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.

Biomedical Ontologies integrate diverse biomedical data and enable intelligent data-mining and help translate basic research into useful clinical knowledge. We present the RNA Ontology (RNAO), an o...

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 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 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)

An important book for philosophers of religion and students of Buddhism. It attempts to translate... the Mādhyamika articulation of the Buddhist dharma by comparing it with the language analysis of Ludwig Wittgenstein... Chris Gudmunsen has made a persuasive case for showing overlapping philosophical concerns and claims in different cultural traditions separated by two millennia.

Analyzes the intellectual roots and philosophy of Ayn Rand. Second edition adds a new preface and an analysis of transcripts documenting Rand's education at Petrograd State University"--Provided by publisher.

> Wealthy nations must step up support for Africa and vulnerable countries in addressing past, present and future impacts of climate change The 2022 report of the Intergovernmental Panel on Climate Change paints a dark picture of the future of life on earth, characterised by ecosystem collapse, species extinction and climate hazards such as heatwaves and floods.1 These are all linked to physical and mental health problems, with direct and indirect consequences of increased morbidity and mortality. To avoid these catastrophic (...) health effects across all regions of the globe, there is broad agreement—as 231 health journals argued together in 2021—that the rise in global temperature must be limited to <1.5°C compared with pre-industrial levels. While the Paris Agreement of 2015 outlines a global action framework that incorporates providing climate finance to low-income and middle-income countries, this support has yet to materialise.2 COP27 is the fifth Conference of the Parties (COP) to be organised in Africa since its inception in 1995. Ahead of this meeting, we—as health journal editors from across the continent—call for urgent action to ensure it is the COP that finally delivers climate justice for Africa and vulnerable countries. This is essential for the health of those countries, and for the health of the whole world. The climate crisis has had an impact on the environmental and social determinants of health across Africa, leading to devastating health effects.3 Impacts on health can result directly from environmental shocks and indirectly through socially mediated effects.4 Climate change-related risks in Africa include flooding, drought, heatwaves, reduced food production and reduced labour productivity.5 Droughts in sub-Saharan Africa …. (shrink)

Continuum's Guides for the Perplexed are clear, concise and accessible introductions to thinkers, writers and subjects that students and readers can find especially challenging. Concentrating specifically on what it is that makes the subject difficult to fathom, these books explain and explore key themes and ideas, guiding the reader towards a thorough and confident understanding of demanding material. Hans-Georg Gadamer is one of the formeost European philosophers of recent times. His work on philosophical hermeneutics defined the whole subject, and Truth (...) and Method , his magnum opus, is a landmark text in modern philosophy. However, Gadamer's ideas, the complex relationship between them, and the often opaque way they are expressed, undoubtedly pose a considerable challenge for the reader. Gadamer: A Guide for the Perplexed is the ideal text for anyone trying to get to grips with Gadamer's work. Providing a clear account of the central tenets of Gadamer's philosophy, the book does not shy away from the more complex material and provides an invaluably thorough and fully engaged account of Gadamer's hermeneutics. There is clear exposition and analysis of such key terms - often problematic for the reader - as 'fusion of horizons', 'effective historical consciousness' and 'the logic of question and answer', as well as Gadamer's redefinition of such concepts as 'prejudice', 'authority' and 'tradition'. The book also discusses Gadamer's influence in other areas of philosophy; the response of other philosophers to his work; and criticisms of his work on the grounds of relativism. (shrink)

Practical reasoning is reasoning about what to do. Practical wisdom is the traditional ideal of practical reasoning associated with virtue ethics. Practical wisdom requires the knowledge and skills necessary to act rightly across a wide range of situations. Critics allege that this notion does not cohere well with what contemporary cognitive science tells us about the production of human behavior. After briefly discussing these criticisms, I sketch an alternative account of these cognitive processes that I call affective engine theory. I (...) then discuss a normative conception of practical reasoning that complements this account. Finally, adopting an approach according to which the virtues are those character traits necessary for excellence in practical reasoning, I argue that these accounts can provide the basis for a nontraditional theory of virtue. I discuss three traits that are plausible candidates for virtues on such an account. (shrink)

Foucault and Social Dialogue; Beyond Fragmentation is a compelling yet extremely clear investigation of these options and offers a new way forward. Christopher Falzon argues that the proper alternative to foundationalism is not fragmentation but dialogue and that such a dialogical picture can be found in the work of Michel Foucault. Such a reading of Foucault allows us to see, for the first time, the ethical and political position implicit in Foucault's work and how his work contributes to the larger (...) debate concerning the death of man. (shrink)

Among the many striking features of the philosophy of the Zhuāngzǐ is that it advocates a life unperturbed by emotions, including even pleasurable, positive emotions such as joy or delight. Many of us see emotions as an ineluctable part of life, and some would argue they are a crucial component of a well-developed moral sensitivity and a good life. The Zhuangist approach to emotion challenges such commonsense views so radically that it amounts to a test case for the fundamental plausibility (...) of the Daoist ethical orientation: If the Zhuangist stance on emotion is untenable, then other aspects of Daoist ethics may founder as well. In this essay, I explore what I call a Zhuangist ‘Virtuoso View’ of emotion and its connections with human agency, attempting to show that at least one version of a Zhuangist approach to emotion passes the ‘basic plausibility’ test. I begin by describing the Virtuoso View and sketching its theoretical foundation, which involves claims about human agency, the self, psychophysical hygiene, the good life, epistemology, and metaphysics. Next, I defend the Virtuoso View against three objections, namely that it abandons intentionality, that it interferes with a good life, and that it yields a schizophrenic conception of agency. I argue for three major theses. First, the Virtuoso View is easily intelligible and largely defensible. Second, it reflects a crucial insight into a fundamental dichotomy at the core of human agency: the unavoidable conflict within a self-aware human agent between an internal, engaged perspective and an external, detached one. Third, I suggest that certain problems or conflicts arising from the Virtuoso View actually reflect inherent features of the human predicament and thus are not mere conceptual defects. Hence even if we do not find the Virtuoso View wholly convincing, we can nevertheless gain much insight from it. (shrink)

This introduction to the twentieth anniversary volume of The Journal of Ayn Rand Studies celebrates the creating and sustaining of a forum in which writers coming from virtually every discipline, representing a diverse range of critical perspectives, have advanced the scholarly study of Ayn Rand and her times.

The behaviour of presupposition triggers in human language has been extensively studied and given rise to many distinct theoretical proposals. One intuitively appealing way of characterising presupposition is to argue that it constitutes backgrounded meaning, which does not contribute to updating the conversational record, and consequently may not be challenged or refuted by discourse participants. However, there are a wide range of presupposition triggers, some of which can systematically be used to introduce new information. Is there, then, a clear psychological (...) distinction between presupposition and assertion? Do certain expressions vacillate between presupposing and asserting information? And is information backgrounding a categorical or a gradient phenomenon? In this paper we argue for the value of experimental methods in addressing these questions, and present a pilot study demonstrating backgrounding effects of presupposition triggers, and suggesting their gradience in nature. We discuss the implications of these findings for theoretical categorisations of presupposition triggers. (shrink)

Context: The evolution of perceptual systems and hence of observers remains largely disconnected from the question of the emergence of classical objects and spacetime. This disconnection between the biosciences and physics impedes progress toward understanding the role of the “observer” in physical theory. Problem: In this article we consider the problem of how to understand objects and spacetime in observer-relative evolutionary terms. Method: We rely on a comparative analysis using multiple formal frameworks. Results: The eigenform construct of von Foerster is (...) compared to other formal representations of observer-environment interactions. Eigenforms are shown to be encoded on observer-environment interfaces and to encode fitness consequences of actions. Space and time are components of observational outcomes in this framework; it is suggested that spacetime constitutes an error-correcting code for fitness consequences. Implications: Our results contribute to an understanding of the world in which neither objects nor spacetime are observer-independent. Constructivist content: The eigenform concept of von Foerster is linked to the concepts of decoherence and holographic encoding from physics and the concept of fitness from evolutionary biology. (shrink)

The concept of noncombatant immunity prohibits the intentional targeting of noncombatants. The availability of nonlethal weapons (NLW) may weaken this prohibition, especially since using NLWs against noncombatants may, in some cases, actually save the noncombatants' lives. Given the advancement of NLWs, I argue that their probable appearance on the battlefield demands close scrutiny due to the moral problems associated with their use. In this paper, I examine four distinct cases and determine whether the use of NLWs is morally permissible. While (...) it seems that the reduced harm caused by NLWs makes their use more acceptable, adhering to noncombatant immunity requires more than not killing noncombatants. It also requires that military forces treat noncombatants a certain way. In the cases I present, to use NLWs against noncombatants treats them as combatants and coerces them to do something against their will. While a consequentialist foundation for noncombatant immunity may permit this action, a rights-based concept of noncombatant immunity does not. I contend that only a rights-based concept of noncombatant immunity is viable, and that the availability of NLWs should not significantly alter the prohibitions prescribed by noncombatant immunity. (shrink)

Alienation theory has acted as the stimulus for a great deal of research and writing in the history of sociology. It has formed the basis of many sociological ‘classics’ focused on the workplace and the experiences of workers, and has also been mobilized to chart wider social malaise and individual troubles. Alienation theory usage has, however, declined significantly since its heyday of the 1960s and 1970s. Here, the reasons why alienation theory was ‘forgotten’ and what can be gained by ‘remembering’ (...) alienation theory are explored. To realize this ambition this article proceeds by (1) briefly visiting differing definitions of alienation theory, before charting its high point, and the various debates and tensions of the time, during the 1960s and 1970s; (2) analysing the reasons why alienation theory fell from grace from the 1980s onwards; (3) elaborating how and why alienation theory is still relevant for sociology and the wider social sciences today. (shrink)

First, we consider an argument due to Popper for maximal strength in choice of logic. We dispute this argument, taking a lead from some remarks by Susan Haack; but we defend a set of contrary considerations for minimal strength in logic. Finally, we consider the objection that Popper presupposes the distinctness of logic from science. We conclude from this that all claims to logical truth may be in equal epistemological trouble.

Complexity is pleased to announce the installment of Prof Hiroki Sayama as its new Chief Editor. In this Editorial, Prof Sayama describes his feelings about his recent appointment, discusses some of the journal’s journey and relevance to current issues, and shares his vision and aspirations for its future.

In his short review of The Political Philosophy of Herbert Spencer , Timothy Virkkala (May 1999) praises Tim S. Gray's discussion of the great classical liberal's methodology as a synthesis of "individualist" and "holist" approaches to social theory. But Virkkala remarks This method -I'm tempted to call it "dialectical," but Spencer's prose and position seem so far from Hegel's that the term is almost indecent -confuses many readers. But it is surely his strength. Gray is one of the few Spencer (...) scholars to see this method as fundamental, and to present sophisticated analyses of Spencer's syntheses. It is unfortunate that Virkkala refuses to give into his temptation, because crucially significant aspects of Herbert Spencer's work are, indeed, dialectical. (shrink)

Gray has expanded his account of schizophrenia to explain consciousness as well. His theory explains neither phenomenon adequately because he treats individual minds (and brains) in isolation. The primary function of consciousness is to permit high level interactions with other conscious beings. The key symptoms of schizophrenia reflect a failure of this mechanism.

In the appropriate contexts reasoning is a powerful tool for producing intersubjective agreement about what counts as the best answer to a question that generates inquiry; sometimes employing arguments can lead to agreement about what is the right answer. In this paper we hope to show, however, that unabashed optimism about the power of argument is misplaced. Such optimism rests on an implausible picture of the power of articulation. Sentences cashed out as reasons to believe another sentence is true cannot (...) bridge large gaps in substantive understanding. A failure to realize this fact, moreover, leads to an uncautious and unreflective optimism about the power of argument that ultimately threatens the very reasons-giving process. What is needed, then, is a much more modest sense of the role of argument. (shrink)

By making plausible the Diversity Thesis (different people have systematically different and incompatible packages of epistemic intuitions), experimental epistemology raises the specter of the shifting-sands problem: the evidence base for epistemology contains systematic inconsistencies. In response to this problem, some philosophers deny the Diversity Thesis, while others flirt with denying the Evidence Thesis (in normal circumstances, the epistemic intuition that p is prima facie evidence that p is true). We propose to accept both theses. The trick to living with the (...) shifting-sands problem is to expand epistemology’s evidential base so as to include scientific evidence. This evidence can provide principled grounds on which to decide between incompatible intuitions. The idea of resolving inconsistencies in an evidential base by adding more independent lines of evidence is commonplace in science. And in philosophy, it is simplyWide Reflective Equilibrium.We contend that the idea that epistemology would depend crucially on scientific evidence seems radical because many traditional epistemologists practice reflective equilibrium that is WINO, Wide In Name Only. We suggest five different lines of scientific evidence that can be, and have been, used in support of non-WINO epistemological theories. (shrink)

Recently, the Dimension Problem for effective Hausdorff dimension was solved by J. Miller in [14], where the author constructs a Turing degree of non-integral Hausdorff dimension. In this article we settle the Dimension Problem for effective packing dimension by constructing a real of strictly positive effective packing dimension that does not compute a real of effective packing dimension one (on the other hand, it is known via [10, 3, 7] that every real of strictly positive effective Hausdorff dimension computes reals (...) whose effective packing dimensions are arbitrarily close to, but not necessarily equal to, one). (shrink)

(1987). The crisis of libertarian dualism. Critical Review: Vol. 1, No. 4, pp. 86-99.