The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

The global pesticide complex has transformed over the past two decades, but social science research has not kept pace. The rise of an enormous generics sector, shifts in geographies of pesticide production, and dynamics of agrarian change have led to more pesticide use, expanding to farm systems that hitherto used few such inputs. Declining effectiveness due to pesticide resistance and anemic institutional support for non-chemical alternatives also have driven intensification in conventional systems. As an inter-disciplinary network of pesticide scholars, we (...) seek to renew the social science research agenda on pesticides to better understand this suite of contemporary changes. To identify research priorities, challenges, and opportunities, we develop the pesticide complex as a heuristic device to highlight the reciprocal and iterative interactions among agricultural practice, the agrochemical industry, civil society-shaped regulatory actions, and contested knowledge of toxicity. Ultimately, collaborations among social scientists and across the social and biophysical sciences can illuminate recent transformations and their uneven socioecological effects. A reinvigorated critical scholarship that embraces the multifaceted nature of pesticides can identify the social and ecological constraints that drive pesticide use and support alternatives to chemically driven industrial agriculture. (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)

Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need (...) to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. (shrink)

Formalised knowledge systems, including universities and research institutes, are important for contemporary societies. They are, however, also arguably failing humanity when their impact is measured against the level of progress being made in stimulating the societal changes needed to address challenges like climate change. In this research we used a novel futures-oriented and participatory approach that asked what future envisioned knowledge systems might need to look like and how we might get there. Findings suggest that envisioned future systems will need (...) to be much more collaborative, open, diverse, egalitarian, and able to work with values and systemic issues. They will also need to go beyond producing knowledge about our world to generating wisdom about how to act within it. To get to envisioned systems we will need to rapidly scale methodological innovations, connect innovators, and creatively accelerate learning about working with intractable challenges. We will also need to create new funding schemes, a global knowledge commons, and challenge deeply held assumptions. To genuinely be a creative force in supporting longevity of human and non-human life on our planet, the shift in knowledge systems will probably need to be at the scale of the enlightenment and speed of the scientific and technological revolution accompanying the second World War. This will require bold and strategic action from governments, scientists, civic society and sustained transformational intent. (shrink)

Barry Allen, in his 2005 Knowledge and Civilization and his 2008 Artifice and Design, argues in favor of an epistemic system that is both praxical and performative; knowledge, rather than being expressed propositionally, is a kind of performance that is expressed in artifacts of all kinds, of which propositions are but an example. However, although he makes a compelling case, it is rather less clear the extent to which we are able to make judgments about the world beneath the (...) artifacts. That is to say: it seems clear that we need to provide some account of how the world is, if only so that we have some kind of coherent characterization of what it is exactly that an artifact captures. Accordingly, if we are to buy into Allen’s model, what can we subsequently say about Allen’s metaphysics? This paper is an attempt to tease out some of these concerns. (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 merit system is based on a person’s ability to achieve. The concept of merit hence rejects a process that awards any particular entitlement explicitly based on disability. Brian Barry says that under the merit principle, people can compete for positions or advantage. This paper argues that the idea of merit, as explained by Barry, is unjust. Iris Marion Young points out that a person with cognitive disability faces a different situation compared to other people. Under normal circumstances, (...) persons can have skills that enable them to do things with ease, something that is not readily available to individuals with autism or Asperger’s syndrome. The problem is also exacerbated by policies that do not recognize the diverse needs of individuals with impairment. In this regard, practical ethics demands that a law or national policy must ensure a level playing field for everyone. (shrink)

For several decades, renewed interest in the connection between perception and knowledge has sustained a robust debate over external world skepticism. Recently, however, a growing consensus claims the skeptical challenge has been substantially met, and that realism in some robust form has emerged a clear victor. I invite us to rethink this consensus in a two-part response. The first forges a temporary alliance with skepticism against prominent forms of contemporary realism. That these fail to rebuff ews bolsters Barry Stroud’s (...) call for a new paradigm of objectivity. In the second part I sketch such a paradigm based upon a transactional interpretation of John Dewey’s pragmatism, and indicate its resilience to skeptical attacks. (shrink)

This dissertation examines the relationship that exists between two distinct and seemingly incompatible bodies of scholarship within the field of contemporary philosophy of technology. The first, as argued by postmodern pragmatist Barry Allen, posits that our tools and what we make with them are epistemically important; disputing the idea that knowledge is strictly sentential or propositional, he claims instead that knowledge is the product of a performance that is both superlative and artefactual, rendering technology importantly world-constituting. The second, as (...) argued by Heidegger and his inheritors, is that technology is ontologically problematic; rather than technology being evidence of performative knowledge, it is instead existentially threatening by virtue of the fact that it changes the tenor of our relationship with the world-as-given. Despite the fact that these claims seem prima facie incompatible, I argue that they may be successfully reconciled by introducing a third body of scholarship: the philosophy of photography. For it is the case, I argue, that although we, qua human beings, occupy lifeworlds that are necessarily constituted by technology, technology also induces a kind of phenomenological scepticism: a concern that mediated action precludes us from the possibility of authentic experience. Arguing in favour of the sentiment that photographs serve as a kind of phenomenal anchor—a kind of machine for living—I claim that photographic images provide a panacea to this existential concern: despite being epistemically problematic, it is this selfsame epistemic “specialness” of photographs that forces us to phenomenologically recommit, if only temporarily, to the world in a serious way. Consequently, it is my belief that an analysis of our artefacts and the way they function is fundamentally incomplete without an analysis of the epistemic and ontological problems introduced of the photographic image; as I will demonstrate, the photographic image casts an extremely long shadow over the philosophy of technology. (shrink)

This article looks at Colossians 2-3:17 and John 17:13-26 as the base texts to see the commonalities between Johannine and Pauline conceptions of Theosis. First, the article looks at indwelling and participation as the methods of Theosis in the two traditions. Second, the role of mimesis is seen to be integral in these texts' concepts of Theosis. Third, the article looks at hope and glory that believers have and look forward to as indicative of their deification. The study begins by (...) defining the term Theosis and its cognate terms - deification and divinisation - properly, within an Orthodox Christian context. CONTRIBUTION: The goal is to see and detail the concept of Theosis in Pauline and Johannine literature, looking at Colossians 2-3:17 and John 17:13-26 specifically. As such, the present study will broaden the discussion the doctrine of Theosis as it appears in the Christian scriptures. (shrink)

The inclusion of engineering standards in US science education standards is potentially important because of how limited engineering education for K-12 learners is, despite the ubiquity of engineering in students’ lives. However, the majority of learners experience science education throughout their compulsory schooling. If improved engineering literacy is to be achieved, then its inclusion in science curricula is perhaps the most efficient means. One significant challenge that arises, however, is in the framing of engineering relative to science by both teachers (...) and curriculum. Science and engineering are both distinct and interdependent. The nature of the contributions of science and engineering to one another has been an area of some examination in philosophy of technology and engineering, but little framing of this relationship has been conducted with K-12 science and engineering education contexts in mind. Nature of science is a critical layer of scientific understanding that has been used to explicitly support literacy in K-16 science classrooms for decades. However, engineering cannot be authentically and appropriately supported by NOS framing. There is an immediate need for discourse on the nature of engineering knowledge but not in isolation of NOS. Given the increasing inclusion of engineering in science classrooms, relationships between NOS and NOEK are in need of explication and argument. Our purpose is to promote a discussion about NOS, engineering, and the relationship between them without misrepresenting engineering as a subdomain of science or as an oversimplification of itself. (shrink)

Modern Christians often polarize the otherwise inseparable realities of academic reading and personal reading of Scripture. While generally not declared outright, many Christians consider the two methods discontinuous. This article deems this bifurcation unnecessary and dangerous to the spiritual formation of individuals and the spiritual health of the church. It examines Bonaventure's insightful use of the quadriga in order to contribute to today's discussion of spiritual reading of Scripture. The article shall argue that Bonaventure's quadrigal method ought to be retrieved (...) today for the spiritual health of scholarship and the church. This thesis will be attained organically. It will first survey his proposed method of interpretation in his Breviloquium and Commentary on the Gospel of Luke; then, it will appeal to scriptural and pastoral support to show that his method is a helpful route for retrieval. (shrink)

"Pace" michael devitt and other recent writers, this paper argues that realism essentially involves commitment to a substantial theory of truth. it also tries to chart the ways whereby the commitment arises.

In this paper we apply the popular Best System Account of laws to typical eternal worlds – both classical eternal worlds and eternal worlds of the kind posited by popular contemporary cosmological theories. We show that, according to the Best System Account, such worlds will have no laws that meaningfully constrain boundary conditions. It’s generally thought that lawful constraints on boundary conditions are required to avoid skeptical arguments. Thus the lack of such laws given the Best System Account may seem (...) like a severe problem for the view. We show, however, that at eternal worlds, lawful constraints on boundary conditions do little to help fend off skeptical worries. So with respect to handling these skeptical worries, the proponent of the Best System Account is no worse off than their competitors. (shrink)

There are two intriguing paradoxes in molecular biology-the inconsistent relationship between organismal complexity and (1) cellular DNA content and (2) the number of protein-coding genes-referred to as the C-value and G-value paradoxes, respectively. The C-value paradox may be largely explained by varying ploidy. The G-value paradox is more problematic, as the extent of protein coding sequence remains relatively static over a wide range of developmental complexity. We show by analysis of sequenced genomes that the relative amount of non-protein-coding sequence increases (...) consistently with complexity. We also show that the distribution of introns in complex organisms is non-random. Genes composed of large amounts of intronic sequence are significantly overrepresented amongst genes that are highly expressed in the nervous system, and amongst genes downregulated in embryonic stem cells and cancers. We suggest that the informational paradox in complex organisms may be explained by the expansion of cis-acting regulatory elements and genes specifying trans-acting non-protein-coding RNAs. (shrink)

The beatific vision is a subject of considerable importance both in the Christian Scriptures and in the history of Christian dogmatics. In it, humans experience and see the perfect immaterial God, which represents the final end for the saints. However, this doctrine has received less attention in the contemporary theological literature, arguably, due in part to the growing trend toward materialism and the sole emphasis on bodily resurrection in Reformed eschatology. As a piece of retrieval by drawing from the Scriptures, (...) Medieval Christianity, and Reformed Christianity, we motivate a case for the Reformed emphasis on the immaterial and intellectual aspects of human personal eschatology and offer some constructive thoughts on how to link it to the contemporary emphasis of the body. We draw a link between the soul and the body in the vision with the help of Christology as reflected in the theology of John Calvin, and, to a greater extent, the theology of both John Owen and Jonathan Edwards. (shrink)

In this paper I argue that the propositional model of Divine revelation deserves renewed attention due to both criticisms stemming from misunderstanding and recent arguments in favor of the propositional model. I begin by clarifying what I mean by the propositional model of Divine revelation and by pointing out misunderstandings of the implications of this model. Subsequently, I offer a few arguments in favor of the propositional model of Divine revelation based on three assumptions that I take to be basic (...) elements of Christianity. Finally, I explain why I think the propositional model is doctrinally significant for the Christian Faith. (shrink)

What may seem astonishing is the near dismissal of the beatific vision doctrine in the last 50+ years of biblical and theological scholarship in contrast to the emphasis given to it throughout church history. The state of theological scholarship is changing. In what follows, we set forth a short survey of a theology of the beatific vision, while also introducing the rest of the volume on the beatific vision and theosis, of which we take to have an intimate and overlapping (...) relationship. The editorial article has four parts: it begins by (1) introducing some of the relevant biblical material on the vision, proceeding to (2) develop a theological interpretation of those passages, and then (3) offer a short historical survey of the doctrine, focusing on the relevant medieval and Reformed developments. It finally (4) introduces the articles of the issue. (shrink)

Le présent article est une tentative nouvelle d’articuler le rôle d’une théorie des vérifacteurs. Nous soutenons que la théorie de la vérifaction constitue une pierre angulaire dans une bonne méthodologie en métaphysique, mais que l’amalgame entre la théorie de la vérifaction et la théorie de la vérité a été responsable de certains excès associés aux approches vérifactionnistes dans la littérature récente. Nous montrons que la théorie de la vérifaction conserve son attrait comme instrument d’investigation métaphysique, et ce, malgré notre accord (...) avec les doctrines déflationnistes telles que celles défendues par Ayer, Quine, Field et Horwich (ou, du moins, malgré notre neutralité à leur égard). Nous soutenons en outre que les intuitions sous-jacentes à la théorie de la vérifaction s’éclairent quand nous les dissocions d’une théorie de la vérité et, par-dessus tout, de la tentative de fournir une définition de la vérité. (shrink)

Henri Bergson (1859-1941) was once the most famous philosopher in the world, but his reputation waned in the latter half of the 20th century. Barry Allen here makes the case for Bergson as a great philosopher, one whose thought has much to contribute to contemporary philosophical questions. Living in Time presents chapters on each of Bergson's four major works, explaining his theories of time, perception, memory, and panpsychic consciousness, his innovative concept of virtual existence, his objection to Darwin, his (...) controversy with Einstein, his philosophy of creative evolution, and his social philosophy of closed and open society. In particular Allen focusses on Bergson's powerful ideas on time. Classical arguments for determinism fallaciously apply spatial concepts to consciousness; once we take time seriously, which means acknowledging its reality as duration and its difference from space, Bergson showed that the arguments for determinism become insupportable. Bergson's ideas on time and evolution offer a comparison with Nietzsche, which Allen develops, exposing both philosophical concurrence and systematic difference. The book's conclusion discusses the question of Bergson and naturalism and summarizes the ontology of the virtual that emerges as a core part of Bergson's thought. (shrink)

In recent years, there has been a distinct shift in the relationship between science and society. We have moved away from the classic unidirectional “deficit” model (Simis et al. 2016) focused on t...

We use normative reasons in a bewildering variety of different ways. And yet, as many recent theorists have shown, one can discern systematic distinctions underlying this complexity. This paper is a contribution to this project of constructive normative metaphysics. We aim to bring a black sheep back into the flock: the balancing model of weighing reasons. This model is threatened by a variety of cases in which distinct reasons overlap, in the sense that they do not contribute separate weight for (...) or against an option. Our response is to distinguish between derivative reasons and load-bearing reasons, only the latter of which contribute non-overlapping weight to an option. This distinction is close at hand for analyses of reasons in terms of the promotion of significant outcomes. But we also develop an account of this distinction for fundamentalist theories of normative reasons. (shrink)

Today the study of African aesthetics constitutes one of the most exciting and dynamic subdisciplines in African and intercultural studies. Yet, because it is also a discipline in which African meanings must of necessity be translated into and expressed by one of the few ‘world’ languages (English, French), it is in the interests of all concerned—Africans and non-Africans—to work together to ensure that the highest possible professional standards are maintained. For it is intercultural dialogue based upon reciprocal language fluency that (...) will best enable researchers to see where Western and African values and beliefs overlap and where they diverge. (shrink)

The debate over persistence is often cast as a disagreement between two rival theories—the perdurantist theory that objects persist through time by having different temporal parts at different times, and the endurantist theory that objects persist through time by being wholly present at different times. This way of framing the debate over persistence involves both an important insight and an important error. Unfortunately, the error is often embraced and the insight is often ignored. This paper aims to correct both of (...) these mistakes, and thus clarify the debate over persistence. (shrink)

The idea that research should become more interdisciplinary has become commonplace. According to influential commentators, the unprecedented complexity of problems such as climate change or the social implications of biomedicine demand interdisciplinary efforts integrating both the social and natural sciences. In this context, the question of whether a given knowledge practice is too disciplinary, or interdisciplinary, or not disciplinary enough has become an issue for governments, research policy makers and funding agencies. Interdisciplinarity, in short, has emerged as a key political (...) preoccupation; yet the term tends to obscure as much as illuminate the diverse practices gathered under its rubric. This volume offers a new approach to theorising interdisciplinarity, showing how the boundaries between the social and natural sciences are being reconfigured. It examines the current preoccupation with interdisciplinarity, notably the ascendance of a particular discourse in which it is associated with a transformation in the relations between science, technology and society. Contributors address attempts to promote collaboration between, on the one hand, the natural sciences and engineering and, on the other, the social sciences, arts and humanities. From ethnography in the IT industry to science and technology studies, environmental science to medical humanities, cybernetics to art-science, the collection interrogates how interdisciplinarity has come to be seen as a solution not only to enhancing relations between science and society, but the pursuit of accountability and the need to foster innovation. Interdisciplinarity is essential reading for scholars, students and policy makers across the social sciences, arts and humanities, including anthropology, geography, sociology, science and technology studies and cultural studies, as well as all those engaged in interdisciplinary research. It will have particular relevance for those concerned with the knowledge economy, science policy, environmental politics, applied anthropology, ELSI research, medical humanities, and art-science. (shrink)

A collection of newly commissioned papers on themes from David Albert's Time and Chance (HUP, 2000), with replies by Albert. Introduction [Barry Loewer, Brad Weslake, and Eric Winsberg] I. Overview of Time and Chance 1. The Mentaculus: A Probability Map of the Universe [Barry Loewer] II. Philosophical Foundations 2. The Metaphysical Foundations of Statistical Mechanics: On the Status of PROB and PH [Eric Winsberg] 3. The Logic of the Past Hypothesis [David Wallace] 4. In What Sense Is the (...) Early Universe Fine-Tuned? [Sean M. Carroll] 5. The Meta-Reversibility Objection [Christopher J. G. Meacham] 6. Typicality versus Humean Probabilities as the Foundation of Statistical Mechanics [Dustin Lazarovici] 7. The Past Hypothesis and the Nature of Physical Laws [Eddy Keming Chen] 8. On the Albertian Demon [Tim Maudlin] III. Underwriting the Asymmetries of Knowledge and Intervention 9. Reading the Past in the Present [Nick Huggett] 10. Causes, Randomness, and the Past Hypothesis [Mathias Frisch] 11. Time, Flies, and Why We Can’t Control the Past [Alison Fernandes] 12. The Concept of Intervention in Time and Chance [Sidney Felder] Conclusion [David Albert]. (shrink)

In this original and rewarding combination of intellectual and political history, Ryan Balot offers a thorough historical and sociological interpretation of classical Athens centered on the notion of greed. Integrating ancient philosophy, poetry, and history, and drawing on modern political thought, the author demonstrates that the Athenian discourse on greed was an essential component of Greek social development and political history. Over time, the Athenians developed sophisticated psychological and political accounts of acquisitiveness and a correspondingly rich vocabulary to describe (...) and condemn it. Greed figures repeatedly as an object of criticism in authors as diverse as Solon, Thucydides, and Plato--all of whom addressed the social disruptions caused by it, as well as the inadequacy of lives focused on it. Because of its ethical significance, greed surfaced frequently in theoretical debates about democracy and oligarchy. Ultimately, critiques of greed--particularly the charge that it is unjust--were built into the robust accounts of justice formulated by many philosophers, including Plato and Aristotle. Such critiques of greed both reflected and were inextricably knitted into economic history and political events, including the coups of 411 and 404 B.C. Balot contrasts ancient Greek thought on distributive justice with later Western traditions, with implications for political and economic history well beyond the classical period. Because the belief that greed is good holds a dominant position in modern justifications of capitalism, this study provides a deep historical context within which such justifications can be reexamined and, perhaps, found wanting. (shrink)