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.

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 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)

The Plant Ontology (PO) is a community resource consisting of standardized terms, definitions, and logical relations describing plant structures and development stages, augmented by a large database of annotations from genomic and phenomic studies. This paper describes the structure of the ontology and the design principles we used in constructing PO terms for plant development stages. It also provides details of the methodology and rationale behind our revision and expansion of the PO to cover development stages for all plants, particularly (...) the land plants (bryophytes through angiosperms). As a case study to illustrate the general approach, we examine variation in gene expression across embryo development stages in Arabidopsis and maize, demonstrating how the PO can be used to compare patterns of expression across stages and in developmentally different species. Although many genes appear to be active throughout embryo development, we identified a small set of uniquely expressed genes for each stage of embryo development and also between the two species. Evaluating the different sets of genes expressed during embryo development in Arabidopsis or maize may inform future studies of the divergent developmental pathways observed in monocotyledonous versus dicotyledonous species. The PO and its annotation databasemake plant data for any species more discoverable and accessible through common formats, thus providing support for applications in plant pathology, image analysis, and comparative development and evolution. (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)

Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the Semantic Web. This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, (...) with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results: Ontologies can advance plant science in four keys areas: 1. comparative genetics, genomics, phenomics, and development, 2. taxonomy and systematics, 3. semantic applications and 4. education. Conclusions: Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. (shrink)

Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal (...) rigor of ontologies to better support computation. 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 computation and for cross-species data integration. Results: To enhance the CL's utility for computational analyses, 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. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org. (shrink)

As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (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)

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)

This paper deals with what I take to be one woman’s literary response to a philosophical problem. The woman is Jane Austen, the problem is the rationality of Hume’s ‘sensible knave’, and Austen’s response is to deepen the problem. Despite his enthusiasm for virtue, Hume reluctantly concedes in the EPM that injustice can be a rational strategy for ‘sensible knaves’, intelligent but selfish agents who feel no aversion towards thoughts of villainy or baseness. Austen agrees, but adds that ABSENT (...) CONSIDERATIONS OF A FUTURE STATE, other vices besides injustice can be rationally indulged with tolerable prospects of worldly happiness. Austen’s creation Mr Elliot in Persuasion is just such an agent – sensible and knavish but not technically ‘unjust’. Despite and partly because of his vices – ingratitude, avarice and duplicity – he manages to be both successful and reasonably happy. There are plenty of other reasonably happy knaves in Jane Austen, some of whom are not particularly sensible. This is not to say that either Austen or Hume is in favor of knavery It is just that they both think that only those with the right sensibility can be argued out of it. (shrink)

This paper argues that the activist, feminist and pragmatist Jane Addams was an experimental philosopher. To defend this claim, I argue for capacious notions of both philosophical pragmatism and experimental philosophy. I begin in Section 2 with a new defence of Rose and Danks’ [‘In Defense of a Broad Conception of Experimental Philosophy’. Metaphilosophy 44, no. 4 : 512–32] argument in favour of a broad conception of experimental philosophy. Koopman [‘Pragmatist Resources for Experimental Philosophy: Inquiry in Place of Intuition’. (...) Journal of Speculative Philosophy 26, no. 1 : 1–24] argues that many twentieth-century American pragmatists can make important contributions to contemporary experimental philosophy. In Section 3, I argue that while this may be true, it is also true that under the broad conception, many of the pragmatists just were experimental philosophers. In Section 4, I argue that as a pragmatist philosopher in her own right, Jane... (shrink)

The sublime is an aspect of experience that has attracted a great deal of scholarship, not only for scholarly reasons but because it connotes aspects of experience not exhausted by what Descartes once called clear distinct perception. That is, the sublime is an experience of the world which involves us in orientating ourselves within it, and this orientation, our human orientation, elevates us in comparison to the non-human world according to traditional accounts of the sublime. The sublime tells us something (...) about our relation to the world rather than anything about the world per se. Nonetheless there is an objective sense of the sublime in that the narratives involved are culturally endorsed rather than invented by an individual. This means that objects can be judged worthy or not of evoking experiences of the sublime. In other words, it is not an idiosyncratic matter. Immanuel Kant’s formulation of this involved explaining how such an experience is possible in terms of his system of the mind. Jane Forsey notes that Kant takes the features of the sublime as given and extrapolates from them certain features of the mind as if any concept of the sublime must implicate the mental architecture of his account (2007). Further to this she argues that in fact the concept of the sublime does implicate a particular system of the mind but neither Kant nor anyone else can successfully formulate it because the concept itself frames certain contradictions. According to Forsey, two consequences follow. First she argues that Kant’s system of the mind does not support the features of the sublime; and secondly that no system could as the very concept is incoherent. If Forsey can show that Kant was mistaken in presenting his account as coherent given his commitments, this would be of interest in its own right. However, her stronger claim is that we cannot separate any concept of the sublime out from Kant’s theoretical underpinnings. That the way the features of the mind are meant to operate in experiences of the sublime are contradictory simply points to the fatal flaws in the whole concept. Her conclusion is that there is no coherent account of the sublime available to us. I will argue that Forsey bases her reasoning on the assumption that a foundational empiricist or direct perception holds; and she interprets Kant’s notions of imagination, understanding and reason as though they are grounded in just such an account of perception. This is revealed in her interpretation of Kant’s phrase “beyond cognition”. Once this foundationalism is replaced with an account of perception more aligned with current research on perception, both philosophical and empirical, then an account of the sublime is available. Further to this however, I argue that what constitutes the narrative of the sublime is historically contingent. Before setting out my arguments, I consider Forsey’s argument in more detail. (shrink)

This article examines ethical themes in the works of the celebrated writer on urban affairs, Jane Jacobs. Jacobs' early works on cities develop an implicit, 'ecological' conception of the human good, one that connects it closely with economic and political goals while emphasizing the intrinsic good of the community formed in pursuit of those goals. Later works develop an explicit ethics, arguing that governing and trading require two different schemes of values and virtues. While Jacobs intended this ethics to (...) apply to all forms of productive activity, it is particularly illuminating when applied to her own urban ideas and activism. (shrink)

The allure of perennial questions in biology: temporary excitement or substantive advance? Content Type Journal Article Pages 1-4 DOI 10.1007/s11016-011-9533-5 Authors Alan C. Love, Department of Philosophy, Minnesota Center for Philosophy of Science, University of Minnesota, 831 Heller Hall, 271 19th Ave. S, Minneapolis, MN 55455-0310, USA Journal Metascience Online ISSN 1467-9981 Print ISSN 0815-0796.

In a series of recent papers, Jane Friedman has argued that attitudes like wondering, enquiring, and suspending judgement are question-directed and have the function of moving someone from a position of ignorance to one of knowledge. Call such attitudes interrogative attitudes. Friedman insists that all IAs are governed by the following Ignorance Norm: Necessarily, if one knows Q at t, then one ought not have an IA towards Q at t. However, I argue that key premisses in Friedman’s argument (...) actually point towards an opposing conclusion; namely, that IAs are not governed by the Ignorance Norm, and IAs have functions other than moving someone from a position of ignorance to one of knowledge. I conclude that the Ignorance Norm should be rejected. (shrink)

Analytic philosophers have a tendency to forget that they are human beings, and one of the reasons that P. F. Strawson’s 1962 essay, “Freedom and Resentment”, has been so influential is that it promises to bring discussions of moral responsibility back down to earth. Strawson encouraged us to “keep before our minds...what it is actually like to be involved in ordinary interpersonal relationships”, which is, after all, the context in which questions about responsibility arise in the first place. In this (...) essay I explore what we can learn about ordinary interpersonal relationships from three works of literature – Shakespeare’s King Lear, Jane Austen’s Persuasion, and Graham Greene’s The End of the Affair. My intention is to try to heed Strawson’s advice without imposing upon the data any particular theoretical agenda, and my hope is that the data collected will prove useful for future theorizing about responsibility. (shrink)


Someone who believes “I believe it will rain” can easily be mistaken about the rain. But it does not seem likely, and might even be impossible, that he is wrong about the fact that he believes that it is going to rain. How can we account for this authority about our own beliefs – the phenomenon known as first person authority? In this paper I examine a type of theory proposed, in distinct forms, by Crispin Wright and Jane Heal (...) for an explanation of our authority. Both authors claim that our second-order beliefs (of the form “I believe that p”) are constitutive of the first-order beliefs that are self-ascribed in them (beliefs of the form “p”) and both try to derive the necessity of first person authority from this constitutive relation. My paper analyses and criticizes the two proposals and suggests a non-constitutive, alternative account of first person authority. (shrink)

This is just an initial finding and needs to be verified by a larger, more thorough study. Part 1 of this paper demonstrates that we unconsciously select words based on letter sounds that we like or dislike. Part 2 demonstrates that there may be harmony and dissonance in the pattern of frequency of letter usage, at least in the case of the vowels. To the best of my knowledge this is a new idea/discovery. The following paper contains graphs of the (...) data collected from 15 classic works of literature including 4 works of HG Wells and 4 works of Jane Austen. Also a separate analysis is done using just the vowels from Shakespeare’s Sonnets and the Eminem Recovery album. (shrink)

This paper examines the settlement movement (a social reform movement during the Progressive Era, roughly 1890–1920) in order to illustrate what pragmatism is and is not. In 1906, Mary Kingsbury Simkhovitch proposed an analysis of settlement house methods. Because of her emphasis on interpretation and action, and because of the nature of the settlement movement as a social reform effort with vitally important consequences for everyone involved, it might be thought that her analysis would be pragmatist in character. This paper (...) shows that her analysis is empiricist, not pragmatist, and offers an alternative pragmatist sketch of settlement house methodology. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

We argue that generic generalizations about racial groups are pernicious in what they communicate (both to members of that racial group and to members of other racial groups), and may be central to the construction of social categories like racial groups. We then consider how we should change and challenge uses of generic generalizations about racial groups.

Two major lines of argument support the notion that Hildegard of Bingen’s metaphysics is peculiarly gynocentric. Contra the standard commentary on her work, the focus is not on the notion of viriditas; rather, the first line of argument presents a specific delineation of her ontology, demonstrating that it is a graded hierarchy of beings, many of which present feminine aspects of the divine, and all of which establish the metaphysical notion of interpenetrability. The second line of argument specifically contrasts her (...) thought to that of Aquinas and Meister Eckhart, noting areas of similarity and difference. It is concluded that the visionary origins of Hildegard’s work may have to some extent precluded our understanding of it, and that her work merits consideration not only philosophically and theologically but from the standpoint of its early presentation of a gynocentric worldview. (shrink)

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

This paper examines distinctive discourse properties of preposed negative 'yes/no' questions (NPQs), such as 'Isn’t Jane coming too?'. Unlike with other 'yes/no' questions, using an NPQ '∼p?' invariably conveys a bias toward a particular answer, where the polarity of the bias is opposite of the polarity of the question: using the negative question '∼p?' invariably expresses that the speaker previously expected the positive answer p to be correct. A prominent approach—what I call the context-management approach, developed most extensively by (...) Romero and Han (2004)—attempts to capture speaker expectation biases by treating NPQs fundamentally as epistemic questions about the proper discourse status of a proposition. I raise challenges for existing context-managing accounts to provide more adequate formalizations of the posited context-managing content, its implementation in the compositional semantics and discourse dynamics, and its role in generating the observed biases. New data regarding discourse differences between NPQs and associated epistemic modal questions are introduced. I argue that we can capture the roles of NPQs in expressing speakers’ states of mind and managing the discourse common ground without positing special context-managing operators or treating NPQs as questions directly about the context. I suggest that we treat the operator introduced with preposed negation as having an ordinary semantics of epistemic necessity, though lexically associated with a general kind of endorsing use observed with modal expressions. The expressive and context-managing roles of NPQs are explained in terms of a general kind of discourse-oriented use of context-sensitive language. The distinctive expectation biases and discourse properties observed with NPQs are derived from the proposed semantics and a general principle of Discourse Relevance. (shrink)

This paper explores the role of generics in social cognition. First, we explore the nature and effects of the most common form of generics about social kinds. Second, we discuss the nature and effects of a less common but equally important form of generics about social kinds. Finally, we consider the implications of this discussion for how we ought to use language about the social world.

Intentionality, or the power of minds to be about, to represent, or to stand for things, remains central in the philosophy of mind. But the study of intentionality in the analytic tradition has been dominated by discussions of propositional attitudes such as belief, desire, and visual perception. There are, however, intentional states that aren't obviously propositional attitudes. For example, Indiana Jones fears snakes, Antony loves Cleopatra, and Jane hates the monster under her bed. The present paper explores such mental (...) states in an introductory but opinionated way. (shrink)

A discussion of L.A. Paul's 'Transformative Experience' from an Author Meets Critics session at the 2015 Pacific APA.

Over the last thirty years, once staunchly historical cinema scholars such as Thomas Elsaesser, Jane Gaines, Siegfried Zielinski, and André Gaudreault have abandoned history for historiography and film studies for media archaeology. With increasing attention on the “database” as a symbolic metaphor for postmodernity and the decentered, networked tenants of the global present, cinema is taking on the characteristics of new media, existing in intertextual space. Thus, the term “post-cinema” has been co-opted as a viable intermediary that accounts for (...) new media conditions, as cinema is no longer emblematic of our cultural climate. As Giorgio Agamben wrote in 1992, “[t]he end of the cinema truly sounds the death knell of the ultimate metaphysical adventure of Dasein. In the twilight of post-cinema…human quasi-existence, now stripped of any metaphysical hypostasis and deprived of any theological model, will have to seek its proper generic consistency elsewhere." Accordingly, we are no longer “moviegoing animals” who seek images of ourselves among a collective in the dark but, rather, users interfacing within a network of moving images. (shrink)

A term expresses a thick concept if it expresses a specific evaluative concept that is also substantially descriptive. It is a matter of debate how this rough account should be unpacked, but examples can help to convey the basic idea. Thick concepts are often illustrated with virtue concepts like courageous and generous, action concepts like murder and betray, epistemic concepts like dogmatic and wise, and aesthetic concepts like gaudy and brilliant. These concepts seem to be evaluative, unlike purely descriptive concepts (...) such as red and water. But they also seem different from general evaluative concepts. In particular, thick concepts are typically contrasted with thin concepts like good, wrong, permissible, and ought, which are general evaluative concepts that do not seem substantially descriptive. When Jane says that Max is good, she appears to be evaluating him without providing much description, if any. Thick concepts, on the other hand, are evaluative and substantially descriptive at the same time. For instance, when Max says that Jane is courageous, he seems to be doing two things: evaluating her positively and describing her as willing to face risk. Because of their descriptiveness, thick concepts are especially good candidates for evaluative concepts that pick out properties in the world. Thus they provide an avenue for thinking about ethical claims as being about the world in the same way as descriptive claims. -/- Thick concepts became a focal point in ethics during the second half of the twentieth century. At that time, discussions of thick concepts began to emerge in response to certain disagreements about thin concepts. For example, in twentieth-century ethics, consequentialists and deontologists hotly debated various accounts of good and right. It was also claimed by non-cognitivists and error-theorists that these thin concepts do not correspond to any properties in the world. Dissatisfaction with these viewpoints prompted many ethicists to consider the implications of thick concepts. The notion of a thick concept was thought to provide insight into meta-ethical questions such as whether there is a fact-value distinction, whether there are ethical truths, and, if there are such truths, whether these truths are objective. Some ethicists also theorized about the role that thick concepts can play in normative ethics, such as in virtue theory. By the beginning of the twenty-first century, the interest in thick concepts had spread to other philosophical disciplines such as epistemology, aesthetics, metaphysics, moral psychology, and the philosophy of law. -/- Nevertheless, the emerging interest in thick concepts has sparked debates over many questions: How exactly are thick concepts evaluative? How do they combine evaluation and description? How are thick concepts related to thin concepts? And do thick concepts have the sort of significance commonly attributed to them? This article surveys various attempts at answering these questions. (shrink)

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)

Recent work in the philosophy of biology argues that we must rethink the biological individual beyond the boundary of the species, given that a key part of our essential functioning is carried out by the bacteria in our intestines in a way that challenges any strictly genetic account of what is involved for the biological human. The gut is a kind of ambiguous other within our understanding of ourselves, particularly when we also consider the status of gastro-intestinal disorders. Hegel offers (...) us theoretical tools to describe and understand our relationship to our gut. His description of our selves as continually mediated through otherness is strikingly compatible with the kind of structure contemporary biology presents us with. His accounts of digestion and habit, contextualized by his logic, help point toward an understanding of selfhood as porous and yet still capable of being sufficiently unified for us to make sense of ourselves, one which allows us to acknowledge otherness within us while still having enough unity for agency. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Beauty is truth, truth beauty.If this epigraph only rarely escapes English class, something like it has fascinated philosophers for a long time. Iris Murdoch remembers that "Kant said that beauty was an analogon of good, Plato said it was the nearest clue."2 I want to go further and posit that our means of perception of the aesthetic and the ethical share an organic connection, an understanding of which will help elucidate moral perception, a critical component of moral education.Or moral education (...) as it should be. But what currently counts as such is, directly or almost directly, simple instruction. I ask why this does not work. I ask why Jane Austen said, "We all love to instruct, though we can teach only what is... (shrink)

Evolutionary developmental biology (Evo-Devo) is a new and rapidly developing field of biology which focuses on questions in the intersection of evolution and development and has been seen by many as a potential synthesis of these two fields. This synthesis is the topic of the books reviewed here. Integrating Evolution and Development (edited by Roger Sansom and Robert Brandon), is a collection of papers on conceptual issues in Evo-Devo, while From Embryology to Evo-Devo (edited by Manfred Laubichler and Jane (...) Maienschein) is a history of the problem of the relations between ontogeny and phylogeny. (shrink)

Translation of "Von der Armut am Geiste; ein Dialog des jungen Lukács," by Ágnes Heller. This translation originally appeared in The Philosophical Forum, Spring-Summer 1972.

As part of a trend in modern cognitive science, cognitive linguist, George Lakoff, and philosopher, Mark Johnson claim to provide a biologically-based account of subsymbolic meaningful experiences. They argue that human beings understand objects by extrapolating from their sensory motor activities and primary perceptions. Lakoff and Johnson’s writings have generated a good deal of interest among scholars of Early China because they maintain that “our common embodiment allows for common stable truths.” Although there are many grounds on which Lakoff and (...) Johnson’s theories have been criticized, this essay focuses in particular on problems related to their schema of Self as Container. Lakoff and Johnson contend that there are no pure experiences outside of culture, while nevertheless arguing that the experience of being a closed-off container is “direct.” “The concepts OBJECT, SUBSTANCE and CONTAINER emerge directly,” they write. “We experience ourselves as entities, separate from the rest of the world—as containers with an inside and an outside.” By “emerge directly,” they do not mean emerging free of culture, but rather that some experiences within culture, specifically physical experiences, are more directly given than others. My study explores the pitfalls of presuming the “direct” experience of containment makes good sense of texts from Early China (ca. 500–100 B.C.E). (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (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)

ABSTRACT Temporal dynamists argue that we should believe that there exists temporal passage because there being passage is the best explanation for the presence of our temporal phenomenology. Presentists argue that presentism is the best version of temporal dynamism. Therefore, conditional on us accepting temporal dynamism, we should accept presentism. In this paper it is argued that if we understand temporal passage as the presentist does, such an argument can succeed only if dualism is true. Thus, we conclude, either presentists (...) should embrace dualism, or they should reject any argument for presentism that proceeds via any such argument for temporal passage that proceeds via considerations of what best explains our temporal phenomenology. (shrink)

In the fall of 1990 I had just began my doc- toral studies at the University of Connecticut. Freshly arrived from Italy, I came to the United States to work with Carl Schlichting on something to do with phenotypic plastic- ity. I spent most of that semester discussing with other graduate students what I thought was a momentous paper by Mary Jane West- Eberhard (1989) in the Annual Review of Ecol- ogy and Systematics. That paper, entitled Phe- notypic Plasticity (...) and the Origins of Diversity, was a (quite lengthy) forerunner of the (also quite bulky) book I am reviewing now. Like the paper, this volume has the potential to be momentous in the development of our ideas on phenotypic evolution. (shrink)

Deep Democracy draws upon the insights of American thinkers whose work has received less attention than the "holy trinity" of Peierce, James and Dewey, in order to investigate current philosophical problems and questions. The work does carry out a sustained interaction with the work of Dewey, in the course of exploring the nature of, obstacles to, and prospects for strengthening the fabric of democracy in the contemporary world. But Green also puts Dewey in conversation with Jane Addams, Alain Locke, (...) Martin Luther King, Malcolm X and Cornel West. Green draws these thinkers together—and draws out the links between them—in order to develop her notion of “deep democracy.”. (shrink)

Three professors reflect on the experience of creating a learning community of 22 students by linking courses in Literature and Ethics. The project demonstrates practical strategies for incorporating feminist scholarship and pedagogy into the core curriculum and for integrating core courses from diverse disciplines.