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 Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (shrink)

Focusing on the production of lists of evaluative criteria has oversimplified our judgments of qualitative research. On the one hand, aspirations for global criteria applicable to “qualitative” or “interpretive” research have glossed over crucial analytic differences among specific types of inquiry. On the other hand, the methodological concern with appropriate ways of acquiring trustworthy data has led to an overly narrow proceduralism. I suggest that rational evaluations of analytic worth require the delineation of species of analytic tasks and the exercise (...) of genre-appropriate judgments, to determine what constitutes explanatory, interpretive, or explicatory adequacy. I focus on the parameters of judgment for interpretations and explications because their analytic differences have not yet been made distinct in qualitative research. (shrink)

Plants from a handful of species provide the primary source of food for all people, yet this source is vulnerable to multiple stressors, such as disease, drought, and nutrient deficiency. With rapid population growth and climate uncertainty, the need to produce crops that can tolerate or resist plant stressors is more crucial than ever. Traditional plant breeding methods may not be sufficient to overcome this challenge, and methods such as highOthroughput sequencing and automated scoring of phenotypes can provide significant new (...) insights. Ontologies are essential tools for accessing and analysing the large quantities of data that come with these newer methods. As part of a larger project to develop ontologies that describe plant phenotypes and stresses, we are developing a plant disease extension of the Infectious Disease Ontology (IDOPlant). The IDOPlant is envisioned as a reference ontology designed to cover any plant infectious disease. In addition to novel terms for infectious diseases, IDOPlant includes terms imported from other ontologies that describe plants, pathogens, and vectors, the geographic location and ecology of diseases and hosts, and molecular functions and interactions of hosts and pathogens. To encompass this range of data, we are suggesting inOhouse ontology development complemented with reuse of terms from orthogonal ontologies developed as part of the Open Biomedical Ontologies (OBO) Foundry. The study of plant diseases provides an example of how an ontological framework can be used to model complex biological phenomena such as plant disease, and how plant infectious diseases differ from, and are similar to, infectious diseases in other organism. (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)

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)

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)

In cognitive science, there is a tacit norm that phenomena such as cultural variation or synaesthesia are worthy examples of cognitive diversity that contribute to a better understanding of cognition, but that other forms of cognitive diversity (e.g., autism, attention deficit hyperactivity disorder/ADHD, and dyslexia) are primarily interesting only as examples of deficit, dysfunction, or impairment. This status quo is dehumanizing and holds back much-needed research. In contrast, the neurodiversity paradigm argues that such experiences are not necessarily deficits but rather (...) are natural reflections of biodiversity. Here, we propose that neurodiversity is an important topic for future research in cognitive science. We discuss why cognitive science has thus far failed to engage with neurodiversity, why this gap presents both ethical and scientific challenges for the field, and, crucially, why cognitive science will produce better theories of human cognition if the field engages with neurodiversity in the same way that it values other forms of cognitive diversity. Doing so will not only empower marginalized researchers but will also present an opportunity for cognitive science to benefit from the unique contributions of neurodivergent researchers and communities. (shrink)

In a recent paper, Lee Kerckhove and Sara Waller (hereafter K & W) argue that the concept of personhood is irrelevant for the abortion debate.1 Surprisingly, this irrelevance is due merely to the fact that the predicate ‘being a person’ — hereafter ‘personhood’ — is inherently vague. This vagueness, they argue, reduces ‘personhood’ to incoherency and disqualifies the notion from being a useful moral concept. In other words, if ‘personhood’ isn’t a precise notion with well-defined boundaries, then it cannot be (...) of any use in the debate over the permissibility of abortion. This argument is mistaken. While it may be true that ‘personhood’ is irrelevant for the debate over abortion (a substantive issue not dealt with in this paper), it is not true that ‘personhood’ should be disqualified merely because it is vague. Section 2 of the paper is a quick survey in which I briefly review the importance of ‘personhood’ in some of the more recent literature concerning the moral status of abortion. Section 3 is a reconstruction of K & W’s argument against the relevancy of ‘personhood’ and a criticism showing why their argument fails. Section 4 approaches the use of a vague predicate in moral debate and explores the application of ‘personhood’ given three contemporary solutions to vagueness: degree theory, epistemicism and supervaluationism. (shrink)

Review of What Every Science Student Should Know by J. L. Bauer, Y. J. Kim, A. H. Zureick and D. K. Lee, U of Chicago Press, 2016.

The four experiments presented support Boyer's theory that counterintuitive concepts have transmission advantages that account for the commonness and ease of communicating many non-natural cultural concepts. In Experiment 1, 48 American college students recalled expectation-violating items from culturally unfamiliar folk stories better than more mundane items in the stories. In Experiment 2, 52 American college students in a modified serial reproduction task transmitted expectation-violating items in a written narrative more successfully than bizarre or common items. In Experiments 3 and 4, (...) these findings were replicated with orally presented and transmitted stimuli, and found to persist even after three months. To sum, concepts with single expectation-violating features were more successfully transmitted than concepts that were entirely congruent with category-level expectations, even if they were highly unusual or bizarre. This transmission advantage for counterintuitive concepts may explain, in part, why such concepts are so prevalent across cultures and so readily spread. (shrink)

Research on the relationship between religious commitment and business ethics has produced widely varying results and made the impact of such commitment unclear. This study presents an empirical investigation based on a questionnaire survey of business managers and professionals in the United States yielding a database of 1234 respondents. Respondents evaluated the ethical acceptability of 16 business decisions. Findings varied with the way in which the religion variable was measured. Little relationship between religious commitment and ethical judgment was found when (...) responses were compared on the basis of broad faith categories – Catholic, Protestant, Jewish, other religions, and no religion. However, respondents who indicated that religious interests were of high or moderate importance to them demonstrated a higher level of ethical judgment (less accepting of unethical decisions) than others in their evaluations. Evangelical Christians also showed a higher level of ethical judgment. (shrink)

Using the latest cognitive and psychological scientific data and theory, this book answers the question "why would anyone believe in God?".

I examine how particular social arrangements and incentive structures encourage the honest reporting of experimental results and minimize fraudulent scientific work. In particular I investigate how epistemic communities can achieve this goal by promoting members to police the community. Using some basic tools from game theory, I explore a simple model in which scientists both conduct research and have the option of investigating the findings of their peers. I find that this system of peer policing can in many cases ensure (...) high levels of honesty. (shrink)

Iris Murdoch was a notable philosopher before she was a notable novelist and her work was brave, brilliant, and independent. She made her name first for her challenges to Gilbert Ryle and behaviourism, and later for her book on Sartre, but she had the greatest impact with her work in moral philosophy—and especially her book The Sovereignty of Good. She turned expectantly from British linguistic philosophy to continental existentialism, but was dissatisfied there too; she devised a philosophy and a style (...) of philosophy that were distinctively her own. Murdoch aimed to draw out the implications, for metaphysics and the conception of the world, of rejecting the standard dichotomy of language into the 'descriptive' and the 'emotive'. She aimed, in Wittgensteinian spirit, to describe the phenomena of moral thinking more accurately than the 'linguistic behaviourists' like R. M. Hare. This 'empiricist' task could be acheived, Murdoch thought, only with help from the idealist tradition of Kant, Hegel, and Bradley. And she combined with this a moral psychology, or theory of motivation, that went back to Plato, but was influenced by Freud and Simone Weil. Murdoch's impact can be seen in the moral philosophy of John McDowell and, in different ways, in Richard Rorty and Charles Taylor, as well as in the recent movements under the headings of moral realism, particularism, moral perception, and virtue theory. This volume brings together essays by critics and admirers of Murdoch's work, and includes a longer Introduction on Murdoch's career, reception, and achievement. It also contains a previously unpublished chapter from the book on Heidegger that Murdoch had been working on shortly before her death, and a Memoir by her husband John Bayley. It gives not only an introduction to Murdoch's important philosophical life and work, but also a picture of British philosophy in one of its heydays and at an important moment of transition.Readership: Students and scholars of philosophy and literature. (shrink)

This article critically examines the competitive, adversarial nature of the Western neoliberal style of democracy. Specifically, this article focuses on Amartya Sen’s notion of a “universal democracy” as a means of addressing socio-economic inequalities through Sen’s capability approach. Sen’s capability theory has become an acclaimed and widely used theory to evaluate and understand development and inequalities. However, we employ a distinctive critique by engaging Amartya Sen through Herbert Marcuse’s analysis of one dimensionality and the adversarial nature of Western democracy. We (...) further highlight how contemporary neoliberal society employ a particular, adversarial form of public participation. Through this, we underline the various neoliberal problemata, such as Western idealism, political passivity, and a “flattening of choice,” within contemporary democracies and locate how their competitive, winner-take-all nature has become essential to contemporary, Western democratic models. Consequently, we argue that democracy, as a functional concept and form of public engagement, should be fundamentally re-examined in order to address inequalities. (shrink)

Peter Vanderschraaf’s Strategic Justice provides a defense of the egalitarian bargaining solution. Vanderschraaf’s discussion of the egalitarian solution invokes three arguments typically given to support the Nash bargaining solution. Overall, we reinforce Vanderschraaf’s criticism of arguments in favor of the Nash solution and point to potential weaknesses in Vanderschraaf’s positive case for the egalitarian solution.

This book compares and contrasts the ideas of some of the leading twentieth-century critics of rationalism: Gadamer, Hayek, Kolnai, MacIntyre, Oakeshott, Polanyi, Ryle, Voegelin, and Wittgenstein. This book provides important insights into this major intellectual trend of the past century.

Recently, philosophers have investigated the emergence and evolution of the social contract. Yet extant work is limited as it focuses on the use of simple behavioral norms in rather rigid strategic settings. Drawing on axiomatic bargaining theory, we explore the dynamics of more sophisticated norms capable of guiding behavior in a wide range of scenarios. Overall, our investigation suggests the utilitarian bargaining solution has a privileged status as it has certain stability properties other social arrangements lack.

The present study sought to determine whether Barrett's counterintuitiveness coding and quantifying scheme could be applied to cultural materials with sufficient intercoder reliability, provide evidence concerning just how counterintuitive is too counterintuitive for a concept to be a recurrent cultural idea, and test whether counterintuitive intentional agent concepts are more common in folktales than other classes of counterintuitive concepts. Seventy-three folktales from around the world were sampled from larger collections. Using Barrett's CI-Scheme, two independent coders identified 116 counterintuitive objects and (...) scored them for degree of counterintuitiveness with very high inter-rater concordance. Of folktales, 79% had one or two counterintuitive objects. Of the counterintuitive objects 93% had a counterintuitiveness score of only one. Of counterintuitive objects, 98% were agents. Results suggest the CI-Scheme may have utility for analyzing cultural materials, that the cognitive optimum for cultural transmission falls around one counterintuitive feature, and that counterintuitive agents are more common than other types of counterintuitive objects in folktales. (shrink)

What is the significance of Arendt considering the title Amor Mundi for what we now are familiar with as The Human Condition? Read alongside Native American philosophers, it is clear that The Human Condition does not explain what it is like to love the world. Instead, it is a powerful genealogy of world alienation and earth alienation in the Western tradition. In other words, The Human Condition shows how Western thought lost and/or undermines amor mundi. By comparing and contrasting Arendt (...) with Vine Deloria Jr. and Daniel Wildcat, we can better understand what Arendt means by the distinction between ‘world’ and ‘earth’ and see the limitations of her concept of world. My claim is that reading these thinkers together enriches our understanding of world alienation, earth alienation, and amor mundi. (shrink)

Mental internalists hold that an individuals mental features at a given time supervene upon what is in that individuals head at that time. While many people reject mental internalism about content and justification, mental internalism is commonly accepted regarding such other mental features as rationality, emotion-types, propositional-attitude-types, moral character, and phenomenology. I construct a counter-example to mental internalism regarding all these features. My counter-example involves two creatures: a human and an alien from Pulse World. These creatures environments, behavioral dispositions and (...) histories are such that it is intuitively clear that they are mentally quite different, even while they are, for a moment, exactly alike with respect to whats in their heads. I offer positive reasons for thinking that the case I describe is indeed possible. I then consider ways in which mental internalists might attempt to account for this case, but conclude that the only plausible option is to reject mental internalism and to adopt a particular externalist alternative a history-oriented version of teleo-functionalism. (shrink)