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; 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 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)

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)

We argue that Lewis would have rejected recent appeals to the notions of ‘metaphysical dependency’, ‘grounding’ and ‘ontological priority’, because he would have held that they’re not needed and they’re not intelligible. We argue our case by drawing upon Lewis’s views on supervenience, the metaphysics of singletons and the dubiousness of Kripke’s essentialism.

In the article, Twin pregnancy, fetal reduction and the ‘all or nothing problem’, I argued that there is a moral problem in multifetal pregnancy reduction from a twin to a singleton pregnancy. Drawing on Horton’s original version of the ‘all or nothing problem’, I argued that there are two intuitively plausible claims in 2-to-1 MFPR: aborting both fetuses is morally permissible, aborting only one of the twin fetuses is morally wrong. Yet, with the assumption that one should select permissible (...) choice over impermissible choice, the two claims lead to a counter-intuitive conclusion: the woman ought to abort both fetuses rather than only one. It would be odd to promote such a pro-death view. Begović _et al_ discuss my article and offer insightful criticism, claiming, that there is no ‘all or nothing problem’ present in 2-to-1 MFPR. In this short reply, I respond to some of their criticism. (shrink)

We investigate an enrichment of the propositional modal language L with a "universal" modality ■ having semantics x ⊧ ■φ iff ∀y(y ⊧ φ), and a countable set of "names" - a special kind of propositional variables ranging over singleton sets of worlds. The obtained language ℒ $_{c}$ proves to have a great expressive power. It is equivalent with respect to modal definability to another enrichment ℒ(⍯) of ℒ, where ⍯ is an additional modality with the semantics x ⊧ (...) ⍯φ iff Vy(y ≠ x → y ⊧ φ). Model-theoretic characterizations of modal definability in these languages are obtained. Further we consider deductive systems in ℒ $_{c}$ . Strong completeness of the normal ℒ $_{c}$ logics is proved with respect to models in which all worlds are named. Every ℒ $_{c}$ -logic axiomatized by formulae containing only names (but not propositional variables) is proved to be strongly frame-complete. Problems concerning transfer of properties ([in]completeness, filtration, finite model property etc.) from ℒ to ℒ $_{c}$ are discussed. Finally, further perspectives for names in multimodal environment are briefly sketched. (shrink)

The causal impacts of genes and environment on any one biological trait are inextricably entangled, and consequently it is widely accepted that it makes no sense in singleton cases to privilege either factor for particular credit. On the other hand, at a population level it may well be the case that one of the factors is responsible for more variation than the other. Standard methodological practice in biology uses the statistical technique of analysis of variance to measure this latter (...) kind of causal efficacy. In this paper, I argue that: 1) analysis of variance is in fact badly suited to this role; and. (shrink)

Fetal reduction is the practice of reducing the number of fetuses in a multiple pregnancy, such as quadruplets, to a twin or singleton pregnancy. Use of assisted reproductive technologies increases the likelihood of multiple pregnancies, and many fetal reductions are done after in vitro fertilisation and embryo transfer, either because of social or health-related reasons. In this paper, I apply Joe Horton’s all or nothing problem to the ethics of fetal reduction in the case of a twin pregnancy. I (...) argue that in the case of a twin pregnancy, there are two intuitively plausible claims: abortion is morally permissible, and it is morally wrong to abort just one of the fetuses. But since we should choose morally permissible acts rather than impermissible ones, the two claims lead to another highly implausible claim: the woman ought to abort both fetuses rather than only one. Yet, this does not seem right. A plausible moral theory cannot advocate such a pro-death view. Or can it? I suggest ways to solve this problem and draw implications for each solution. There are no data in this work. (shrink)

In a recent paper, Chunghyoung Lee argues that, because zygotes are developmentally plastic, they cannot be numerically identical to the singletons into which they develop, thereby undermining conceptionism. In this short paper, I respond to Lee. I argue, first, that, on the most popular theories of personal identity, zygotic plasticity does not undermine conceptionism, and, second, that, even overlooking this first issue, Lee’s plasticity argument is problematic. My goal in all of this is not to take a stand in the (...) abortion debate, which I remain silent on here, but, rather, to push for the conclusion that transitivity fails when we are talking about numerical identity of non-abstract objects. (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)

A set of parameters for classifying composition operations is introduced. These parameters determine whether a composition operation is 1) universal, 2) determinate, 3) whether there is a difference between possible and actual compositions, 4) whether there can be singleton compositions, 5) whether they give rise to a hierarchy, and 6) whether components of compositions can be repeated. Philosophical implications of these parameters (in particular in relation to set theory) and mereology are discussed.

The problem of personal identity is a longstanding philosophical topic albeit without final consensus. In this article the somewhat similar problem of AI identity is discussed, which has not gained much traction yet, although this investigation is increasingly relevant for different fields, such as ownership issues, personhood of AI, AI welfare, brain–machine interfaces, the distinction between singletons and multi-agent systems as well as to potentially support finding a solution to the problem of personal identity. The AI identity problem analyses the (...) criteria for two AIs to be considered the same at different points in time. Two approaches to tackle the problem are proposed: One is based on the personal identity problem and the concept of computational irreducibility, while the other one applies multi-factor authentication to the AI identity problem. Also, a range of scenarios is examined regarding AI identity, such as replication, fission, fusion, switch off, resurrection, change of hardware, transition from non-sentient to sentient, journey to the past, offspring and identity change. (shrink)

Before the 2007–2008 global financial crisis, the vast majority of social scientists were not paying much attention to the politics of central banking, despite the fact that, since their creation, central banks have been pivotal institutions between private financial institutions and public authorities (Singleton, 2010). During the past decades, central banks acquired considerable independence from public officials under the Central Bank Independence (CBI) template (McNamara, 2002). Governments justified their decisions to delegate monetary competences by relying on a narrow conception (...) of monetary policy, in which central bankers should only seek to control inflation and ignore the implications of their policies on other economic issues such as financial stability or wealth inequalities (Issing et al., 2001; Marcussen, 2009). Heterodox economists and critical political economists opposed this view by declaring that monetary policy is fundamentally political as it deals with complicated policy trade-offs, which generates winners and losers (Epstein & Gintis, 1995; Forder, 2005). However, until 2007, their concerns were very marginal and remained at the fringes of the political debate. The vast majority of policy-makers, economists, and central bankers themselves agreed on the fact that the CBI template was the optimal institutional arrangement between fiscal and monetary authorities. (shrink)