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)

The study of anarchism as a philosophical, political, and social movement has burgeoned both in the academy and in the global activist community in recent years. Taking advantage of this boom in anarchist scholarship, Nathan J. Jun and Shane Wahl have compiled twenty-six cutting-edge essays on this timely topic in New Perspectives on Anarchism.

© 2015, Springer-Verlag Berlin Heidelberg.Genetic studies have identified single nucleotide polymorphisms associated with the risk of prostate cancer. It remains unclear whether such genetic variants are associated with disease aggressiveness. The NCI-SPORE Genetics Working Group retrospectively collected clinicopathologic information and genotype data for 36 SNPs which at the time had been validated to be associated with PC risk from 25,674 cases with PC. Cases were grouped according to race, Gleason score and aggressiveness. Statistical analyses were used to compare the frequency (...) of the SNPs between different disease cohorts. After adjusting for multiple testing, only PC-risk SNP rs2735839 was significantly and inversely associated with aggressive and high-grade disease in European men. Similar associations with aggressive and high-grade disease were documented in African-American subjects. The G allele of rs2735839 was associated with disease aggressiveness even at low PSA levels in both European and African-American men. Our results provide further support that a PC-risk SNP rs2735839 near the KLK3 gene on chromosome 19q13 may be associated with aggressive and high-grade PC. Future prospectively designed, case-case GWAS are needed to identify additional SNPs associated with PC aggressiveness. (shrink)

_ Source: _Volume 35, Issue 1, pp 35 - 60 The early-modern French translations of Erasmus’ Praise of Folly show an astonishing adaptability to its ever changing readerships. Much attention has been paid recently to the two sixteenth-century translations and their intended readers—royal and bourgeois respectively. The three French translations of the seventeenth and eighteenth centuries are less known but all the more intriguing. In 1642 Folly addresses herself to the French pre-classicist readers, adepts of Richelieu’s new Académie Française—although her (...) translator, Hélie Poirier, was a Protestant refugee, recently settled in the Netherlands. In 1671 Folly seeks her readers in the Parisian salons, satirizing the same societal wrongs as her great contemporary Molière in Tartuffe and Les femmes savantes. The successful translation by Nicolas Gueudeville is also a chameleon: originally translated and printed in Leiden, the text gradually becomes more Parisian with each passing edition. Folly’s language is bowdlerized according to the principles of bienséance, and Vianen’s illustrations, based on Holbein, are discarded as rude and old-fashioned. In 1751 they are replaced by Charles Eisen’s elegant, long-limbed, periwigged figures, dressed to the latest fashion. Although she changes her name, her language, her appearance and attire, Folly remains much the same through the ages—everlasting and omnipresent, just as the vices she laughs at. (shrink)

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński.

In this article, I identify “spontaneity” as a significant but poorly-analyzed term in social theory and description through an overview of tensions between varying technical accounts of spontaneity in research literature. In contrast to conceptually-slippery “realist” accounts of spontaneity, I argue for viewing spontaneity ethnomethodologically, i.e., as a contextually-emergent social practice. I suggest two directions for future applications of this approach: first, an ethnomethodological approach to rhetorical analysis of unanalyzed use of the term “spontaneity” in research literature, and second, observational (...) studies of improvisational theatre, a social practice in which orientation toward the production of spontaneity by participants is criterial to the identity of the practice. (shrink)

This study is situated within the newly emerging interest in the concept of grace as a legitimate topic for empirical enquiry, and draws on the theoretical framework provided by the SIFT approach to biblical hermeneutics, an approach rooted in reader-perspective hermeneutical theory and in Jungian psychological type theory. Data were draw from two one-day workshops with Anglican Readers (lay ministers). On each occasion the participants were invited to divide into three separate groups according to their preferences for sensing or intuition (...) (the two perceiving functions) and within these groups to explore the messages of grace in Matthew 6: 25–30 (Jesus’ invitation to look at the birds and to consider the lilies). The rich data gathered from these workshops generated insights into contemporary theologies of grace and also confirmed the hypothesis that biblical interpretation is shaped by the reader’s psychological type preference for sensing or for intuition. (shrink)

Research seeking a scientific foundation for the theory of art appreciation has raised controversies at the intersection of the social and cognitive sciences. Though equally relevant to a scientific inquiry into art appreciation, psychological and historical approaches to art developed independently and lack a common core of theoretical principles. Historicists argue that psychological and brain sciences ignore the fact that artworks are artifacts produced and appreciated in the context of unique historical situations and artistic intentions. After revealing flaws in the (...) psychological approach, we introduce a psycho-historical framework for the science of art appreciation. This framework demonstrates that a science of art appreciation must investigate how appreciators process causal and historical information to classify and explain their psychological responses to art. Expanding on research about the cognition of artifacts, we identify three modes of appreciation: basic exposure to an artwork, the artistic design stance, and artistic understanding. The artistic design stance, a requisite for artistic understanding, is an attitude whereby appreciators develop their sensitivity to art-historical contexts by means of inquiries into the making, authorship, and functions of artworks. We defend and illustrate the psycho-historical framework with an analysis of existing studies on art appreciation in empirical aesthetics. Finally, we argue that the fluency theory of aesthetic pleasure can be amended to meet the requirements of the framework. We conclude that scientists can tackle fundamental questions about the nature and appreciation of art within the psycho-historical framework. (shrink)

Has the time come to put to bed the concept of a harm threshold when discussing the ethics of reproductive decision making and the legal limits that should be placed upon it? In this commentary, we defend the claim that there exist good moral reasons, despite the conclusions of the non-identity problem, based on the interests of those we might create, to refrain from bringing to birth individuals whose lives are often described in the philosophical literature as ‘less than worth (...) living’. (shrink)

Critics of the target article objected to our account of art appreciators' sensitivity to art-historical contexts and functions, the relations among the modes of artistic appreciation, and the weaknesses of aesthetic science. To rebut these objections and justify our program, we argue that the current neglect of sensitivity to art-historical contexts persists as a result of a pervasive aesthetic–artistic confound; we further specify our claim that basic exposure and the design stance are necessary conditions of artistic understanding; and we explain (...) why many experimental studies do not belong to a psycho-historical science of art. (shrink)

Many scholars view artworks as the products of cultural history and arbitrary institutional conventions. Others construe art as the result of psychological mechanisms internal to the organism. These historical and psychological approaches are often viewed as foes rather than friends. Is it possible to combine these two approaches in a unified analysis of the perception and consciousness of artworks? I defend a positive answer to this question and propose a psycho-historical theory, which argues that artworks are historical and material artefacts (...) designed to prompt mental activities and elicit the conscious experience of aesthetic worlds. My argument suggests that the material components of artworks--termed their `material substrata'--are crucial mediators between historical contexts and the mental activities elicited by the perception of artworks. (shrink)

This commentary suggests that understanding the “Folk Psychology of Souls” requires studying a problem articulating ontology with psychology: How do human beings, both as perceivers and thinkers, track and refer to (1) living and dead intentional agents and (2) supernatural agents? The problem is discussed in the light of the principle of the ontological commitment in agent tracking.

How do humans manage to keep track of a gradually changing object or person as the same persisting individual despite the fact that the extraction of information about this individual must often rely on heterogeneous information sources and heterogeneous tracking methods? The article introduces the Empirical Tracking of Individuals theory to address this problem. This theory proposes an analysis of the concept of integrated tracking, which refers to the capacity to acquire, store, and update information about the identity and location (...) of individuals in our environment. It hypothesizes that certain functions of attention are a key to explaining how the cognitive flexibility of the human mind overcomes the heterogeneity of sources and methods in integrated tracking. At least two premises lend support to this hypothesis. First, heterogeneity of tracking sources is overcome by the combination of information from multiple perceptual modalities and a phenomenon of multisensory 'transparency'. Second, heterogeneity of tracking sources and methods may also be overcome by inferences that combine information across domains to acquire reasons to believe propositions about the target's location and identity. (shrink)

Abstractabstract:Vaccine hesitancy continues to pose a formidable obstacle to increasing national COVID-19 vaccination rates in the US, but this is not the first time that American vaccination efforts have confronted resistance and apathy. This study examines the history of US vaccination efforts against smallpox, polio, and measles, highlighting persistent drivers of vaccine hesitancy as well as factors that helped overcome it. The research reveals that logistical barriers, negative portrayals in the media, and fears about safety stymied inoculation efforts as early (...) as the 18th century and continue to do so. However, vaccine hesitancy has been markedly diminished when trusted community leaders have guided efforts, when ordinary citizens have felt personally invested in the success of the vaccine, and when vaccination efforts have been tied to broader projects to improve public health and social cohesion. Deliberately cultivating such factors could be an effective strategy for lessening opposition today, when COVID-19's distinctive characteristics make addressing vaccine hesitancy more urgent than it has ever been. (shrink)

Working within the sensing, intuition, feeling, thinking (SIFT) approach to biblical hermeneutics, the present study invited a hermeneutical community of 23 type-aware participants to explore the account of the Death of Lazarus as reported in John 11: 1–17 within type-alike groups differentiated according to the participants’ dominant function-orientation. Five groups were constituted differentiating: introverted sensing, introverted intuition, extraverted intuition, introverted and extraverted feeling and introverted and extraverted thinking. These five groups generated distinctive readings of the narrative that were characteristic of (...) the individual type preference. Contribution: The SIFT method, situated within the reader perspective approach to biblical hermeneutics, is concerned with attending to the influence exerted by the psychological type profile of the reader on interpreting the text. The present study goes beyond previous work by comparing the responses of five hermeneutical communities (each distinguished by a different dominant function-orientation) to the same passage of scripture. (shrink)

Proteins are targeted to plastids by N‐terminal transit peptides, which are recognized by protein import complexes in the organelle membranes. Historically, transit peptide properties have been defined from vascular plant sequences, but recent large‐scale genome sequencing from the many plastid‐containing lineages across the tree of life has provided a much broader representation of targeted proteins. This includes the three lineages containing primary plastids (plants and green algae, rhodophytes and glaucophytes) and also the seven major lineages that contain secondary plastids, “secondhand” (...) plastids derived through eukaryotic endosymbiosis. Despite this extensive spread of plastids throughout Eukaryota, an N‐terminal transit peptide has been maintained as an essential plastid‐targeting motif. This article provides the first global comparison of transit peptide composition and summarizes conservation of some features, the loss of an ancestral motif from the green lineages including plants, and modifications to transit peptides that have occurred in secondary and even tertiary plastids. BioEssays 29:1048–1058, 2007. © 2007 Wiley Periodicals, Inc. (shrink)

To introduce the issue of the tracking and identification of human agents, I examine the ability of an agent to track a human person and distinguish this target from other individuals: The ability to perform person identification. First, I discuss influential mechanistic models of the perceptual recognition of human faces and people. Such models propose detailed hypotheses about the parts and activities of the mental mechanisms that control the perceptual recognition of persons. However, models based on perceptual recognition are incomplete (...) theories of person identification because they do not explain several identification behaviors that are fundamental to human social interactions. Furthermore, recognition-based models tend to appeal to the controversial concept of the “identity” of a person without explaining what determines personal identity and persistence. To overcome these limitations, I propose to integrate the face-recognition program into a broader causal-historical theory of identification. The causal-historical theory of identification complements models focused on perceptual recognition because it can account for the types of non-perceptual identification overlooked by the face-recognition program. Moreover, it can decompose the identification behaviors into tracking processes that succeed or fail to be sensitive to causal characteristics of a target. I illustrate these advantages with a discussion of the difference between the tracking of a person understood as either a causally continuous biological organism or a psychologically continuous mind. Finally, I argue that the causal-historical theory provides a theoretical framework for investigating the tracking of relations between a target and its contextual and historical attributes, such as a target's possessions. (shrink)

Object identification via a perceptual-demonstrative mode of presentation has been studied in cognitive science as a particularly direct and context-dependent means of identifying objects. Several recent works in cognitive science have attempted to clarify the relation between attention, demonstrative identification and context exploration. Assuming a distinction between ‘ demonstrative reference' and ‘perceptual-demonstrative identification', this article aims at specifying the role of attention in the latter and in the linking of conceptual and non conceptual contents while exploring a spatial context. First, (...) the analysis presents an argument to the effect that selection by overt and covert attention is needed for perceptual-demonstrative identification since overt/covert selective attention is required for the situated cognitive access to the target object. Second, it describes a hypothesis that makes explicit some of the roles of attention: the hypothesis of identification by epistemic attention via the control of perceptual routines. (shrink)

To explain agent-identification behaviours, universalist theories in the biological and cognitive sciences have posited mental mechanisms thought to be universal to all humans, such as agent detection and face recognition mechanisms. These universalist theories have paid little attention to how particular sociocultural or historical contexts interact with the psychobiological processes of agent-identification. In contrast to universalist theories, contextualist theories appeal to particular historical and sociocultural contexts for explaining agent-identification. Contextualist theories tend to adopt idiographic methods aimed at recording the heterogeneity (...) of human behaviours across history, space, and cultures. Defenders of the universalist approach tend to criticise idiographic methods because such methods can lead to relativism or may lack generality. To overcome explanatory limitations of proposals that adopt either universalist or contextualist approaches in isolation, I propose a philosophical model that integrates contributions from both traditions: the psycho-historical theory of agent-identification. This theory investigates how the tracking processes that humans use for identifying agents interact with the unique socio-historical contexts that support agent-identification practices. In integrating hypotheses about the history of agents with psychological and epistemological principles regarding agent-identification, the theory can generate novel hypotheses regarding the distinction between recognition-based, heuristic-based, and explanation-based agent-identification. (shrink)

ABSTRACTSocial attentional biases are a core component of social anxiety disorder, but research has not yet determined their direction due to methodological limitations. Here we present preliminary findings from a novel, dynamic eye-tracking paradigm allowing spatial–temporal measurement of attention and gaze-following, a mechanism previously unexplored in social anxiety. 105 participants took part, with those high and low in social anxiety traits entered into the analyses. Participants watched a video of an emotionally-neutral social scene, where two actors periodically shifted their gaze (...) towards the periphery. HSA participants looked more at the actors’ faces during the initial 2s than the LSA group but there were no group differences in proportion of first fixations to the face or latency to first fixate the face, although HSA individuals’ first fixations to the face were shorter. No further differences in eye movements were found, nor in gaze-following beha... (shrink)

From an ethnomethodological perspective, this article describes social actors’ everyday and virtual stances in terms of their practices of provisional doubt and belief for the purpose of fact-establishment. Facts are iterated, reinforced, elaborated, and transformed via phenomenal practices configuring relations of equipment, interpretation, and method organized as “other” than, but relevant to, the everyday. Such practices in scientific research involve forms of suspended belief; in other areas they can instead involve forms of suspended doubt. As an illuminating example of this (...) latter class of virtual fact-establishment practices, I offer an extended analysis of the “yes; and…” principle of information-establishment used in improvisational theatre to progressively develop the content of a performance. (shrink)

We agree with many of the principles proposed by Frost but highlight crucial caveats and report research findings that challenge several assertions made in the target article. We discuss the roles that visual processing, development, and bilingualism play in visual word recognition and reading. These are overlooked in all current models, but are fundamental to any universal model of reading.

To analyze the relations between art and science, philosophers and historians have developed different lines of inquiry. A first type of inquiry considers how artistic and scientific practices have interacted over human history. Another project aims to determine the contributions that scientific research can make to our understanding of art, including the contributions that cognitive science can make to philosophical questions about the nature of art. We rely on contributions made to these projects in order to demonstrate that art and (...) science are codependent phenomena. Specifically, we explore the codependence of art and science in the context of a historical analysis of their interactions and in the context of contemporary debates on the cognitive science of art. (shrink)

Editorial: Objects and Sound Perception Content Type Journal Article Pages 5-17 DOI 10.1007/s13164-009-0006-3 Authors Nicolas J. Bullot, École des Hautes Études en Sciences Sociales Centre de Recherches sur les Arts et le Langage (CRAL/CNRS) 96 Bd Raspail 75006 Paris France Paul Égré, Institut Jean-Nicod (ENS/EHESS/CNRS) Département d’Etudes Cognitives de l’ENS 29 rue d’Ulm 75005 Paris France Journal Review of Philosophy and Psychology Online ISSN 1878-5166 Print ISSN 1878-5158 Journal Volume Volume 1 Journal Issue Volume 1, Number 1.