Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)
The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (shrink)
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)
As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s motivation, (...) content, structure, adoption, and governance approach. (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)
A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing (...) a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. (shrink)
Law and History contains a broad range of essays by prominent legal historians, which explore the ways in which history has been used by lawyers. Largely theoretical in focus, the volume covers a broad range of issues, including discussions of norms in medieval England, the works of Montesquieu, Maine, and Weber, and of the nature of legal argument in nineteenth-century England, and in twentieth- century war crimes trials.Readership: Scholars of law and history, social historians, legal historians.
Within educational philosophy and theory, there has been an international re-turn to envision study as an alternative formation to disrupt the defining learning logic. As an enrichment, this paper articulates “Daoist onto-un-learning” as an Eastern form of study, drawing upon Roger Ames’s interpretation of the ancient Chinese correlative cosmology and relational personhood thinking. This articulation is to dialogue with the conceptualizations of study shared by Giorgio Agamben, Derek Ford, and Tyson Lewis, and unfolds in three steps. First, I examine (...) how their conceptualizations of study constrain the studier-doing-study logic as a commonsensical expression of “foundational individualism” and anthropocentric disordering. Second, re-invoking the ancient Chinese wisdom, I envision “Daoist onto-un-learning” as a non-individualistic and non-anthropocentric form of study, re-configuring study and learning no longer as two disparate, if not necessarily oppositional, formations but into a Daoist bipolar yin-yang movement. Finally, I story-tell my doctoral research experience as a Daoist onto-un-learning journey, a spiralling learning-study movement, to unpack the ways it suspends and overturns the modern-Western trap/trope of anthropocentric-foundational individualism. In so doing, this paper further internationalizes and supplements the current study scholarship in relation to learning in a way so-far hardly explored yet cross-culturally provocative. (shrink)
This paper provides an analysis of the educational use of the Internet and of digital technologies that is neither pessimistic nor optimistic, that is neither critical nor post-critical. Turning to Italian philosopher Giorgio Agamben’s comments on studying and its relationship to the technology of the blank writing tablet, the authors argue that digital devises are a radical transformation in our relationship to the technologies of reading and writing. Traditionally, the scholar was able to experience his or her potentiality to communicate (...) through writing via the blankness of the writing tablet. Yet, according to Agamben, such blankness has become inaccessible in the digital age, where the screen is always full of content. Here the authors argue that Agamben is correct in his diagnosis, yet his own theory of communicability offers up a way to redeem the educational use of digital devices. It is precisely the overflowing saturation of communications on the Internet which produces a new kind of blankness. It is this blankness which should thus become the focus of a studious form of media literacy—one that is not critical or post-critical so much as pre-critical. (shrink)
In this paper, we pose a speculative encounter between Heidegger and the Chinese Song Dynasty landscape painter Xia Gui. Our intention is to reassess Heidegger’s theory of the fourfold. By placing the concept in a cross-cultural context, we argue that Heidegger was essentially correct in that the world is structured as a fold between interrelated elements. At the same time, we challenge the quantity and quality of the folded elements. If one turns to the work of Xia Gui in conjunction (...) with relevant Daoist texts, what one finds is a threefold structure to the world, composed of earth, sky, and mortals without Heidegger’s emphasis on divinities. In conclusion, we suggest that studying the folding structure of the world ought to be done through cultural comparisons of philosophical and aesthetic traditions in order to understand the potentiality for worldhood as an xfold. (shrink)
Following Kenya’s independence in 1963, scientists converged on an ecologically sensitive area in southern Kenya on the northern slope of Mt. Kilimanjaro called Amboseli. This region is the homeland of the Ilkisongo Maasai who grazed this ecosystem along with the wildlife of interest to the scientists. Biologists saw opportunities to study this complex community, an environment rich in biological diversity. The Amboseli landscape proved to be fertile ground for testing new methods and lines of inquiry in the biological sciences that (...) were generalizable and important for shaping natural resource management policies in Kenya. However, the local community was in the midst of its own transformation from a primarily transhumant lifestyle to a largely sedentary one, a complex political situation between local and national authorities, and the introduction of a newly educated generation. This article examines the intersection of African history and field science through the post-colonial Africanization of Kenyan politics, the broadening of scientific practices in Amboseli in previously Western-occupied spaces to include Kenyan participants, and an increasing awareness of the role of local African contexts in the results, methods, and implications of biological research. “Africanization” as an idea in the history of science is multifaceted encompassing not just Africans in the scientific process, but it needs an examination of the larger political and social context on both a local and national level. (shrink)
In this article, we explore the possibilities that works of art might possess for looking in original and unforeseen ways into something that, at first sight, has little to do with arts and artistic practice. To be more precise, we present here three artistic representations, taken from various times and style periods, that depict a well-known figure in art history: angels. A detailed description and analysis of these images give us the opportunity to figure out something about another figure, which (...) is fascinating to us as philosophers of education: the teacher. Our basic intuition is that the way in which three important artists—Albrecht Dürer, William Hogarth, and Paul Klee—have tried to capture and trace out... (shrink)
This study compares the relationship between the moral reasoning modes and leadership orientation of males versus females, and managers versus engineers/scientists. A questionnaire developed by Worthley (1987) was used to measure the degree of each participant's respective independence and justice, and relationships and caring moral reasoning modes. Leadership orientation values and attitudes were measured using the Fiedler and Chemers (1984) Least Preferred Coworker Scale.The results suggest that, although males differ from female in their dominant moral reasoning modes, managers are not (...) distinguishable from the engineers/scientists they manage in terms of their moral reasoning mode or Least Preferred Coworker score. (shrink)
This selection of articles by Lewis E. Hahn addresses the philosophical school of contextualism and four contemporary American philosophers: John Dewey, Henry Nelson Wieman, Stephen C. Pepper, and Brand Blanshard. Stressing the relatively recent contextualistic worldview, which he considers one of the best world hypotheses, Hahn seeks to achieve a broad perspective within which all things may be given their due place. After providing a brief outline, Hahn explains contextualism in relation to other philosophies. In his opening chapter, as (...) in later chapters, he expresses contextualism as a form of pragmatic naturalism. In spite of Hahn’s high regard for contextualism, however, he does not think it would be good if we were limited to a single worldview. “The more different views we have and the more different sources of possible light we have, the better our chances that some of these cosmic maps will shed light on our world and our place in it.”. (shrink)
The editor's introduction discusses Clarence I. Lewis's conceptual pragmatism when compared with post-empiricist epistemology and argues that several Cartesian assumptions play a major role in the work, not unlike those of Logical Positivism. The suggestion is made that the Cartesian legacy still hidden in Logical Positivism turns out to be a rather heavy ballast for Lewis’s project of restructuring epistemology in a pragmatist key. More in detail, the sore point is the nature of inter-subjectivity. For Lewis, no (...) less than for the Logical Positivists at the time of the Protocols Controversy and Husserl in the Cartesian Meditations, this is a problem without a solution. The reason is that all these philosophers are apparently unable to realize that the existence of a plurality of knowing subjects cannot be treated at once both as a speculative problem and a methodological one. Lewis, thanks to his pragmatist approach both comes closer to the right answer and offers an even more naïve unsatisfactory solution to the pseudo-problem under discussion. The fact that he has clear in mind that inter-subjectivity means not only a plurality of linguistic utterances but also a co-existence of different kinds of practical behaviour. Eventually, the very idea of mind, the key-idea in the book, suffers from the above mentioned tension. In fact, if inter-subjective communication and action is considered at a methodological level, the very idea of mind would not need an analysis, and no kind of ‘reflexive’ analysis. Methodology might be limited to a ‘naïve’ level where the existence of the world and a plurality of subjects be taken as a bedrock of uncritically accepted evidence. Philosophical reflection on ultimate evidence, instead, would take a different approach, maybe the one Wittgenstein was putting into practice in the same years when Mind and the world order was written, namely it would be bound to question the very meaning of the idea of ‘mind’ as an undue fiction – the same carried out by Descartes – when he assumed the Cogito to be at once a body of self-evident truths and a thing or substance, the familiar Platonic idea of psyche or soul. (shrink)
Walter Benjamin's Antifascist Education is the first comprehensive analysis of educational themes across the entirety of the critical theorist's diverse writings. Starting with Benjamin's early reflections on teaching and learning, Tyson E. Lewis argues that the aesthetic and cultural forms to which Benjamin so often turned-namely, radio broadcasts, children's theatrical productions, collections, cityscapes, public cinemas, and word games-swell with educational potentialities. What emerges from Lewis's reading is a constellational curriculum composed of minor practices such as poor teaching, absentminded (...) learning, and nondurational studying. This curriculum carries political significance, offering an antidote to past and present forms of fascist manipulation, hardness, and coldness. Walter Benjamin's Antifascist Education is a testimony to Benjamin's belief that "everyone is an educator and everyone needs to be educated and everything is education.". (shrink)
D. Compaeetti, Leggi antiche delta città di Gortyna, Firenze, 1885 F. Bücheler and E. Zitelmann, Rheinisches Museum N. F. Bd. 40 J. and T. Baunack, Die Inschrift von Gortyn, Stuttgart, 1886H. Lewy, Stadtrecht von Gortyn, Berlin, 1885Museo Italiano di Antickità classiche, edited by D. Comparetti, Florence, 1885 sqq. Vols. i, ii.
The strong weak truth table (sw) reducibility was suggested by Downey, Hirschfeldt, and LaForte as a measure of relative randomness, alternative to the Solovay reducibility. It also occurs naturally in proofs in classical computability theory as well as in the recent work of Soare, Nabutovsky, and Weinberger on applications of computability to differential geometry. We study the sw-degrees of c.e. reals and construct a c.e. real which has no random c.e. real (i.e., Ω number) sw-above it.