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)

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)

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.

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)

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 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.

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)

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)

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)

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)

Last year at VSS, Bullot, Droulez & Pylyshyn reported studies using a Modified Traveling Salesman Paradigm in which a virtual vehicle had to visit up to 10 targets once and only once, and in which the invisible targets were identified only by line segments pointing from the vehicle toward each target. We hypothesized that subjects used two distinct strategies: A “location-based strategy”, which kept track of where targets were located in screen coordinates, and a “segment-based strategy” that kept track of (...) which segments corresponded to visited targets. We report new studies that further explore these two strategies. Subjects passively observed a computer-controlled virtual vehicle that visited a number of targets. Two forms of display were used: an “Allocentric” display, in which the vehicle moved and the targets remained fixed in screen coordinates, and an “Egocentric” display, in which the vehicle's position on the screen remained fixed while the targets moved -- as if the environment were being viewed by an observer on the vehicle. At the end of each trial, the directional segments were extended to the edge of the screen and subjects were asked to perform two tasks by referring to these segments. In the “status task” observers had to indicate for each segment whether the corresponding target had been visited or not. In the “locating task” they had to locate each target along its directional segment. Performance on these two tasks measures the use of the two hypothesized strategies. Results showed that observers do well on the status task with 4 or 6 targets in both display conditions, but do poorly on the locating task, especially in the egocentric condition when there are more targets. These results are consistent with the hypothesis that in the egocentric condition the MTSP task is carried out primarily by segment-tracking, which can be viewed as a deictic strategy. (shrink)

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)

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)

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)

This study investigates a new experimental paradigm called the Modified Traveling Salesman Problem. This task requires subjects to visit once and only once n invisible targets in a 2D display, using a virtual vehicle controlled by the subject. Subjects can only see the directions of the targets from the current location of the vehicle, displayed by a set of oriented segments that can be viewed inside a circular window surrounding the vehicle. Two conditions were compared. In the “allocentric” condition, subjects (...) see the vehicle move across the screen and change orientation under their command. The “egocentric” condition is similar except for how the information is provided: the position and orientation of the vehicle icon remains fixed at the center of the screen and only target directions, as indicated by the oriented segments, change as the subject “moves” the vehicle. The unexpected finding was that this task can be performed, in either condition, for up to 10 targets. We consider two possible strategies that might be used, a location-based strategy and a segment strategy. The location-based strategy relies on spatial memory and attempts to infer the locations of all the targets. The segment strategy is more local and focuses on the directional segments themselves, keeping track of the ones that represent already-visited targets. A number of observations suggest that the segment strategy was used, at least for larger numbers of targets. According to our hypothesis, keeping track of the segments requires one to use indexical reference for associating the segments with their status in the task - given by current status predicates Visited or Not-visited -, perhaps using visual indexes, deictic pointers, or object files. (shrink)

This article puts forward an hypothesis on the aesthetic use of attention. Some artistic situations favour such a use of attention and may contribute to the conscious access to cognitive and emotional contents and effects, as well as to their discussion in the public sphere.

This text aims at presenting a general characterization of the act of perceiving a particular object, in a framework in which perception is conceived of as a mental and cognitive faculty having specific functions that other faculties such as imagination and memory do not possess. I introduce the problem of determining the occurrence of singular perception of a physical object, as opposed to the occurrence of other mental states or attitudes. I propose that clarifying this occurrence problem requires making explicit (...) the conditions of perceptual competence/faculty so as to explain the occurrence of each perceptual performance on the basis of the use of this competence. I argue then for a direct relational model according to which the singular perception of an object depends on a competence of connecting the perceiver directly with each target object. This model is compatible with a disjunctive approach to perception according to which each particular experience of an object corresponds either to a direct perceptual relation with this object or to the illusion of having the experience of this object. The arguments in favour of this relational model rest on the idea that the faculty of perception grounds the capacity to demonstratively identify physical objects. (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)

Stem cell science is advancing at an unprecedented rate, with thousands of research papers being published every year and many clinical trials for a wide range of conditions underway as registered on ClinicalTrials.gov. This rapidly expanding and alluring field has brought with it ever more complex and multifaceted ethical issues, many of which require new guidelines, consent protocols and even change in legislation, since they do not fit comfortably in the existing bioethical regulations and protocols. Keeping up with the ethical (...) implications of stem cell research is daunting to the expert and non-expert. We review the various types of stem cells and then focus on multipotent and pluripotent cell types, since it is these cell types that bring with them the greatest research and therapeutic potential, while concurrently delivering novel ethical conundrums. Certain key considerations are currently lacking and what is needed is how to obtain permission from individuals who donate their biological material for both scientific inquiry and eventually, for their potential therapeutic utility. (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)

Research seeking to explain the perpetration of violence and atrocities by humans against other humans offers both social and individualistic explanations, which differ namely in the roles attributed to empathy. Prominent social models suggest that some manifestations of inter-human violence are caused by parochial attitudes and obedience reinforced by within-group empathy. Individualistic explanations of violence, by contrast, posit that stable intra-individual characteristics of the brain and personality of some individuals lead them to commit violence and atrocities. An individualistic explanation argues (...) that the chief cause of violence is the perpetrator’'s lack of empathy with the victim. To offer the rudiments of a critique of the individualistic approach, I critically examine a model stating that violence is caused by empathy erosion. Specifically, the discussion of the empathy-erosion model is applied to the case of honour-based violence, a type of violence known for its communal character. Building from prior enquiries into violence and social cognition, I argue that an empathy-erosion explanation of HBV is defective because it does not consider important cultural and historical enablers of violence. Finally, as an alternative to individualism, I propose a psychohistorical approach to HBV in the migration context. This alternative combines psychological and philosophical enquiry with historical and ethnographical analysis. The psychohistorical approach hypothesises that distinct processes of cultural learning of honour codes both scaffold HBV and modulate the perpetrators’ emotions and empathy. (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.