Biological ontologies are used to organize, curate, and interpret the vast quantities of data arising from biological experiments. While this works well when using a single ontology, integrating multiple ontologies can be problematic, as they are developed independently, which can lead to incompatibilities. The Open Biological and Biomedical Ontologies Foundry was created to address this by facilitating the development, harmonization, application, and sharing of ontologies, guided by a set of overarching principles. One challenge in reaching these goals was that the (...) OBO principles were not originally encoded in a precise fashion, and interpretation was subjective. Here we show how we have addressed this by formally encoding the OBO principles as operational rules and implementing a suite of automated validation checks and a dashboard for objectively evaluating each ontology’s compliance with each principle. This entailed a substantial effort to curate metadata across all ontologies and to coordinate with individual stakeholders. We have applied these checks across the full OBO suite of ontologies, revealing areas where individual ontologies require changes to conform to our principles. Our work demonstrates how a sizable federated community can be organized and evaluated on objective criteria that help improve overall quality and interoperability, which is vital for the sustenance of the OBO project and towards the overall goals of making data FAIR. Competing Interest StatementThe authors have declared no competing interest. (shrink)

[R]eflection is a system of thought no less closed than insanity, with this difference that it understands itself and the madman too, whereas the madman does not understand it.– Merleau-Ponty, Phen...

The book that the French reader holds in his hands is one of the century’s most fascinating and liberating. It does nothing less than instigate the psychoanalytic approach as a universal method of...

Il est assez commun de se représenter le bûcheron comme un être plutôt fruste, qualifié avant tout par sa force au service d’une tâche peu valorisée. Or cette représentation se révèle tronquée, car l’équation qui associe la force à l’outil ne peut se réaliser sans le contrôle du geste. Plus encore, l’écoute des témoignages recueillis auprès des forestiers nous apprend que ce travail réclame d’efficaces systèmes de précision. C’est là une qualification oubliée, pourtant reconnue à part entière dès l’Iliade, qui (...) nous en donne deux témoins privilégiés par l’anthropologie historique de la Grèce, la mètis, l’« intelligence rusée », prêtée au kybérnêtês, le pilote du navire, au conducteur de char et, en bonne première place, au bûcheron. La théorie du contrôle nous permet maintenant de dépasser le flou conceptuel de la notion historiquement pré-théorique de mètis, la ruse s’appliquant à des cas bien trop divers, pour lui préférer les développements les plus récents d’une science du contrôle de l’action, théorisée depuis Wiener, nourrissant aujourd’hui les projets les mieux financés de cyber-cerveaux informatiques, au service des neurosciences et de la médecine. Le travail forestier, qui réclame une coordination maîtrisée des gestes, y compris de leurs commandes vocales dans le chant de travail — qu’un seul ou plusieurs bûcherons en équipe soient mobilisés —, nous en fournit une parfaite illustration. The woodcutter is commonly represented as a fairly boorish person, reduced to brute force and low-level tasks. But this representation is partial because a simplistic inferential link between an axe and strength obliterates that nothing can happen without any modus operandi, i.e. a set of neural controls over gestures. Indeed, listening to woodcutter’s testimonies led us to elicit that this work needs efficient precision systems. This high level of qualification was acknowledged at least since Homer’s Iliad as evidenced by two favourite telltales from historical anthropology of Ancient Greece: mètis ascribed to kybérnêtês, the ship’s pilot as to the chariot-driver and in the first rank to the woodcutter. Control theory allows now to avoid the fuzziness of meaning of the pre-theoretical notion of mètis to focus on a domain steadily developed since Wiener, now part of costly cyber-brain projects in informatics, for neuroscience and medicine. Forest work, which requires skilled gesture coordination, with vocal commands in a worksong—for one or more woodcutters being engaged in the task—is such a telling case. (shrink)

This paper offers a framework for consciousness of internal reality. Recent PET experiments are reviewed, showing partial overlap of cortical activation during self-produced actions and actions observed from other people. This overlap suggests that representations for actions may be shared by several individuals, a situation which creates a potential problem for correctly attributing an action to its agent. The neural conditions for correct agency judgments are thus assigned a key role in self/other distinction and self-consciousness. A series of behavioral experiments (...) that demonstrate, in normal subjects, the poor monitoring of action-related signals and the difficulty in recognizing self-produced actions are described. In patients presenting delusions, this difficulty dramatically increases and actions become systematically misattributed. These results point to schizophrenia and related disorders as a paradigmatic alteration of a ''Who?'' system for self-consciousness. (shrink)

D'où vient que tous les régimes politiques prétendent rétablir ou défendre la liberté et qu'il n'y en ait pas un qui ne semble la confisquer ou la dévoyer? Pourquoi les diverses représentations que nous en formons spontanément sont-elles en outre si contradicctoires que nous ne puissions jouir d'aucune liberté sans nous sentir privés d'une autre? Certains mathématiciens croient parfois avoir contribué à l'élucidation d'un problème en démontrant qu'il ne peut avoir de solution. A leur exemple, cet essai tente de montrer (...) pourquoi la conception de la liberté tombe en d'insurmontables antinomies dès qu'on l'associe au temps en la définissant comme pouvoir d'accomplir ce qu'on désire ou de faire ce qu'on veut. Seule échapperait aux antinomies de la contingence et de la nécessité, de la différence et de l'identié, de la médiation et de l'immédiation, une liberté affranchie du désir et du temps. Mais il faudrait pour cela nous être délivrés des obsessions de l'ego et du prestige de ses images. Quoiqu'il n'y ait rien dont le monde contemporain parle autant que de la liberté, il est donc à craindre que rien ne lui soit plus étranger. C'est cette diversité que l'auteur traduit par la description de quelques exemples, avant d'en rechercher l'origine. (shrink)

(in press, under contract with MIT Press, accepted on June 30th, 2006). Attention, Information and Epistemic Perception. In Terzis, G. & Arp, R. (Eds) Information and the Living Systems: Essays in the Philosophy of Biology. The MIT Press. (14,000 words).

While visiting her grandmother, Nora joins with the animated toys from an old chest to bring the stars down from the night sky, but their loss makes the sky black and sad.

As Russell's paradox of "the set of all sets that do not contain themselves" indicated long ago, matters go seriously amiss if one operates an ontology of unrestricted totalization. Some sort of restriction must be placed on such items as "the set of all sets that have the feature F' or "the conjunction of all truths that have the feature G." But generally, logicians here introduce such formalized and complex devices as the theory of types or the doctrine of impredictivity. (...) The present paper argues for the informal and elementary idea that the items invoked in a proper identification have themselves already been identified. Even as an explanation is not satisfactory that proceeds in terms of items that themselves require prior explanation, so the same holds with identification. And heed of this elementary idea suffices to sideline those otherwise paradoxical perplexities. (shrink)

Can animals be agents? Do they want to be free? Can they have meaningful lives? If so, should we change the way we treat them? This paper offers an account of animal agency and of two continuums: between human and nonhuman agency, and between wildness and captivity. It describes how a wide range of human activities impede on animals’ freedom and argues that, in doing so, we deprive a wide range of animals of opportunities to exercise their agency in ways (...) that can give meaning to their lives. (shrink)

El presente artículo analiza la recepción de la _Germania_ de Tácito como documento histórico fidedigno en la Alemania nazi, y las operaciones de lectura que el régimen nacionalsocialista realizó sobre la obra con el objetivo de instalarla como fuente de su ideología. De allí, se demostrará cómo se subvirtió la función primordial de la _Germania_, de ficción a historia mediante el recorte, la traducción sesgada, la cita apócrifa y la desvinculación con su contexto de producción inmediato. Esto produjo una interpretación (...) de la _Germania_ como espejo de la ideología oficial de conflicto racial en la Alemania de la década de 1930. (shrink)

En este artículo se presenta una aplicación del análisis de las proyecciones funcionales del Sintagma Determinante desarrollado por Borer a dos fenómenos relacionados que involucran a estructuras en función de complemento de estar: por un lado, encontramos la lectura no locativa de sintagmas preposicionales encabezados por en y complementados por un nominal escueto, y la lectura locativa de sintagmas encabezados por la misma preposición y complementados por un SDet con el mismo núcleo léxico N. Por otro lado, encontramos la alternancia (...) de un gerundio en estar entrenando con la estructura preposicional presente en estar en entrenamiento. Considerando, además, que solo en la lectura no locativa el sujeto de la cláusula corresponde a un participante semántico del evento, se propone que la presencia de determinante bloquea la posibilidad de establecer una relación de identidad referencial entre el sujeto de v y el sujeto de P, contribuyéndose así a la producción de una lectura locativa. La ausencia de bloqueo a la relación de identidad referencial mencionada permite producir una lectura no locativa que posibilita, al menos parcialmente, la alternancia entre las estructuras con gerundio y con nominal escueto. (shrink)

This paper demonstrates the central role of the Socratic elenchus in the Sophist. In the first part, I defend the position that the Stranger describes the Socratic elenchus in the sixth division of the Sophist. In the second part, I show that the Socratic elenchus is actually used when the Stranger scrutinizes the accounts of being put forward by his predecessors. In the final part, I explain the function of the Socratic elenchus in the argument of the dialogue. By contrast (...) with standard scholarly interpretations, this way of reading the text provides all the puzzles about being (241c4–251a4) with a definite function in the dialogue. It also reveals that Plato’s methodology includes a plurality of method and is more continuous than what is often believed. (shrink)

ABSTRACT This paper examines consequences of the computer revolution in mathematics. By comparing its repercussions with those of conceptual developments that unfolded in the nineteenth century, I argue that the key epistemological lesson to draw from the two transformative periods is that effective and successful mathematical practices in science result from integrating the computational and conceptual styles of mathematics, and not that one of the two styles of mathematical reasoning is superior. Finally, I show that the methodology deployed by applied (...) mathematicians in modern scientific computing is a paradigmatic instance of this key lesson. (shrink)

This article presents an applied discussion of the possibility of integrating conversation analysis (CA) methodology into that of machine learning. The aim is to improve the detection of that which resembles disengagement in the interaction between a robot and a human. We offer a novel analytical assemblage at the heart of the two disciplines, and namely on the level of the annotation schemes provided by conversation analysis transcription methods. First, we demonstrate that the need for a stable structure in establishing (...) an interaction scenario and in designing robot behaviours does not prevent the emergence of ordinariness or creativity among the participants engaged in this interaction. Secondly, based on an actual case, we emphasize the possibility of systematicness in CA transcription to support the choice (a) of the categories targeted by prediction methods and defined by the annotation scheme, and (b) of the verbal and non-verbal features used to create prediction models. (shrink)

It is commonly assumed that moral deliberation requires that the alternatives available in a choice situation are evaluatively comparable. This comparability assumption is threatened by claims of incomparability, which is often established by means of the small improvement argument (SIA). In this paper I argue that SIA does not establish incomparability in a stricter sense. The reason is that it fails to distinguish incomparability from a kind of evaluative indeterminacy which may arise due to the vagueness of the evaluative comparatives (...) ‘better than,’ ‘worse than,’ and ‘equally as good as.’. (shrink)

Recent research has challenged our view of the Abrahamic religious traditions as unilaterally intolerant and incapable of recognizing otherness in all its diversity and richness; but a diachronic and comparative study of how these traditions deal with otherness is yet to appear. This volume aims to contribute to such a study by presenting different treatments of otherness in medieval and early modern thought. Part I: Altruism deals with attitudes and behaviors that benefit others, regardless of its motives. We deal with (...) the social rights and emotions as well as the moral obligations that the very existence of other human beings, whatever their characteristics, creates for a community. Part II: Religious recognition and toleration considers identity, toleration and mutual recognition created by the existence of religious or ethnic otherness in a given social, religious or political community. Part III: Evil deals with religious otherness that is considered evil and rejected such as heretics and malevolent, demonic entities. The volume will ultimately inform the reader on the nature of religious toleration (including beliefs and doctrines, even emotions) as well as of the self-definition of religious communities when encountering and defining otherness in different ways. (shrink)

This paper demonstrates the importance of the reception and development of Goethe’s metamorphosis of plants as a methodological and philosophical framework in the history of botanical theories. It proposes a focus on the textbooks written by the German botanist Ludwig Reichenbach and his first attempt to use Goethe’s idea of metamorphosis of plants as fundamental to his natural system of plants published under the title ‘Botany for Women’, in German Botanik für Damen. In this book, Reichenbach paid particular attention to (...) Goethe’s sensitive views on the essence of nature; he regarded Goethe’s idea of metamorphosis in the plant kingdom as an ideal model to interpret connections of natural phenomena, in particular as a conceptual frame for a natural system. Furthermore, he aimed to develop the philosophical statement of the metamorphosis, in which he called for nature-philosophical conceptions in order to materialize his representation of plant “affinities,” and of a kind of “ontogeny” of the whole plant kingdom. This paper demonstrates that, between speculative views and empirical attempts, the extent to which Reichenbach actually belonged to a new “school” of thought, which left its mark on the history and philosophy of botany. (shrink)

Dans cet article j’envisage la problématique du « discours rattrapé par la situation » non comme un fait rare, mais comme une propriété générique de tout événement social : l’organisation du discours en interaction (la conversation, une conférence, une performance poétique) suppose un contexte qu’il contribue réflexivement à structurer. Je souhaite le montrer en ayant recours à l’analyse de situations a priori extra-ordinaires, où des aspects troublants, angoissants, morbides font enfler des phénomènes humains structurant des pratiques sociales en général. Par (...) là, je m’appuierai sur une perspective endogène du contexte, et j’introduirai une discussion sur l’approche interactioniste vis-à-vis de notions telles que l’information, ou la normalité. (shrink)

Para calificar la estética posmodernista, que responde a la entrada en la era posmoderna, marcada por la ausencia de una visión unitaria y global del mundo, los teóricos de los años 70 privilegiaron el concepto de “heterogeneidad”, que en la década siguiente y parte de los años 90, dejó paso al de “sincretismo”, “mestizaje” o “creolidad”. A partir de los años 90 y, sobre todo, desde la primera década del tercer milenio, el concepto de “hibridez” ocupa un lugar destacado debido, (...) en parte, a la influencia de los estudios poscoloniales. Uno de los primeros en utilizar dicho concepto, en 1990, fue el crítico cultural argentino Néstor García Canclini, pero no profundizó sobre la hibridez de las obras literarias. Por consiguiente, cabe definir, en primer lugar, esta noción proteiforme, utilizada en nuestros días en numerosos campos. (shrink)

There seems to be an inconsistency at the heart of Aristotle’s Metaphysics: a differentia is said both to presuppose its genus (in vii 12) and to be logically independent from it (in x 7). I argue that the relation of analogy resolves this inconsistency, restores the coherence of the concepts of differentia and species, and gives x 7 its rightful place in the development of the Metaphysics.