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)

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)

Jennifer Nagel (2010) has recently proposed a fascinating account of the decreased tendency to attribute knowledge in conversational contexts in which unrealized possibilities of error have been mentioned. Her account appeals to epistemic egocentrism, or what is sometimes called the curse of knowledge, an egocentric bias to attribute our own mental states to other people (and sometimes our own future and past selves). Our aim in this paper is to investigate the empirical merits of Nagel’s hypothesis about the psychology involved (...) in knowledge attribution. (shrink)

Pinillos’ Why We Doubt presents a powerful critique of such global skeptical assertions as “I don’t know I am not a brain-in-a-vat (BIV)” by introducing a cognitive mechanism that is sensitive to error possibilities and a Bayesian rule of rationality that this mechanism is designed to approximate. This multifaceted argument offers a novel counter to global skepticism, contending that our basis for believing such premises is underminable. In this work, we engage with Pinillos’ adoption of Bayesianism, questioning whether the Bayesian (...) principle that he invokes truly does fail to generate the verdict that we don’t we aren’t BIVs, contrary to what Pinillos asserts. Furthermore, we argue that Pinillos’ empirical argument is not empirical enough; we need a lot more empirical work if we are going to counter global skepticism and win over neutral bystanders. (shrink)

Pinillos’ Why We Doubt presents a powerful critique of such global skeptical assertions as “I don’t know I am not a brain-in-a-vat (BIV)” by introducing a cognitive mechanism that is sensitive to error possibilities and a Bayesian rule of rationality that this mechanism is designed to approximate. This multifaceted argument offers a novel counter to global skepticism, contending that our basis for believing such premises is underminable. In this work, we engage with Pinillos’ adoption of Bayesianism, questioning whether the Bayesian (...) principle that he invokes truly does fail to generate the verdict that we don’t we aren’t BIVs, contrary to what Pinillos asserts. Furthermore, we argue that Pinillos’ empirical argument is not empirical enough; we need a lot more empirical work if we are going to counter global skepticism and win over neutral bystanders. (shrink)

The issue of musical identity—of what defines works of music, gives each its unique character and distinguishes them from one another—is one of the central issues in the philosophy of music. Too often in the philosophical literature it is approached as a purely theoretical question, one that can be answered adequately through careful intellectual consideration of scores and performances. The typical philosophical approach to the performance of Western art music, particularly that composed between the Baroque and Romantic eras, is to (...) offer descriptions of how musical works come into being, what their origins may be, which of their structural and aesthetic elements must be observed and conserved in their representations, and so on. It takes the written notation of a musical work, the score, to be a kind of blueprint created by a composer, defining and describing an autonomous musical entity, the musical work, such that another person might perform it. The work is recognized paradoxically as something existing independently of, yet deriving its identity from, its origins with the composer. (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 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)

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)

This is an appendix containing the stimulus materials for the experiments reported in the paper ‘Salient Alternatives in Perspective.’.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

Following Freud’s analysis of the fragile line between the uncanny double and its comic redoubling, I identify the doubling of the double found in critical moments of Hegelian dialectic as producing a kind of comic effect. It almost goes without saying that two provides greater pleasure than one, the loneliest number. Many also find two to be preferable to three, the tired trope of dialectic as a teleological waltz. Two seems to offer lightness, relieving one from her loneliness and lacking (...) the complications of a third who comes in between. And yet, we learn through Marx and Freud that the double (even the double of tragedy and farce) borders on something closer to horror than comedy. -/- In the following, I would like to explore why four is funnier than two in my staging of dialectic as the doubling of the double or, to borrow a movie title from Laurel and Hardy, “Twice Two” (Roach et al. 1933a). I will begin by exploring the formulations of the double in the form of a pair of opposites and in the form of a pair of twins. The literary tropes of the double as the odd couple, on one side, and the twins, on the other, appear to serve very different narrative functions, which incite different kinds of affective responses from the audience. However, the form of the opposed double sometimes conceals the realization that the empty or fragmented content of the first is only reduplicated in the second. The “straight man” of the odd couple cannot see himself in his counterpart “the comic.” The redoubling of the double, however, forces not only the audience, but the original double on stage to confront what was already present, but unrealized, from the beginning. To illustrate this redoubling of the double within the opening of Hegel’s Science of Logic, I consider two short films by Laurel and Hardy in which the comic duo redoubles itself. The formula (2 x 2) produces a comic excess through the dialectical redoubling of there uncanny double. (shrink)

I intend to dismantle a piece of historiographic mythology created by self-styled ‘Revisionists’ (Hill, Alvey, Oslington, etc.). According to the myth, Adam Smith endorsed several of the traditional proofs of God’s existence; he believed that the order existing in the world is a morally good order implemented by Divine Providence; he believed that evil in the world is part of an all-encompassing Divine Plan; and that the ‘invisible hand’ is the hand of the Christian God who leads the rich to (...) employ their wealth for the greater benefit of the greatest number. I argue instead that there is a remarkable analogy between Smith’s and Kant’s theory of religion. Smith’s philosophy is a third way between Rationalism and Phyrronism, arguing that doctrines confirmed by reason in every field, from natural science to theology, are nothing more than combinations of ideas agreeable to the imagination; if we try, on the basis of both Smithian texts and their context and co-text, to reconstruct his lectures on natural theology, all kind of evidence converge in indicating that he reduced proofs of God´s existence to ‘inventions of the imagination’ and argued that philosophical theism is not different in status from primitive belief in invisible beings, or that it is as unwarranted as any system is, and besides that it generates a moral conundrum; he argued also that teleological explanations are no more and no less imaginary than those based on efficient causes, that the teleological order we may imagine in the world is not too bad from a ‘consequentialist’ point of view, and yet it is far below any moral standard; I argued that this is by no means a proof of Smith’s ‘irreligion’ and also that no convincing proof of any turn from religion to irreligion on his part has been provided so far, and finally that the two viable options he left open were either dismal unbelief or Theism on a moral basis. I defend this third way by proving that what Smith’s lost lectures on natural religion said can be reconstruct with some plausibility and what they did not say with absolute certainty; I argue that he developed a sharp criticism of natural theology, that he argued that at the root of religion there are a number of principles of the mind that make religious belief a ‘natural belief’; I do so by reconstructing, first, the context of the missing lectures (sect. 2); then the contents of their first part, considering the proofs of God’s existence and his attributes (sects 3-4); the ‘principles of the mind’ lying at the root of polytheism (sect. 5), of philosophical monotheism (par. 6), and of pure and rational religion (par.7); I contend, then, that his vindication of toleration is consistent with ‘pure and rational religion’ (par. 8) and that attempts to prove a phantom conversion to ‘natural religion’ or ‘irreligion’ result from misreading (par.9). My conclusions are the following: i) Adam Smith claimed that any natural theology is impossible; ii) There is in fact some kind of order in the world, and it proves useful to a point in allowing for humankind’s survival, but it doesn’t meet any minimal moral criterion; iii) the world is not teleologically ordered; we may indeed imagine such order for mental economy, but the world abounds in misery and depravity; iv) consequences of human wickedness and insanity do, happily enough, deviate from intended outcomes; we may feign invisible mechanisms at work behind, but to mistake them for a hidden mechanism is as childish as the primitive’s belief in ‘invisible beings’. v) there are indeed themes from theological doctrines in Smithian economic theory, but they not the kind of rational theology ‘discovered’ by the ‘New View’; they are instead Augustinian and Jansenist themes. vi) Smith’s theological doctrines did – as suggested by Waterman – have a bearing on his economic theory not by ‘doctrinal dependence’ but – as suggested by Harrison – in the more modest role of source of blueprints for economic explanation. (shrink)