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)

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 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)

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)

En général, un agent peut dire ce qu’il est en train de faire sans l’observer au préalable, et il possède une certaine autorité sur ce qu’il en dit. Partant de ce fait, Elizabeth Anscombe a soutenu que la connaissance qu’un agent a de ses actions intentionnelles est un «savoir pratique» (practical knowledge) «sans observation». Cette thèse a été abondamment commentée, critiquée et reprise depuis la publication d’Intention il y a bientôt 70 ans. Ce qui a plus rarement été abordé est (...) l’étonnant parallèle entre ce que dit Anscombe à ce sujet, et certaines descriptions sartriennes de la conscience d’un agent intentionnel. Cet article tâchera de montrer que les pensées respectives de ce drôle de couple philosophique convergent sur l’idée que nous avons la capacité de dire ce que nous sommes en train de faire sans observation ni réflexion préalable. En critiquant une certaine image de l’intériorité de l'esprit, leur objectif commun est de rendre compte de cette conscience de soi toute particulière qui permet aux agents de savoir ce qu’ils font dans et par cette action même. Comment faut-il comprendre le rapport entre ces deux approches ? Sont-elles complémentaires ? Concurrentes ? Nous considérons qu’une réponse simple et tranchée à ces questions n’est pas possible d’avance, exige une étude comparative relativement poussée. Notre hypothèse est que le savoir pratique d’un agent est indissociable d’une certaine expérience de l’engagement pratique dans le monde que décrit Sartre. (shrink)

A sustained challenge to the view that artworks are physical objects relates to the alleged inability of physical objects to possess representational properties, which some artworks clearly do possess. I argue that the challenge is subject to confusions about representational properties and aesthetic experience. I show that a challenge to artwork-object identity put forward by Danto is vulnerable to a similar criticism. I conclude by noting that the identity of artworks and physical objects is consistent with the insight that attending (...) exclusively to the object’s individual physical properties may prevent us from grasping the nature of the work. // Contre l’opinion voulant que les œuvres d’art soient des objets physiques, d’aucuns font régulièrement valoir la présumée incapacité des objets physiques à possedér des propriétés représentationnelles, propriétés que certaines œuvres d’art possèdent a l’evidence. Je fais valoir que cette remise en question est sujette à des confusions à propos des propriétés représentationnelles et de l’experience esthétique. Je montre que de même, la remise en question par Danto de l’identité œuvre d’art-objet prête le flanc à une critique similaire. Je conclus pour finir que l’identité entre œuvres d’art et objets physiques est compatible avec l’intuition voulant que prêter attention exclusivement aux propriétés physiques d’un certain objet peut nous empêcher de saisir la nature de l’œuvre. (shrink)

Deux idées centrales sont défendues dans cet article. La première concerne les liens entre les concepts de matérialisme émergentiste et de réalisme critique dans la métaphysique bungéenne. Je défends la thèse que le réalisme critique bungéen doit intégrer épistémologiquement celui de matérialisme afin de se développer en tant que doctrine méthodologique. J’y analyse ce que je considère être les fondements de la méthode de la construction de cette même métaphysique, soit l’affirmation du postulat de l’extériorité du monde concret et son (...) rôle dans la méthode en question. La seconde thèse a pour objet une analyse de cette méthode au moyen de l’étude que j’y fais des concepts ontologiques bungéens d’objet, de substance et de propriétés objectales. Je compare ensuite cette méthode à certains aspects de la philosophie des mathématiques et en particulier au rôle attribué dans cette même philosophie à la méthode axiomatique en tant que méthode de construction théorique et de preuve. Je conclus en une certaine circularité de l’argument qui justifie le réalisme critique à partir du postulat ontologique de l’extériorité du monde concret. (shrink)

The corporate meltdowns of this and the previous decade in the US - WorldCom, Enron, Tyco, and in Australia - FAI, HIH and AWB being among the many examples - have resulted in the governments of those two countries introducing legislation and policy guidelines aimed at minimising future corporate misbehaviour. -/- The US has introduced the Sarbanes Oxley Act, with requirements on corporate accountants and auditors, as well as its whistleblowing provisions. It has revised the Federal Sentencing Guidelines for Organizations. (...) New rules for the NYSE and NASDAQ have also been introduced. In addition, the U.S. Securities and Exchange Commission and U.S. Department of Justice have further strengthened the Foreign Corrupt Practices Act 1977, last revised in 1997. -/- Australia has revised the Corporations Act to include whistleblower protection clauses as well as adopted the ASX Corporate Governance guidelines. Standards Australia has issued its handbook on corporate governance. Although not a business issue, the Australian government has also announced that it will introduce whistleblower protection legislation for the public sector by the end of its first term in office. This legislation will likely influence whatever the private sector does in this respect. The inclusion of whistleblower protection in both Sarbanes–Oxley and the Corporations Act reflects a growing body of research that finds that people internal to an organisation are the most effective way to identify corporate wrongs. The Commonwealth Treasury has recently issued an options paper, stating that the Corporations Act has been ineffectual. It has sought submissions on revisions to the legislation that the Australian Government could take. This paper examines the policies advocated by over 20 organisations and academics concerned with whistleblowing issues. It draws the conclusion that on current indications, even after further reform, Australian legislation and policies are still likely to be less effectual than overseas practices. -/- --------------------------------- . (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)

À propos de la possibilité de voyager dans le temps sur la base de plusieurs ouvrages spécialisés, notamment ceux de Nicholas J. J. Smith (« Time Travel »), William Grey (« Troubles with Time Travel »), Ulrich Meyer (« Explaining causal loops »), Simon Keller and Michael Nelson (« Presentists should believe in time-travel »), Frank Arntzenius and Tim Maudlin (« Time Travel and Modern Physics »), et David Lewis (« The Paradoxes of Time Travel »). L'article commence par une (...) Introduction dans laquelle je fais une brève présentation du voyage dans le temps et poursuit par une Histoire du concept de voyage dans le temps, les principaux aspects physiques du voyage dans le temps, y compris les voyages dans le temps dans le passé dans la relativité générale et la physique quantique , et les voyages dans le temps dans le futur, puis une présentation du Paradoxe du grand-père abordé dans presque toutes les œuvres spécialisées, suivie d’une section consacrée à la Philosophie du voyage dans le temps et d’une section dans laquelle j’analyse les Boucles causales pour le voyage dans le temps. Je termine mon travail avec Conclusions, dans laquelle je maintiens mes opinions personnelles sur le voyage dans le temps et la Bibliographie sur laquelle repose le travail. -/- TABLE: -/- Abstract Introducere Istoria conceptului de călătorie în timp Paradoxul bunicului Filosofía călătoriei în timp Buclele cauzale Concluzii Note Bibliografie -/- DOI: 10.13140/RG.2.2.27116.51841. (shrink)

L'America e il mondo sono in procinto di collassare a causa dell'eccessiva crescita demografica, la maggior parte per il secolo scorso, e ora tutto questo, a causa della gente del terzo mondo. Il consumo di risorse e l'aggiunta di altri 4 miliardi di ca. 2100 crolleranno la civiltà industriale e porterà alla fame, alle malattie, alla violenza e alla guerra su scala impressionante. La terra perde almeno l'1% del suo suolo superiore ogni anno, così come si avvicina a 2100, la (...) maggior parte della sua capacità di coltivazione alimentare sarà andato. Miliardi moriranno e la guerra nucleare è tutt'altro che certa. In America, questo è stato enormemente accelerato dalla massiccia immigrazione e dalla riproduzione degli immigrati, unite agli abusi resi possibili dalla democrazia. La natura umana depravata trasforma inesorabilmente il sogno della democrazia e della diversità in un incubo di criminalità e povertà. La Cina continuerà a travolgere l'America e il mondo, finché manterrà la dittatura che limita l'egoismo. La causa principale del collasso è l'incapacità della nostra psicologia innata di adattarsi al mondo moderno, che porta le persone a trattare le persone non correlate come se avessero interessi comuni. L'idea dei diritti umani è una fantasia malvagia promossa dalla sinistra per distogliere l'attenzione dalla spietata distruzione della terra da parte della sfrenata maternità del terzo mondo. Questo, oltre all'ignoranza della biologia e della psicologia di base, porta alle illusioni di ingegneria sociale dei parzialmente istruiti che controllano le società democratiche. Pochi capiscono che se aiuti una persona che fai del male a qualcun altro, non c'è pranzo gratuito e ogni singolo oggetto che qualcuno consuma distrugge la terra in modo irreparabile. Di conseguenza, le politiche sociali ovunque sono insostenibili e una dopo l'altra tutte le società senza rigorosi controlli sull'egoismo crolleranno nell'anarchia o nella dittatura. I fatti più basilari, quasi mai menzionati, sono che non ci sono abbastanza risorse in America o nel mondo per sollevare una percentuale significativa dei poveri dalla povertà e tenerli lì. Il tentativo di farlo sta mandando in bancarotta l'America e distruggendo il mondo. La capacità della terra di produrre cibo diminuisce ogni giorno, così come la nostra qualità genetica. E ora, come sempre, di gran lunga il più grande nemico dei poveri sono gli altri poveri e non i ricchi. Senza cambiamenti drammatici e immediati, non c'è speranza di prevenire il crollo dell'America, o di qualsiasi paese che segua un sistema democratico. (shrink)

L’ambition du présent article est de montrer la filiation entre le naturalisme d’Henry David Thoreau et ses positions antiesclavagistes. Je défends que cette filiation se fait voir par la façon dont l’éthique de Thoreau s’appuie sur une certaine conception de la nature et par la manière dont ses vues abolitionnistes découlent de cette éthique. Je fais valoir, plus précisément, que la fuite de Thoreau dans la nature n’est pas seulement, comme le prétend le politologue Malcom Ferdinand, un moyen comme (...) un autre qu’emploierait Thoreau pour protester contre l’esclavagisme. Il faut plutôt voir en l’idée que se fait Thoreau de la nature ce qui nourrit ses positions antiesclavagistes. L’éthique de Thoreau est une éthique de la vertu qui repose sur l’idée que l’être humain est un être de nature. L’accomplissement humain doit être pensé en rapport avec une certaine idée de nature – la nature sauvage – et l’esclavage condamné parce qu’il dénature l’homme. L’abolitionnisme de Thoreau n’est donc pas, comme le défend Ferdinand, la cause du naturalisme de Thoreau. C’est bien plutôt de son naturalisme que découlent ses vues abolitionnistes. (shrink)

The questions that have been looming at the thoughts of many African theologians for years have been: How can the Christian faith be made to be at home in Africa, in such a way that it harmo nizes with African beliefs and practices, thus becoming the religion of the African people? What is the relationship between African traditional religion and culture with the Christian faith? Does being a Christian mean that I should distance myself from m y traditional religious and (...) cultural heritages? It is from this background that Igwebuike theology emerges as an African theology , posting that effort towards evangelization must begin from the understanding of the African worldview and the incorporation of such in the processes of the communication and learning of the Christian faith. This work presented the theology of African typo logy ( u di, meaning type, kind or nature) within the context of Igwebuike theology , with a view to creating a balance in the midst of the conflicts between Christianity and African religion and culture by connecting the events of the New Testament to events and persons in African traditional religion and culture. This connection is such that the events, persons, realities, etc., in African traditional religion and culture find meaning and fulfillment in the New Testament Scriptures. The Igwebuike theology of u di has created an aperture for further dialogue of culture with faith. It provided a deeper meaning and wider capacity for the application of the concept , ‘typology’. It has contributed to the continuous search for better ways of making the Christian fai th feel at home in Africa, and also making it possible for the redemption of the African culture through its interaction with faith. For the purpose of this study, the Igwebuike theoretical framework , which emphasizes beginning from and valuing what is kno wn, and using what is already known as a stepping stone to get to the unknown , was adopted. (shrink)

L'America e il mondo sono in procinto di collassare a causa di una crescita eccessiva della popolazione, la maggior parte per il secolo scorso e ora tutto a causa di persone del terzo mondo. Il consumo di risorse e l'aggiunta di uno o due miliardi in più di 2100 crolleranno la civiltà industriale e porterà alla fame, alle malattie, alla violenza e alla guerra su scala impressionante. Miliardi moriranno e la guerra nucleare è tutt'altro che certa. In America questo è (...) stato enormemente accelerato dalla massiccia immigrazione e dalla riproduzione degli immigrati, unite ad abusi resi possibili dalla democrazia. La natura umana depravata trasforma inesorabilmente il sogno della democrazia e della diversità in un incubo di criminalità e povertà. La causa principale del collasso è l'incapacità della nostra psicologia innata di adattarsi al mondo moderno, che porta le persone a trattare le persone non correlate come se avessero interessi comuni. Questo, oltre all'ignoranza della biologia e della psicologia di base, porta alle illusioni di ingegneria sociale dei parzialmente istruiti che controllano le società democratiche. Pochi capiscono che se aiuti una persona che fai del male a qualcun altro, non c'è pranzo gratuito e ogni singolo oggetto che qualcuno consuma distrugge la terra in modo irreparabile. Di conseguenza, le politiche sociali ovunque sono insostenibili e una dopo l'altra tutte le società senza rigorosi controlli sull'egoismo crolleranno nell'anarchia o nella dittatura. Senza cambiamenti drammatici e immediati, non c'è speranza di prevenire il crollo dell'America, o di qualsiasi paese che segua un sistema democratico. Da qui il mio saggio "Suicide by Democracy". È anche ormai chiaro che i sette sociopatici che governano la Cina stanno vincendo la terza guerra mondiale, e quindi il mio saggio conclusivo su di loro. L'unica minaccia più grande è l'Intelligenza Artificiale che commento brevemente. La chiave di tutto ciò che ci riguarda è la biologia, ed è l'ignarietà che porta milioni di persone intelligenti istruite come Obama, Chomsky,Clinton, il Partito Democratico e il Papa a sposare ideali utopici suicidi che portano inesorabilmente direttamente all'Inferno sulla Terra. Come W ha notato, è ciò che è sempre davanti ai nostri occhi che è il più difficile da vedere. Viviamo nel mondo del sistema linguistico deliberativo cosciente 2, ma è inconscio, automatico sistema riflessivo 1 che governa. Questa è la fonte della cecità universale descritta da The Phenomenological Illusion (TPI) di Searle, Pinker's Blank Slate and Tooby and Cosmides' Standard Social Science Model. Il primo gruppo di articoli cerca di dare un'idea di come ci comportiamo che è ragionevolmente privo di illusioni teoriche. Nei prossimi tre gruppi commento tre delle principali illusioni che impediscono un mondo sostenibile: tecnologia, religione e politica (gruppi cooperativi). La gente crede che la società possa essere salvata da loro, quindi fornisco alcuni suggerimenti nel resto del libro sul perché questo è improbabile attraverso brevi articoli e recensioni di libri recenti di scrittori ben noti. Un'altra sezione descrive l'illusione religiosa – che c'è qualche super potere che ci salverà. La sezione successiva descrive le illusioni digitali, che confondono i giochi linguistici del System 2 con gli automatismi del Sistema uno, e quindi non possono distinguere le macchine biologiche (cioè le persone) da altri tipi di macchine (cioè i computer). Altri illusioni digitali sono che saremo salvati dal male puro (egoismo) del Sistema 1 da computer/AI/robotica/nanotecnologia/ingegneria genetica creata dal System 2. Il principale Nessun pranzo libero ci dice che ci saranno conseguenze gravi e forse fatali. L'ultima sezione descrive The One Big Happy Family Delusion, cioè che siamo selezionati per la cooperazione con tutti, e che gli ideali euforici di Democrazia, Diversità e Uguaglianza ci condurranno all'utopia, se ne gestiamo le cose correttamente (la possibilità della politica). Ancora una volta, il No Free Lunch Principle dovrebbe avvertirci che non può essere vero, e vediamo nel corso della storia e in tutto il mondo contemporaneo, che senza controlli rigorosi,egoismo e stupidità guadagnano il sopravvento e presto distruggono qualsiasi nazione che abbracci queste illusioni. Inoltre, la mente scimmia sconti ripida il futuro, e così collaboriamo nel vendere il patrimonio del nostro discendente per comfort temporanei, esacerbando notevolmente i problemi. (shrink)