists; they are highly influential freethinkers, emancipated by an age no longer tethered to the authority of church and state. While acknowledging this fact, the contributors are united in arguing that this is (...) only one side of a complex story. To redress the imbalance of attention to secularism among crucial modern thinkers and to consolidate a more theologically informed view of modernity, they focus on the centrality of the sacred in the thought of these philosophers. The essays, each in its own way, argue that the major figures in modernity are theologically astute, bent not on removing God from philosophy but on putting faith and reason on a more sure footing in light of advancements in science and a perceived need to rethink the relationship between God and world. By highlighting and defending the theologically affirmative dimensions of thinkers such as Thomas Hobbes, Gottfried Leibniz, John Locke, Immanuel Kant, F. W. J. Schelling, G. W. F. Hegel, and others, the essayists present a forceful and timely correction of widely accepted interpretations of these philosophers. To ignore or downplay the theological dimensions of the philosophical works they address, they argue, distorts our understanding of modern thought. "Over the past twenty-five years there has been a gradual change in the study of modern philosophy toward recognizing the centrality of our relation to God in the work of most of the major modern thinkers of the period. _The Persistence of the Sacred in Modern Thought_ is a timely and useful collection that has the potential to crystallize this important development in the study of modern philosophy." —_John E. Hare, Yale Divinity School_. (shrink)

In this book, Chris W. Surprenant puts forward an original position concerning Kant’s practical philosophy and the intersection between his moral and political philosophy. Although Kant provides a detailed account of the nature of morality, the nature of human virtue, and how right manifests itself in civil society, he does not explain fully how individuals are able to become virtuous. This book aims to resolve this problem by showing how an individual is able to cultivate virtue, the aim of (...) Kant’s practical philosophy. Through an examination of Kant’s accounts of autonomy, the state, and religion, and their effects on the cultivation of virtue, Surprenant develops a Kantian framework for moral education, and ultimately raises the question of whether or not Kantian virtue is possible in practice. (shrink)

How ought we to respond to strangers in imminent need? Many people suggest that we need justice to temper the partiality of care. In this paper 1 argue that neither care nor justice adequately motivates attention to the suffering of strangers. Rather, a different virtue, compassion grounded in equanimity, is required. I demonstrate that the virtue of compassion alhws the agent to sustain her engagement with suffering strangers without sacrificing her own flourishing.

Recent clinical trials show that psychedelics such as LSD and psilocybin can be given safely in controlled conditions, and can cause lasting psychological benefits with one or two administrations. Supervised psychedelic sessions can reduce symptoms of anxiety, depression, and addiction, and improve well-being in healthy volunteers, for months or even years. But these benefits seem to be mediated by "mystical" experiences of cosmic consciousness, which prompts a philosophical concern: do psychedelics cause psychological benefits by inducing false or implausible beliefs about (...) the metaphysical nature of reality? This book is the first scholarly monograph in English devoted to the philosophical analysis of psychedelic drugs. Its central focus is the apparent conflict between the growing use of psychedelics in psychiatry and the philosophical worldview of naturalism. Within the book, Letheby integrates empirical evidence and philosophical considerations in the service of a simple conclusion: this "Comforting Delusion Objection" to psychedelic therapy fails. While exotic metaphysical ideas do sometimes come up, they are not, on closer inspection, the central driver of change in psychedelic therapy. Psychedelics lead to lasting benefits by altering the sense of self, and changing how people relate to their own minds and lives-not by changing their beliefs about the ultimate nature of reality. The upshot is that a traditional conception of psychedelics as agents of insight and spirituality can be reconciled with naturalism (the philosophical position that the natural world is all there is). Controlled psychedelic use can lead to genuine forms of knowledge gain and spiritual growth-even if no Cosmic Consciousness or transcendent divine Reality exists. Philosophy of Psychedelics is an indispensable guide to the literature for researchers already engaged in the field of psychedelic psychiatry, and for researchers-especially philosophers-who want to become acquainted with this increasingly topical field. (shrink)

We review Potts' influential book on the semantics of conventional implicature, offering an explication of his technical apparatus and drawing out the proposal's implications, focusing on the class of CIs he calls supplements. While we applaud many facets of this work, we argue that careful considerations of the pragmatics of CIs will be required in order to yield an empirically and explanatorily adequate account.

This book takes concepts developed by researchers in theoretical computer science and adapts and applies them to the study of natural language meaning. Summarizing over a decade of research, Chris Barker and Chung-chieh Shan put forward the Continuation Hypothesis: that the meaning of a natural language expression can depend on its own continuation.

In this incisive study of the biological and cultural origins of the human self, the author challenges readers to re-think ideas about the self and consciousness as being exclusive to humans. In their place, he expounds a metatheoretical approach to the self as a purposeful system of extended cognition common to animal life: the invisible medium maintaining mind, body and environment as an integrated 'field of being'. Supported by recent research in evolutionary and developmental studies together with related discoveries in (...) animal behavior and the neurosciences, the author examines the factors that have shaped the evolution of the animal self across widely different species and times, through to the modern, technologically enmeshed human self; the differences between which, he contends, are relations of degree rather than absolute differences. We are, he concludes, instinctive and 'fuzzy' individuals clinging to fragile identities in an artificial and volatile world of humanity's own making, but which we now struggle to control. This book, which restores the self to its fundamental place in identity formation, will be of great interest for students and academics in the fields of social, developmental and environmental psychology, together with readers from other disciplines in the humanities, especially cultural theory and philosophy. (shrink)

Conflicting accounts of the role of mathematics in our physical theories can be traced to two principles. Mathematics appears to be both (1) theoretically indispensable, as we have no acceptable non-mathematical versions of our theories, and (2) metaphysically dispensable, as mathematical entities, if they existed, would lack a relevant causal role in the physical world. I offer a new account of a role for mathematics in the physical sciences that emphasizes the epistemic benefits of having mathematics around when we do (...) science. This account successfully reconciles theoretical indispensability and metaphysical dispensability and has important consequences for both advocates and critics of indispensability arguments for platonism about mathematics. (shrink)

One of the main challenges confronting Humean accounts of natural law is that Humean laws appear to be unable to play the explanatory role of laws in scientific practice. The worry is roughly that if the laws are just regularities in the particular matters of fact (as the Humean would have it), then they cannot also explain the particular matters of fact, on pain of circularity. Loewer (2012) has defended Humeanism, arguing that this worry only arises if we fail to (...) distinguish between scientific and metaphysical explanations. However, Lange (2013, 2018) has argued that scientific and metaphysical explanations are linked by a transitivity principle, which would undercut Loewer's defense and re-ignite the circularity worry for the Humean. I argue here that the Humean has antecedent reasons to doubt that there are any systematic connections between scientific and metaphysical explanations. The reason is that the Humean should think that scientific and metaphysical explanation have disparate aims, and therefore that neither form of explanation is beholden to the other in its pronouncements about what explains what. Consequently, the Humean has every reason to doubt that Lange's transitivity principle obtains. (shrink)

This paper is an enquiry into the logical, metaphysical, and physical possibility of time travel understood in the sense of the existence of closed worldlines that can be traced out by physical objects. We argue that none of the purported paradoxes rule out time travel either on grounds of logic or metaphysics. More relevantly, modern spacetime theories such as general relativity seem to permit models that feature closed worldlines. We discuss, in the context of Gödel's infamous argument for the ideality (...) of time based on his eponymous spacetime, what this apparent physical possibility of time travel means. Furthermore, we review the recent literature on so-called time machines, i.e., of devices that produce closed worldlines where none would have existed otherwise. Finally, we investigate what the implications of the quantum behaviour of matter for the possibility of time travel might be and explicate in what sense time travel might be possible according to leading contenders for full quantum theories of gravity such as string theory and loop quantum gravity. (shrink)

In their recent article “A Hierarchy of Classical and Paraconsistent Logics”, Eduardo Barrio, Federico Pailos and Damien Szmuc present novel and striking results about meta-inferential validity in various three valued logics. In the process, they have thrown open the door to a hitherto unrecognized domain of non-classical logics with surprising intrinsic properties, as well as subtle and interesting relations to various familiar logics, including classical logic. One such result is that, for each natural number n, there is a logic which (...) agrees with classical logic on tautologies, inferences, meta-inferences, meta-meta-inferences, meta-meta-...-meta-inferences, but that disagrees with classical logic on n + 1-meta-inferences. They suggest that this shows that classical logic can only be characterized by defining its valid inferences at all orders. In this article, I invoke some simple symmetric generalizations of BPS’s results to show that the problem is worse than they suggest, since in fact there are logics that agree with classical logic on inferential validity to all orders but still intuitively differ from it. I then discuss the relevance of these results for truth theory and the classification problem. (shrink)

Users of psychedelic drugs often report that their sense of being a self or ‘I’ distinct from the rest of the world has diminished or altogether dissolved. Neuroscientific study of such ‘ego dissolution’ experiences offers a window onto the nature of self-awareness. We argue that ego dissolution is best explained by an account that explains self-awareness as resulting from the integrated functioning of hierarchical predictive models which posit the existence of a stable and unchanging entity to which representations are bound. (...) Combining recent work on the ‘integrative self' and the phenomenon of self-binding with predictive processing principles yields an explanation of ego dissolution according to which self-representation is a useful Cartesian fiction: an ultimately false representation of a simple and enduring substance to which attributes are bound which serves to integrate and unify cognitive processing across levels and domains. The self-model is not a mere narrative posit, as some have suggested; it has a more robust and ubiquitous cognitive function than that. But this does not mean, as others have claimed, that the self-model has the right attributes to qualify as a self. It performs some of the right kinds of functions, but it is not the right kind of entity. Ego dissolution experiences reveal that the self-model plays an important binding function in cognitive processing, but the self does not exist. (shrink)

Chris Daly; Tropes, Proceedings of the Aristotelian Society, Volume 94, Issue 1, 1 June 1994, Pages 253–262, https://doi.org/10.1093/aristotelian/94.1.253.

Chris Daly; Tropes, Proceedings of the Aristotelian Society, Volume 94, Issue 1, 1 June 1994, Pages 253–262, https://doi.org/10.1093/aristotelian/94.1.253.

The purpose of this paper is to analyze the relationship between national culture and ethical decision making. Established theories of ethics and moral development are reviewed and a culture-based model of ethical decision making in organizations is derived. Although the body of knowledge in both cross-cultural management and ethics is well documented, researchers have failed to integrate the influence of cultural values into the ethical decision-making paradigm. A conceptual understanding of how managers from different nations make decisions about highly ethical (...) issues will provide business ethics researchers with a sound theoretical foundation upon which future empirical inquiry can be based. (shrink)

Good theory; bad politics - this is how Zizek's works have been described. Now Chris McMillan argues that Zizek's reading of global capitalism could reinvent political subversion. He highlights the political consequences of Zizek's fundamental concepts, such as the Lacanian Real, universality and the communist hypothesis. He argues that Zizek's turn to Communism represents the ultimate significance of Zizek's work for the 21st century and a marked new direction for Zizekian theory. While Zizek's work attracts a lot of labels, (...) most of them pejorative - communist, conservative, anti-semantic - Chris McMillan identifies Zizek's unique and productive contribution to social and political theory, constructing his work as a response to the difficulties of contemporary social theory and the political deadlock of global capitalism. (shrink)

This article explores the arguments for architecture having an identifiable essence equivalent to Heidegger's concept of 'dwelling' and place identity, versus those who claim it is no more than a 'hybrid' collection of many different technical, social and cultural practices. The opposing positions in architecture are compared by analogy with the opposing theories of language which underly them, the latter position being associated with the universalist theory of language propagated by Chomsky, while the purpose of architecture in identity formation is (...) compared with Wittgenstein's theory of the interdependence between language and human behaviour as a 'form of life'. As an example, the author points to colonial architecture as a clear case where people retain 'that part of their identity which is their architecture'. The author concludes that, in so far as objects also have meanings, then the physical environment must also be taken into account in the evolution of mind. (shrink)

This article examines the prospects for an authentic regional architecture in the light of alternative development paradigms. It is argued that the failure of orthodox development strategies and the domination of western culture, including architecture, over non-Western cultures, is due to fundamental imbalances between northern and southern economic structures. By contrast, ecodevelopment, appropriate technology and regional architecture all represent significant devolutionary movements toward a global “eco-culture.” A cultural typology placing eco-culture in historical perspective is outlined. It is concluded that, to (...) be fully effective, changes in development patterns in the south have to be matched by equivalent cultural changes in the North. (shrink)

BackgroundMedical ethics has recently seen a drive away from multiple prescriptive approaches, where physicians are inundated with guidelines and principles, towards alternative, less deontological perspectives. This represents a clear call for theory building that does not produce more guidelines. Phronesis offers an alternative approach for ethical decision-making based on an application of accumulated wisdom gained through previous practice dilemmas and decisions experienced by practitioners. Phronesis, as an ‘executive virtue’, offers a way to navigate the practice virtues for any given case (...) to reach a final decision on the way forward. However, very limited empirical data exist to support the theory of phronesis-based medical decision-making, and what does exist tends to focus on individual practitioners rather than practice-based communities of physicians.MethodsThe primary research question was: What does it mean to medical practitioners to make ethically wise decisions for patients and their communities? A three-year ethnographic study explored the practical wisdom of doctors and used their narratives to develop theoretical understanding of the concepts of ethical decision-making. Data collection included narrative interviews and observations with hospital doctors and General Practitioners at all stages in career progression. The analysis draws on neo-Aristotelian, MacIntyrean concepts of practice- based virtue ethics and was supported by an arts-based film production process.ResultsWe found that individually doctors conveyed many different practice virtues and those were consolidated into fifteen virtue continua that convey the participants’ ‘collective practical wisdom’, including the phronesis virtue. This study advances the existing theory and practice on phronesis as a decision-making approach due to the availability of these continua.ConclusionGiven the arguments that doctors feel professionally and personally vulnerable in the context of ethical decision-making, the continua in the form of a video series and app based moral debating resource can support before, during and after decision-making reflection. The potential implications are that these theoretical findings can be used by educators and practitioners as a non-prescriptive alternative to improve ethical decision-making, thereby addressing the call in the literature, and benefit patients and their communities, as well. (shrink)