Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Scottish philosophy and intellectual history have become the increasingly fashionable fields of academic studies. Alexander Broadie, one of the pioneers and an accomplished scholar of the Scottish Enlightenment, returns to the basic question, namely, “what is Scottish philosophy?”, and presents a comprehensive work on the history of Scottish philosophy. Broadie successfully elucidates the nature and significance of Scottish philosophy both historically and philosophically. He argues that Scottish philosophy must be studied in its historical context, for it is not only (...) a philosophical enterprise but also a persistent tradition which has united the Scottish nation for centuries. The advancements in science, literature, politics, and culture in Scotland would be extremely unlikely, if not impossible, without such an intellectual culture established by thinkers in that tradition. This article is intended as a review of Broadie’s A History of Scottish Philosophy in the background of his shifting academic interests from philosophy to history while he holds the professorship in University of Glasgow. His commitment to Scottish philosophical culture deserves the attention of contemporary historians and philosophers, for his work opens up a space for dialogue between intellectual history and history of philosophy, an issue addressed at the end of this paper. (shrink)

A collaborative article by the Editorial Collective of Social Imaginaries. Investigations into social imaginaries have burgeoned in recent years. From ‘the capitalist imaginary’ to the ‘democratic imaginary’, from the ‘ecological imaginary’ to ‘the global imaginary’ – and beyond – the social imaginaries field has expanded across disciplines and beyond the academy. The recent debates on social imaginaries and potential new imaginaries reveal a recognisable field and paradigm-in-the-making. We argue that Castoriadis, Ricoeur, and Taylor have articulated the most important theoretical frameworks (...) for understanding social imaginaries, although the field as a whole remains heterogeneous. We further argue that the notion of social imaginaries draws on the modern understanding of the imagination as authentically creative. We contend that an elaboration of social imaginaries involves a significant, qualitative shift in the understanding of societies as collectively and politically-instituted formations that are irreducible to inter-subjectivity or systemic logics. After marking out the contours of the field and recounting a philosophical history of the imagination, the essay turns to debates on social imaginaries in more concrete contexts, specifically political-economic imaginaries, the ecological imaginary, multiple modernities and their inter-civilisational encounters. The social imaginaries field imparts powerful messages for the human sciences and wider publics. In particular, social imaginaries hold significant implications for ontological, phenomenological and philosophical anthropological questions; for the cultural, social, and political horizons of contemporary worlds; and for ecological and economic phenomena. The essay concludes with the argument that social imaginaries as a paradigm-in-the-making offers valuable means by which movements towards social change can be elucidated as well providing an open horizon for the critiques of existing social practices. (shrink)

Boundary colors are observed when light from a scene is dispersed by a prism or diffraction grating. We discovered that patterns with repeating black and white stripes can produce repeating bands of boundary colors with two hues. These hues are virtually constant as measured by chromaticity or CIELAB. We found seven cases of this kind using a new appearance model for boundary colors. The model correctly predicts that green and magenta bands recur as stripe widths and dispersion strength vary. The (...) first green/magenta case in the sequence traces out an accurate ellipse in XYZ color space. Green and magenta bands are prominent in supernumerary rainbows and interference rings, and we explain why that might be the case. The explanation is based on an interesting property of the visible spectrum. In addition to the green/magenta cases, the other cases are orange/cyan, yellowish-green/purple, and yellow/violet. The success of the boundary color appearance model implies that bands are perceived as if the wavelength responses of the cones were essentially independent, which contradicts the actual behavior of cones. (shrink)

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 Repugnant Conclusion served an important purpose in catalyzing and inspiring the pioneering stage of population ethics research. We believe, however, that the Repugnant Conclusion now receives too much focus. Avoiding the Repugnant Conclusion should no longer be the central goal driving population ethics research, despite its importance to the fundamental accomplishments of the existing literature.

Are the real numbers rich enough to measure intelligence? We generalize a result of Alexander and Hutter about the so-called Legg-Hutter intelligence measures of reinforcement learning agents. Using the generalized result, we exhibit a paradox: in one particular version of the Legg-Hutter intelligence measure, certain agents all have intelligence 0, even though in a certain sense some of them outperform others. We show that this paradox disappears if we vary the Legg-Hutter intelligence measure to be hyperreal-valued rather than real-valued.

This paper provides a method for characterizing space events using the framework of conceptual spaces. We focus specifically on estimating and ranking the likelihood of collisions between space objects. The objective is to design an approach for anticipatory decision support for space operators who can take preventive actions on the basis of assessments of relative risk. To make this possible our approach draws on the fusion of both hard and soft data within a single decision support framework. Contextual data is (...) also taken into account, for example data about space weather effects, by drawing on the Space Domain Ontologies, a large system of ontologies designed to support all aspects of space situational awareness. The framework is coupled with a mathematical programming scheme that frames a mathematically optimal approach for decision support, providing a quantitative basis for ranking potential for collision across multiple satellite pairs. The goal is to provide the broadest possible information foundation for critical assessments of collision likelihood. (shrink)

Background: Ontologies and taxonomies are among the most important computational resources for molecular biology and bioinformatics. A series of recent papers has shown that the Gene Ontology (GO), the most prominent taxonomic resource in these fields, is marked by flaws of certain characteristic types, which flow from a failure to address basic ontological principles. As yet, no methods have been proposed which would allow ontology curators to pinpoint flawed terms or definitions in ontologies in a systematic way. Results: We present (...) computational methods that automatically identify terms and definitions which are defined in a circular or unintelligible way. We further demonstrate the potential of these methods by applying them to isolate a subset of 6001 problematic GO terms. By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms. This allows us to demonstrate that these other resources do not contain definitions superior to those supplied by GO. Conclusion: Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies. Further, they are well suited to assist ontology curators in drawing their attention to those terms that are ill-defined. We have further shown the limitations of ontology mapping and alignment in assisting ontology curators in rectifying problems, thus pointing to the need for manual curation. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

Neurath’s scientific utopianism is the proposal that the social sciences should engage in the elaboration, development, and comparison of counterfactual scenarios, the ‘utopias’. Such scenarios can be understood as centerpieces of scientific thought experiments, that is, in exercises of imagination that not only promote conceptual revision, but also stimulate creativity to deal with experienced problems, as utopias are efforts to imagine what the future could look like. Moreover, utopian thought experiments can offer scientific knowledge to inform political debates and decisions, (...) contributing to the shaping of society. This essay reconstructs a historical event as an example of Neurath’s utopianist methodology. In the late 1970s and early 1980s, a scientific and political commission appointed by the Western German Parliament devised and compared four scenarios for future energetic-economic policies. Conclusions of the commission informed political decisions that put Western (later reunified) Germany in a route towards becoming a green industrial power. A fundamental part of the commission’s work involved an appeal to imagination, allowing for the characterization under Neurath’s methodology. (shrink)

In contrast to the successful previous year, 2020 turned out to be difficult, not only for the earth’s population due to COVID-19 but also for JDDM with an unusually small sixth volume. Looking back at these two very different years back-to-back led us to some reflection: As the COVID-19 pandemic forcefully illustrates, dynamic decision-making with all its complications and uncertainty is a topic of high relevance for modern societies.

The Molyneux question asks: would a blind person, who knows spheres and cubes only from touch, be able to recognize these shapes visually immediately upon becoming sighted, without touching them? Molyneux himself answered no. Locke accepted Molyneux’s negative answer. But Locke’s answer appears inconsistent with the doctrine of common sensibles, according to which some ideas are given in more than one sense modality. Motivated by alleviating this tension, philosophers have put forth several interpretations of Locke’s views on shape perception. Here (...) I motivate a novel interpretation of Locke that can better resolve the tension. (shrink)

Discussion of the relevance of grounding to substantiveness, theory-choice, and “location problems” in metaphysics.

What happens when scholars come together to study Buddhist and German Idealist perspectives on mind and representation? We explore this question and reflect on methodological considerations in what is often referred to as "comparative philosophy.".

This is a reply to de Sousa's 'Emotional Truth', in which he argues that emotions can be objective, as propositional truths are. I say that it is better to distinguish between truth and accuracy, and agree with de Sousa to the extent of arguing that emotions can be more or less accurate, that is, based on the facts as they are.

As formal theoretical linguistic methodology has matured, recent years have seen the advent of applying it to objects of study that transcend language, e.g., to the syntax and semantics of music (Lerdahl & Jackendoff 1983, Schlenker 2017a; see also Rebuschat et al. 2011). One of the aims of such extensions is to shed new light on how meaning is construed in a range of communicative systems. In this paper, we approach this goal by looking at narrative dance in the form (...) of Bharatanatyam. We argue that a semantic approach to dance can be modeled closely after the formal semantics of visual narrative proposed by Abusch (2013, 2014, 2021). A central conclusion is that dance not only shares properties of other fundamentally human means of expression, such as visual narrative and music, but that it also exhibits similarities to sign languages and the gestures of non-signers (see, e.g., Schlenker 2020) in that it uses space to track individuals in a narrative and performatively portray the actions of those individuals. From the perspective of general human cognition, these conclusions corroborate the idea that linguistic investigations beyond language (see Patel-Grosz et al. forthcoming) can yield insights into the very nature of the human mind and of the communicative devices that it avails. (shrink)

Monoclonal antibodies are essential biomedical research and clinical reagents that are produced by companies and research laboratories. The NIAID ImmPort (Immunology Database and Analysis Portal) resource provides a long-term, sustainable data warehouse for immunological data generated by NIAID, DAIT and DMID funded investigators for data archiving and re-use. A variety of immunological data is generated using techniques that rely upon monoclonal antibody reagents, including flow cytometry, immunofluorescence, and ELISA. In order to facilitate querying, integration, and reuse of data, standardized terminology (...) for describing monoclonal antibody reagents and their targets needs to be used for annotating data submitted to ImmPort. (shrink)

The overall goal of the approach developed in this paper is to estimate the likelihood of a given kinetic kill scenario between hostile spacebased adversaries using the mathematical framework of Complex Conceptual Spaces Single Observation. Conceptual spaces are a cognitive model that provide a method for systematically and automatically mimicking human decision making. For accurate decisions to be made, the fusion of both hard and soft data into a single decision framework is required. This presents several challenges to this data (...) fusion framework. The first is the challenge involved in handling multiple complex terminologies, which is addressed by drawing on a set of Space Domain Ontologies. Another challenge is the complex combinatorics involved when considering all possible feature combinations. This can be mitigated by using integer linear programming optimization that is outlined by the Complex Conceptual Spaces Single Observation mathematical model framework. A third challenge is the complicated physics that is involved in a spacecraft collision that must be addressed to obtain a better understanding of threat assessment. Overcoming these various challenges allows for a quantitative ranking for the potential of a kinetic kill collision across multiple spacecraft pairs. In addition to overcoming these challenges this paper will break down threat assessment into four domains and identify a ranking of threat both for each individual domain and for the four domains combined. Simulation results are shown to verify the developed concepts. (shrink)

Unterrichtsreihe inklusive didaktischen Erläuterungen zur Problemfrage: Inwiefern befördert der Einsatz von Algorithmen bei Entscheidungsprozessen Diskriminierung?

The Cell Ontology (CL) is designed to provide a standardized representation of cell types for data annotation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL’s utility for cross-species data integration. To address this problem, we developed a method for the ontological representation of cells and applied this method to develop a (...) dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. 104. Barry Smith, “Toward a Realistic Science of Environments”, Ecological Psychology, 2009, 21 (2), April-June, 121-130. Abstract: The perceptual psychologist J. J. Gibson embraces a radically externalistic view of mind and action. We have, for Gibson, not a Cartesian mind or soul, with its interior theater of contents and the consequent problem of explaining how this mind or soul and its psychological environment can succeed in grasping physical objects external to itself. Rather, we have a perceiving, acting organism, whose perceptions and actions are always already tuned to the parts and moments, the things and surfaces, of its external environment. We describe how on this basis Gibson sought to develop a realist science of environments which will be ‘consistent with physics, mechanics, optics, acoustics, and chemistry’. (shrink)

Dieser Beitrag setzt sich mit der unterrichtspraktischen Frage nach der Einführung und Vertiefung von Begriffsverständnissen im Philosophie- und Ethikunterricht aus- einander. Als Ausgangspunkt dient dazu Sistermanns Bonbonmodell. Es wird dafür argumentiert, dass dieses Modell sowie die Leitidee der Problemorientierung erweitert werden sollten, so man dem Anspruch einer Vermittlung tiefgehender Begriffsverständnisse gerecht werden will. Um eine solche Erweiterung vorzuschlagen, werden erstens ein lernproduktorientiertes Lehr-Lern-Modell aus der Physikdidaktik und zweitens lernpsychologische Grundlagen, die als Darstellungsebenenwechsel in der Mathematikdidaktik Anwendung finden, hinzugezogen.

An increasing number of financial services (FS) companies are adopting solutions driven by artificial intelligence (AI) to gain operational efficiencies, derive strategic insights, and improve customer engagement. However, the rate of adoption has been low, in part due to the apprehension around its complexity and self-learning capability, which makes auditability a challenge in a highly regulated industry. There is limited literature on how FS companies can implement the governance and controls specific to AI-driven solutions. AI auditing cannot be performed in (...) a vacuum; the risks are not confined to the algorithm itself, but rather permeates the entire organization. Using the risk of unfairness as an example, this paper will introduce the overarching governance strategy and control framework to address the practical challenges in mitigating risks AI introduces. With regulatory implications and industry use cases, this framework will enable leaders to innovate with confidence. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

The comprehension of anaphoric relations may be guided not only by discourse, but also syntactic information. In the literature on online processing, however, the focus has been on audible pronouns and descriptions whose reference is resolved mainly on the former. This paper examines one relation that both lacks overt exponence, and relies almost exclusively on syntax for its resolution: adjunct control, or the dependency between the null subject of a non-finite adjunct and its antecedent in sentences such as Mickey talked (...) to Minnie before ___ eating. Using visual world eyetracking, we compare the time course of interpreting this null subject and overt pronouns (Mickey talked to Minnie before he ate). We show that when control structures are highly frequent, listeners are just as quick to resolve reference in either case. When control structures are less frequent, reference resolution based on structural information still occurs upon hearing the non-finite verb, but more slowly, especially when unaided by structural and referential predictions. This may be due to increased difficulty in recognizing that a referential dependency is necessary. These results indicate that in at least some contexts, referential expressions whose resolution depends on very different sources of information can be resolved approximately equally rapidly, and that the speed of interpretation is largely independent of whether or not the dependency is cued by an overt referring expression. (shrink)

I begin with an initial sketch of French and Phillips’ brand of naive realism, which appeals to "ways of perceiving". Then I consider two arguments for it: their own argument concerning illusion, and another argument based on what I have called "internal dependence". Next I turn to criticism. I argue that their “quietism” about "ways of perceiving" is unmotivated; there are several possible positive accounts and it is unclear why French and Phillips reject them. I raise three phenomenological problems for (...) the view. Finally, I raise a problem about sensible qualities. (shrink)

Taong 2019 nang magsimula ang paglaganap ng COVID-19 sa Pilipinas, kaya samu’t saring mga impormasyon ang ipinakalat sa bansa upang maiwasan ang pagkalat ng virus lalo na sa mga lugar na matataas ang bilang ng nag positibo, gaya na lamang sa Lungsod ng Quezon. Hinggil rito, ang saliksik na ito na naglalayong malaman at maitala ang Gampanin ng Wikang Filipino sa pag papalaganap ng impormasyon patungkol sa COVID-19. Upang matugunan ang mga hinihingi sa pananaliksik, ito ay gagwin sa deskriptibong paraan, (...) mag o-obserba ang mga mananaliksik sa mga post mula sa mga social media sites ng Lokal na Pamahalaan ng Lungsod ng Quezon, upang malaman ang ginampanan ng Wikang Filipino sa pagpapalaganap ng impormasyon patungkol sa COVID-19. Bilang proseso sa pagkalap ng mga datos, naghanap ang mga mananaliksik ng mga pages o sites na minamanipula ng Lokal na Pamahalaan ng Lungsod ng Quezon na pinagkunan ng mga post na pumapatungkol sa COVID-19. Mula rito makakagawa ang mga mananaliksik ng content analysis mula sa mga post sa iba’t ibang sites kung paano nagamit ang Wikang Filipino at kung paano ito nakatulong upang mas maiwasan pa ang paglaganap ng virus sa Lungsod ng Quezon. Sa saliksik na ito natuklasan na hindi lamang ang Filipino ang ginamit, marami sa mga post na nakalap ay nasa Tag-lish o pinaghalong Filipino at English, dahil sa bago ito sa mga tao, nilayon ng pamahalaan at maging ang Komisyon ng Wikang Filipino na gamitin ang Wikang Filipino dahil hindi lahat ay may kakayahang umintindi ng wikang banyaga. Gayunpama’y nagkaroon din ng ambag ang wikang Ingles dahil maraming pagkakataong gumamit ng mga teknikal na termino na kadalasang maririnig natin sa agham. Nakatutulong ang saliksik na ito upang mas mabigyang linaw ang ginampanan ng wika at sa kung paano nagiging epektibo ang mga pabatid upang maiwasan ang COVID-19. (shrink)

Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases, and extensive HMI studies have generated large amounts of data. We propose that the logical representation of the knowledge derived from these data and the standardized representation of experimental variables and processes can foster integration of data and reproducibility of experiments and thereby further HMI knowledge discovery. A community-based Ontology of Host-Microbiome Interactions (OHMI) was developed following the OBO Foundry principles. OHMI leverages established (...) ontologies to create logically structured representations of microbiomes, microbial taxonomy, host species, host anatomical entities, and HMIs under different conditions and associated study protocols and types of data analysis and experimental results. (shrink)

Translators’ Abstract: This is a translation of Hans-Georg Gadamer’s recently discovered 1952 Berlin speech. The speech includes several themes that reappear in Truth and Method, as well as in Gadamer’s later writings such as Reason in the Age of Science. For example, Gadamer criticizes positivism, modern philosophy’s orientation toward positivism, and Enlightenment narratives of progress, while presenting his view of philosophy’s tasks in an age of crisis. In addition, he discusses structural power, instrumental reason, the objectification of nature and human (...) beings, the reduction of both to mere means, and the colonization of scientific-technological ways of knowing and being—all of which continue to impact our social and political lives together and threaten the very existence of every living being. This speech is essential reading for Gadamer scholars interested in the social, political, and ethical dimensions of his thought and for those interested in bringing Gadamer into conversation with critical theory. (shrink)

(1) Suppose that you care only about speaking the truth, and are confident that some particular deterministic theory is true. If someone asks you whether that theory is true, are you rationally required to answer "yes"? -/- (2) Suppose that you face a problem in which (as in Newcomb's problem) one of your options---call it "taking two boxes"---causally dominates your only other option. Are you rationally required to take two boxes? -/- Those of us attracted to causal decision theory are (...) under pressure to answer "yes" to both questions. However, it has been shown that many existing decision theories are inconsistent with doing so (Ahmed 2014). A simple proof shows that the same goes for an even wider class of theories: all "suppositional" decision theories. The moral is that causal decision theorists must either answer "no" to one of the above questions, or else abandon suppositional decision theories. (shrink)

This paper employs a case study from the history of neuroscience—brain reward function—to scrutinize the inductive argument for the so-called ‘Heuristic Identity Theory’ (HIT). The case fails to support HIT, illustrating why other case studies previously thought to provide empirical support for HIT also fold under scrutiny. After distinguishing two different ways of understanding the types of identity claims presupposed by HIT and considering other conceptual problems, we conclude that HIT is not an alternative to the traditional identity theory so (...) much as a relabeling of previously discussed strategies for mechanistic discovery. (shrink)

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Significant associations have been found between specific human leukocyte antigen (HLA) alleles and organ transplant rejection, autoimmune disease development, and the response to infection. Traditional searches for disease associations have conventionally measured risk associated with the presence of individual HLA alleles. However, given the high level of HLA polymorphism, the pattern of amino acid variability, and the fact that most of the HLA variation occurs at functionally important sites, it may be that a combination of variable amino acid sites shared (...) by several alleles (shared epitopes) are better descriptors of the actual causative genetic variants. Here we describe a novel approach to genetic association analysis in which genes/proteins are broken down into smaller sequence features and then variant types defined for each feature, allowing for independent analysis of disease association with each sequence feature variant type. We have used this approach to analyze a cohort of systemic sclerosis patients and show that a sequence feature composed of specific amino acid residues in peptide binding pockets 4 and 7 of HLA-DRB1 explains much of the molecular determinant of risk for systemic sclerosis. (shrink)

Since its introduction just over two decades ago, evidence-based medicine (EBM) has come to dominate medical practice, teaching, and policy. There are a growing number of textbooks, journals, and websites dedicated to EBM research, teaching, and evidence dissemination. EBM was most recently defined as a method that integrates best research evidence with clinical expertise and patient values and circumstances in the treatment of patients. There have been debates throughout the early 21st century about what counts as good research evidence between (...) EBM proponents and philosophical critics and even within the EBM community itself. Similar controversy arises about the relative worth of patient values and clinical expertise (and how these can be integrated). EBM has also evolved in ways that have come under scrutiny. Specifically, policymakers have used EBM research methodology to increase the relative importance of clinical guidelines that some clinicians have argued are tyrannical. Philosophers have addressed all of these controversies, and with very few exceptions have been critical of EBM. In addition most philosophical attention has been on the epistemic role of Randomization and evidence hierarchies, with relatively little attention being paid to the role of Diagnosis, expertise, patient values, and Systematic Reviews within EBM. (shrink)

Coherence and correspondence are classical contenders as theories of truth. In this paper we examine them instead as interacting factors in the dynamics of belief across epistemic networks. We construct an agent-based model of network contact in which agents are characterized not in terms of single beliefs but in terms of internal belief suites. Individuals update elements of their belief suites on input from other agents in order both to maximize internal belief coherence and to incorporate ‘trickled in’ elements of (...) truth as correspondence. Results, though often intuitive, prove more complex than in simpler models (Hegselmann & Krause 2002, 2006; Grim, Singer, Reade & Fisher 2015). The optimistic finding is that pressures toward internal coherence can exploit and expand on small elements of truth as correspondence is introduced into epistemic networks. Less optimistic results show that pressures for coherence can also work directly against the incorporation of truth, particularly when coherence is established first and new data is introduced later. (shrink)

La dependencia epistemológica existente en los saberes que integran el quehacer académico, científico y socio-cultural actual hacía las diversas formas de conocer de occidente, han dado como resultado una fragmentación y discriminación epistémica entre el conocimiento científico experimental, las ciencias humanas y los saberes ancestrales y culturales. El presente artículo “diálogo de saberes en las ciencias humanas”, tiene como objetivo indagar acerca de los imaginarios sobre los distintos tipos de saberes que integran el quehacer académico, científico y sociocultural con la (...) finalidad de diagnosticar los estados actuales de la ciencia para su revalorización. Para cumplir con este propósito se aborda la problemática sobre la fragmentación de los saberes en el quehacer académico y científico contemporáneo, a través de un estudio bibliográfico y hermenéutico de textos de filósofos sobre el tema así como el análisis de los datos obtenidos de la encuesta elaborada especialmente para este trabajo. El problema que se aborda está relacionado con la tendencia academicista actual de considerar como conocimiento científico únicamente a aquello que puede ser comprobado experimentalmente; evidenciando con ello una clara fragmentación y discriminación epistémica entre conocimiento científico experimental, ciencias humanas y saberes ancestro culturales. (shrink)

This is a protocol for a Cochrane Review (Intervention). The objectives are as follows: -/- The main aim of this review will be to assess the effects of changing practitioner empathy or patient expectations for all conditions. The main objective is to conduct a systematic review of randomised trials where the intervention involves manipulating either (a) practitioner empathy or (b) patient expectations, or (c) both.

In the first part of this article we survey general similarities and differences between biological and social macroevolution. In the second (and main) part, we consider a concrete mathematical model capable of describing important features of both biological and social macroevolution. In mathematical models of historical macrodynamics, a hyperbolic pattern of world population growth arises from non-linear, second-order positive feedback between demographic growth and technological development. Based on diverse paleontological data and an analogy with macrosociological models, we suggest that the (...) hyperbolic character of biodiversity growth can be similarly accounted for by non-linear, second-order positive feedback between diversity growth and the complexity of community structure. We discuss how such positive feedback mechanisms can be modelled mathematically. (shrink)

Grounding and explanation are said to be intimately connected. Some even maintain that grounding just is a form of explanation. But grounding and explanation also seem importantly different—on the face of it, the former is ‘worldy’ or ‘objective’ while the latter isn’t. In this paper, we develop and respond to an argument to the effect that there is no way to fruitfully address this tension that retains orthodox views about grounding and explanation but doesn’t undermine a central piece of methodology, (...) namely that explanation is a guide to ground. (shrink)

Esta obra colectiva expone diversas concepciones teóricas, ontológicas, epistemológicas, axiológicas y prácticas sobre el origen, sentido, problemáticas, ventajas, detrimentos, alternativas y desafías de la filosofía de la innovación y su incidencia en la educación; reflexiona sobre las contribuciones de la tecnología y responde a interrogantes como: ¿Cuáles son los aporte de la tradición filosófica, del pensamiento ilustrado, de la postmodernidad y de la teoría crítica para la filosofía de la innovación educativa?; ¿Cuál es la función de la filosofía para la (...) comprensión de la innovación?; ¿Cómo se explica el progreso tecno-científico desde la epistemología contemporánea?; ¿Cuál es el componente pedagógico de la innovación?; ¿Cuáles son las aportaciones del Laudato Si para la innovación educativa?. Además, plantea la necesidad de repensar algunos aspectos relacionados con la educación, el Estado y la identidad latinoamericana para determinar las posibilidades, las limitaciones y los retos de la innovación, entendida como un fenómeno en permanente construcción. Este tomo se encuentra conformado por ocho capítulos en los que los autores formulan un conjunto de contribuciones para la generación de nuevas investigaciones. Además, evidencia a la innovación como un procesos que exige reformulaciones. La innovación sigue siendo una de las tareas pendientes de la filosofía. (shrink)

Both books published in 1996 explore the role that gender plays in the psychology of art (dealing with both making and viewing), complicating current philosophical distinctions between the aesthetic and the cognitive, and providing new insights into basic topics in the history and psychology of perception, representation, and disinterestedness.

This article examines two questions about scientists’ search for knowledge. First, which search strategies generate discoveries effectively? Second, is it advantageous to diversify search strategies? We argue pace Weisberg and Muldoon, “Epistemic Landscapes and the Division of Cognitive Labor”, that, on the first question, a search strategy that deliberately seeks novel research approaches need not be optimal. On the second question, we argue they have not shown epistemic reasons exist for the division of cognitive labor, identifying the errors that led (...) to their conclusions. Furthermore, we generalize the epistemic landscape model, showing that one should be skeptical about the benefits of social learning in epistemically complex environments. (shrink)

Can there be grounding without necessitation? Can a fact obtain wholly in virtue of metaphysically more fundamental facts, even though there are possible worlds at which the latter facts obtain but not the former? It is an orthodoxy in recent literature about the nature of grounding, and in first-order philosophical disputes about what grounds what, that the answer is no. I will argue that the correct answer is yes. I present two novel arguments against grounding necessitarianism, and show that grounding (...) contingentism is fully compatible with the various explanatory roles that grounding is widely thought to play. (shrink)

People’s beliefs about normality play an important role in many aspects of cognition and life (e.g., causal cognition, linguistic semantics, cooperative behavior). But how do people determine what sorts of things are normal in the first place? Past research has studied both people’s representations of statistical norms (e.g., the average) and their representations of prescriptive norms (e.g., the ideal). Four studies suggest that people’s notion of normality incorporates both of these types of norms. In particular, people’s representations of what is (...) normal were found to be influenced both by what they believed to be descriptively average and by what they believed to be prescriptively ideal. This is shown across three domains: people’s use of the word ‘‘normal” (Study 1), their use of gradable adjectives (Study 2), and their judgments of concept prototypicality (Study 3). A final study investigated the learning of normality for a novel category, showing that people actively combine statistical and prescriptive information they have learned into an undifferentiated notion of what is normal (Study 4). Taken together, these findings may help to explain how moral norms impact the acquisition of normality and, conversely, how normality impacts the acquisition of moral norms. (shrink)

It is widely held that counterfactuals, unlike attitude ascriptions, preserve the referential transparency of their constituents, i.e., that counterfactuals validate the substitution of identicals when their constituents do. The only putative counterexamples in the literature come from counterpossibles, i.e., counterfactuals with impossible antecedents. Advocates of counterpossibilism, i.e., the view that counterpossibles are not all vacuous, argue that counterpossibles can generate referential opacity. But in order to explain why most substitution inferences into counterfactuals seem valid, counterpossibilists also often maintain that counterfactuals (...) with possible antecedents are transparency‐preserving. I argue that if counterpossibles can generate opacity, then so can ordinary counterfactuals with possible antecedents. Utilizing an analogy between counterfactuals and attitude ascriptions, I provide a counterpossibilist‐friendly explanation for the apparent validity of substitution inferences into counterfactuals. I conclude by suggesting that the debate over counterpossibles is closely tied to questions concerning the extent to which counterfactuals are more like attitude ascriptions and epistemic operators than previously recognized. (shrink)

The objective of Working Group 4 of the COST Action NET4Age-Friendly is to examine existing policies, advocacy, and funding opportunities and to build up relations with policy makers and funding organisations. Also, to synthesize and improve existing knowledge and models to develop from effective business and evaluation models, as well as to guarantee quality and education, proper dissemination and ensure the future of the Action. The Working Group further aims to enable capacity building to improve interdisciplinary participation, to promote knowledge (...) exchange and to foster a cross-European interdisciplinary research capacity, to improve cooperation and co-creation with cross-sectors stakeholders and to introduce and educate students SHAFE implementation and sustainability. To enable the achievement of the objectives of Working Group 4, the Leader of the Working Group, the Chair and Vice-Chair, in close cooperation with the Science Communication Coordinator, developed a template to map the current state of SHAFE policies, funding opportunities and networking in the COST member countries of the Action. On invitation, the Working Group lead received contributions from 37 countries, in a total of 85 Action members. The contributions provide an overview of the diversity of SHAFE policies and opportunities in Europe and beyond. These were not edited or revised and are a result of the main areas of expertise and knowledge of the contributors; thus, gaps in areas or content are possible and these shall be further explored in the following works and reports of this WG. But this preliminary mapping is of huge importance to proceed with the WG activities. In the following chapters, an introduction on the need of SHAFE policies is presented, followed by a summary of the main approaches to be pursued for the next period of work. The deliverable finishes with the opportunities of capacity building, networking and funding that will be relevant to undertake within the frame of Working Group 4 and the total COST Action. The total of country contributions is presented in the annex of this deliverable. (shrink)

The recent literature abounds with accounts of the semantics and pragmatics of so-called predicates of personal taste, i.e. predicates whose application is, in some sense or other, a subjective matter. Relativism and contextualism are the major types of theories. One crucial difference between these theories concerns how we should assess previous taste claims. Relativism predicts that we should assess them in the light of the taste standard governing the context of assessment. Contextualism predicts that we should assess them in the (...) light of the taste standard governing the context of use. We show in a range of experiments that neither prediction is correct. People have no clear preferences either way and which taste standard they choose in evaluating a previous taste claim crucially depends on whether they start out with a favorable attitude towards the object in question and then come to have an unfavorable attitude or vice versa. We suggest an account of the data in terms of what we call hybrid relativism. (shrink)

A supplemental document for "Metalinguistic Gradability".