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 Common Anatomy Reference Ontology (CARO) is being developed to facilitate interoperability between existing anatomy ontologies for different species, and will provide a template for building new anatomy ontologies. CARO has a structural axis of classification based on the top-level nodes of the Foundational Model of Anatomy. CARO will complement the developmental process sub-ontology of the GO Biological Process ontology, using it to ensure the coherent treatment of developmental stages, and to provide a common framework for the model organism communities (...) to classify developmental structures. Definitions for the types and relationships are being generated by a consortium of investigators from diverse backgrounds to ensure applicability to all organisms. CARO will support the coordination of cross-species ontologies at all levels of anatomical granularity by cross-referencing types within the cell type ontology (CL) and the Gene Ontology (GO) Cellular Component ontology. A complete cross-species CARO could be utilized in other ontologies for cross-product generation. (shrink)

An underexamined insight of W. E. B. Du Bois’s John Brown is that John Brown worked for much of his life to cultivate democratic relationships with the Black Americans with and for whom he worked. Brown did so through practicing deference and deliberation, and by seeking authorization. However, Brown’s commitment to these practices faltered at a crucial moment in decision making: when he raided Harpers Ferry absent widespread support. Examining this aspect of John Brown brings into relief an overlooked tragic (...) choice Brown made: To act in accordance with his own substantive vision of what justice required, Brown eschewed democratic ideals and practices that grounded the distinctive relations of equality he had cultivated with the Black communities with and for whom he worked. (shrink)

Informal political representation can be a political lifeline, particularly for oppressed and marginalized groups. Such representation can give these groups some say, however mediate, partial, and imperfect, in how things go for them. Coeval with the political goods such representation offers these groups are its particular dangers to them. Mindful of these dangers, skeptics challenge the practice for being, inter alia, unaccountable, unauthorized, inegalitarian, and oppressive. These challenges provide strong pro tanto reasons to think the practice morally impermissible. This paper (...) considers the question: On what conditions is the informal political representation of oppressed and marginalized groups permissible? By responding to skeptics’ challenges, I develop a systematic account of moral constraints that, if adopted, would make such representation permissible. The account that emerges shows that informal political representatives (IPRs) must aim to fulfill two sets of sometimes conflicting duties to the represented: democracy within duties, which concern how the representative treats and relates to the represented, and justice without duties, which concern how the representative’s actions advance the aims of the representation. (shrink)

Centred on 'Foams', the third volume of his Spheres trilogy, this article questions the privilege granted by Peter Sloterdijk to motifs of inclusion and exclusion, contending that whilst his prioritization of dwelling as a central aspect of human existence provides a promising counterpoint to the dislocative and isolative effects of post-industrial capitalism, it is compromised by its dependence upon an anti-cosmopolitan outlook that views cultural distantiation as a natural and preferable state of human affairs, and valorizes a purported ontological security (...) attained through defensive postures with respect to perceived foreigners or externalities. Sloterdijk’s conceptualization of culture as a kind of immune system, it is argued, although posited as a rebuke to models of essentialism and ethno-nationalism, provides ontological support to the xenophobic critiques of immigration that are today finding increasing currency. (shrink)

Informal political representation—the phenomenon of speaking or acting on behalf of others although one has not been elected or selected to do so by means of a systematized election or selection procedure—plays a crucial role in advancing the interests of groups. Sometimes, those who emerge as informal political representatives (IPRs) do so willingly (voluntary representatives). But, often, people end up being IPRs, either in their private lives or in more public political forums, over their own protests (unwilling representatives) or even (...) without their knowledge (unwitting representatives)—that is, they are conscripted. None of the few theories of informal political representation extant accommodate conscripted IPRs. The account detailed here introduces the phenomenon of conscripted informal political representation and explains its place in a complete theory of informal political representation. Conscripted IPRs can, like their voluntary counterparts, come to have significant power to influence how various audiences regard those for whom the conscripted IPRs speak or act. Upon attaining such power to influence, conscripted IPRs, like their voluntary counterparts, come to have pro tanto duties to those they represent—duties that arise despite IPRs’ unwittingness or unwillingness. Understanding the phenomenon of conscripted informal political representation allows us to surface essential normative questions about informal political representation that are otherwise occluded. (shrink)

It is common for social theorists to utilize the metaphors of ‘flow’, ‘fluidity’, and ‘liquidity’ in order to substantiate the ways in which speed and mobility form the basis for a new kind of information or network society. Yet rarely have these concepts been sufficiently theorized in order to establish their relevance or appropriateness. This article contends that the notion of flow as utilized in social theory is profoundly metaphysical in nature, and needs to be judged as such. Beginning with (...) a discussion of the accelerating timescape that characterizes the network society, it will then move on to examine three main issues with this ‘metaphysics of flux’. First, that the concept of flows unjustly privileges the process of becoming and, as a result, is unable to account for the materiality, substantiality, and agency of the objects being mobilized, and the contingency of their mediation. Second, that it posits the accelerating tendencies of capital as an ontological inevitability, thus discounting resistance to such forces. Finally, that it ignores the human faculty for reason and speculative thought in developing alternative means of political praxis. The solution, it will be argued, is not to abandon metaphysical accounts of the network society, but rather to challenge those accounts that, in exhibiting a crude empiricism, work to justify the status quo. (shrink)

Journal of Political Philosophy, Volume 29, Issue 4, Page 429-455, December 2021.

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

This article examines the ontology and politics of Peter Sloterdijk's Spheres trilogy, focusing in particular upon the notion of microspherical enclosure explicated in the first volume of this series. Noting Sloterdijk's unusual alignment of his philosophy with media theory, three main contentions are put forward. Firstly, that Sloterdijk's reconfiguration of Heidegger's fundamental ontology represents a largely unacknowledged renunciation of the primacy of Being-towards-death in the authentic existence of Dasein, foregrounding instead an originary co-belonging between mother and child. Secondly, that Sloterdijk (...) borrows from media theory a concern regarding the facticity of all communication, grounding philosophical discourse in the determinate locality of its origin, but does so while exalting a pre-natal communicative immediacy that would seem to disparage the everydayness of Dasein. Finally, that Sloterdijk's oft-justified scepticism regarding globalization often retreats into an anti-cosmopolitanism that, in its nostalgia for the comfort, security and immediacy of the matrixial co-belonging, evinces a covert but potentially noxious politics of exclusion. (shrink)

This article considers Friedrich Kittler’s deterministic media theory as both an appropriation and mutation of Michel Foucault’s archaeological method. Focusing on these two thinkers’ similar but divergent conceptions of the “death of man,” it will be argued that Kittler’s approach attempts to expunge archaeology of its last traces of Kantian transcendentalism by locating the causal agents of epistemic change within the domain of empirical experience, but in doing so, actually amplifies the anthropological vestiges that Foucault hoped to eradicate. The result (...) is an alluring but dogmatically positivist theory of mediatic causality that, in spite of its best efforts, can only reify, rather than dispel, the image of “so-called man.”. (shrink)

Focusing upon the five books of his early Hermes series, this article argues that Michel Serres furnishes an accomplished, unconventional philosophical account of communication and mediation-a structuralist epistemology designed to comprehend the sciences in their complexity and plurality-that, even decades after its first publication, has significant value for media theory. Two key themes within this pentalogy are highlighted: firstly, its emphasis upon motifs of communication, transport, and circulation, attempting to grasp the scientific field in topological terms, as a kind of (...) networked encyclopaedia; and secondly, its attempt to account for the intricate relationship between the formal and the empirical in all theorization. (shrink)

Plato’s Phaedrus, perhaps his most enigmatic and structurally convoluted dialogue, could easily be said to inaugurate a pointed critique of mass media that persists to the present day. Indeed, in certain corners of media theory, the origin myth of writing furnished in the Phaedrus (in which the Egyptian god Theuth presents writing as a gift to King Thamus) has in turn come to serve as a kind of origin myth for media theory: a primaeval pharmacopoeia of media effects. And yet, (...) this is an origin myth that can only underwrite not only its own non-originarity and non-truth, insofar as its very status as a written text ensures that it will never meet the criteria that it itself establishes for a reasoned account of things (logos). It remains perpetually orphaned, unable to defend itself, irrevocably cut off from its ‘father’, the speaking subject, and thus from the vitality of living discourse. But this paradox, I argue, is not a failing of the dialogue, but is a device intended to encourage the reader’s active involvement in the text’s status as medium. The Phaedrus is not just diagnostic, but therapeutic. (shrink)

A moral requirement R1 is said to be lexically prior to a moral requirement R2 just in case we are morally obliged to uphold R1 at the expense of R2 – no matter how many times R2 must be violated thereby. While lexical priority is a feature of many ethical theories, and arguably a part of common sense morality, attempts to model it within the framework of decision theory have led to a series of problems – a fact which is (...) sometimes spun as a ‘decision theoretic critique’ of lexical priority. In this paper, I develop an enriched decision theoretic framework that is capable of modelling lexical priority while avoiding all extant problems. This will involve introducing several new ingredients into the standard decision theoretic framework, including multidimensional utilities, de minimis risks, and the means to represent two different conceptions of risk. (shrink)

Many healthcare practices expose people to risks of harmful outcomes. However, the major theories of moral philosophy struggle to assess whether, when and why it is ethically justifiable to expose individuals to risks, as opposed to actually harming them. Sven Ove Hansson has proposed an approach to the ethical assessment of risk imposition that encourages attention to factors including questions of justice in the distribution of advantage and risk, people’s acceptance or otherwise of risks, and the scope individuals have to (...) influence the practices that generate risk. This paper investigates the ethical justifiability of preventive healthcare practices that expose people to risks including overdiagnosis. We applied Hansson’s framework to three such practices: an ‘ideal’ breast screening service, a commercial personal genome testing service, and a guideline that lowers the diagnostic threshold for hypertension. The framework was challenging to apply, not least because healthcare has unclear boundaries and involves highly complex practices. Nonetheless, the framework encouraged attention to issues that would be widely recognised as morally pertinent. Our assessment supports the view that at least some preventive healthcare practices that impose risks including that of overdiagnosis are not ethically justifiable. Further work is however needed to develop and/or test refined assessment criteria and guidance for applying them. (shrink)

Definitions vary according to context of use and target audience. They must be made relevant for each context to fulfill their cognitive and linguistic goals. This involves adapting their logical structure, type of content, and form to each context of use. We examine from these perspectives the case of definitions in ontologies.

In this article, I introduce and examine the novel concept of bench representation. Jurists and scholars have extensively examined whether judges are or ought to be considered symbolic representatives of abstract concepts (for instance, the law, equality, or justice), representatives of society as a whole, or descriptive representatives of the social groups from which they hail. However, little attention has been paid to the question whether judges act as representatives for the parties before them through their everyday work on the (...) bench. This article examines that question. Bench representation occurs when a judge, through statements or actions undertaken during the performance of official duties, speaks or acts for a party to the proceeding before them. I argue that serving as a bench representative is a common and valuable feature of what it is to be a judge and, despite appearances, usually undermines neither impartiality nor fairness. (shrink)

The main point in this chapter isthat SDG 4 targets cannot be achieved without education justice, which entails that every child, young person and adult benefit from quality education and lifelong learning. There is no justification for the injustices arising from poor-quality education and exclusion as they exist today. Accordingly, tackling the problem of social, political and economic exclusion that emerges from the education sector, and the limitations they impose on the prospects of some individuals, must be prioritised to expedite (...) the realisation of SDG 4. That entails, among other things, ensuring inclusive and equitable quality education and promoting lifelong learning opportunities for all. Drawing a nexus between education justice in basic education and higher education, the chapter exposes the nature of the challenges that sustain the injustices of educational exclusion and poor-quality education. These include the knock-on effects that injustices in basic education have on higher education, especially for students from marginalised schools. Interventions that seek to advance education justice towards attaining SDG 4 are also discussed. (shrink)

In the literature on philosophical progress it is often assumed that agreement is a necessary condition for progress. This assumption is sensible only if agreement is a reliable sign of the truth, since agreement on false answers to philosophical questions would not constitute progress. This paper asks whether agreement among philosophers is (or would be) likely to be a reliable sign of truth. Insights from social choice theory are used to identify the conditions under which agreement among philosophers would be (...) a reliable indicator of the truth, and it is argued that we lack good reason to think that philosophical inquiry meets these conditions. The upshot is that philosophical agreement is epistemically uninformative: agreement on the answer to a philosophical question does not supply even a prima facie reason to think that the agreed-upon view is true. However, the epistemic uninformativeness of philosophical agreement is not an indictment of philosophy's progress, because philosophy is valuable independent of its ability to generate agreement on the correct answers to philosophical questions. (shrink)

The manufacturing industry is evolving rapidly, becoming more complex, more interconnected, and more geographically distributed. Competitive pressure and diversity of consumer demand are driving manufacturing companies to rely more and more on improved knowledge management practices. As a result, multiple software systems are being created to support the integration of data across the product life cycle. Unfortunately, these systems manifest a low degree of interoperability, and this creates problems, for instance when different enterprises or different branches of an enterprise interact. (...) Common ontologies (consensus-based controlled vocabularies) have proved themselves in various domains as a valuable tool for solving such problems. In this paper, we present a consensus-based Additive Manufacturing Ontology (AMO) and illustrate its application in promoting re-usability in the field of dentistry product manufacturing. (shrink)

A belief one has is safe if either (i) it could not easily be false or (ii) in any nearby world in which it is false, it is not formed using the method one uses to form one’s actual belief. It seems our mathematical beliefs are safe if mathematical pluralism is true: if, loosely put, almost any consistent mathematical theory is true. It seems, after all, that in any nearby world where one’s mathematical beliefs differ from one’s actual beliefs, one (...) would believe some other true, consistent theory. Focusing on Justin Clarke-Doane’s recent discussion, I argue the thesis that mathematical beliefs are safe given pluralism faces some obstacles. I argue (i) is true of mathematical belief given pluralism only if we deny plausible claims about the interpretation of non-pluralists who many of us could easily be. Unless strong metasemantic theses are true, it is plausible many of us could easily deny or refuse to believe a consistent and true mathematical theory we actually believe. Since philosophical arguments and controversies permeate the methodology of foundational mathematics, I argue we cannot confidently distinguish the methods we use in mathematics between worlds, thus raising doubts about (ii). (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

A political philosopher dissects the duties and dilemmas of the unelected spokesperson, from Martin Luther King, Jr., to Greta Thunberg. -/- Political representation is typically assumed to be the purview of formal institutions and elected officials. But many of the people who represent us are not senators or city councilors—think of Martin Luther King, Jr., or Malala Yousafzai or even a neighbor who speaks up at a school board meeting. Informal political representatives are in fact ubiquitous, often powerful, and some (...) bear enormous responsibility. In Speaking for Others, political philosopher Wendy Salkin develops the first systematic conceptual and moral analysis of informal political representation. -/- Salkin argues that informal representation can be a political lifeline, particularly for oppressed and marginalized groups that are denied representation in formal political institutions. Yet informal political representatives exert outsized influence over the ways these groups’ interests are understood by the public, without the represented having much recourse to hold them accountable. And many informal political representatives are selected not by the groups they represent but by outsiders, sticking these groups with representatives they would not choose but cannot shake. The role of informal political representatives is therefore fraught with moral questions. What exactly are their duties and to whom are they owed? Should they be members of the groups they represent? When is informal representation permissible and when is it best avoided? -/- Informal political representation is taking place all around us. In fact, you yourself may be an informal political representative without knowing it. Speaking for Others explores the tensions central to this pervasive yet underexamined practice, bringing light to both its perils and its promise. (shrink)

In her recent paper ‘The Epistemology of Propaganda’ Rachel McKinnon discusses what she refers to as ‘TERF propaganda’. We take issue with three points in her paper. The first is her rejection of the claim that ‘TERF’ is a misogynistic slur. The second is the examples she presents as commitments of so-called ‘TERFs’, in order to establish that radical (and gender critical) feminists rely on a flawed ideology. The third is her claim that standpoint epistemology can be used to establish (...) that such feminists are wrong to worry about a threat of male violence in relation to trans women. In Section 1 we argue that ‘TERF’ is not a merely descriptive term; that to the extent that McKinnon offers considerations in support of the claim that ‘TERF’ is not a slur, these considerations fail; and that ‘TERF’ is a slur according to several prominent accounts in the contemporary literature. In Section 2, we argue that McKinnon misrepresents the position of gender critical feminists, and in doing so fails to establish the claim that the ideology behind these positions is flawed. In Section 3 we argue that McKinnon’s criticism of Stanley fails, and one implication of this is that those she characterizes as ‘positively privileged’ cannot rely on the standpoint-relative knowledge of those she characterizes as ‘negatively privileged’. We also emphasize in this section McKinnon’s failure to understand and account for multiple axes of oppression, of which the cis/trans axis is only one. (shrink)

Objective We reviewed human–robot interaction (HRI) participatory design (PD) research with older adults. The goal was to identify methods used, determine their value for design of robots with older adults, and provide guidance for best practices. Background Assistive robots may promote aging-in-place and quality of life for older adults. However, the robots must be designed to meet older adults’ specific needs and preferences. PD and other user-centered methods may be used to engage older adults in the robot development process to (...) accommodate their needs and preferences and to assure usability of emergent assistive robots. Method This targeted review of HRI PD studies with older adults draws on a detailed review of 26 articles. Our assessment focused on the HRI methods and their utility for use with older adults who have a range of needs and capabilities. Results Our review highlighted the importance of using mixed methods and including multiple stakeholders throughout the design process. These approaches can encourage mutual learning (to improve design by developers and to increase acceptance by users). We identified key phases used in HRI PD workshops (e.g., initial interview phase, series of focus groups phase, and presentation phase). These approaches can provide inspiration for future efforts. Conclusion HRI PD strategies can support designers in developing assistive robots that meet older adults’ needs, capabilities, and preferences to promote acceptance. More HRI research is needed to understand potential implications for aging-in-place. PD methods provide a promising approach. (shrink)

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

Trigger warnings captured national attention in 2014 when students from several U.S. universities called for inclusion of the warnings on course syllabi and in classrooms. Opinions spread through news outlets across the spectrum, and those weighing in were quick to pronounce trigger warnings as either unnecessary coddling and an affront to free speech, or as a responsible pedagogical practice that treats students with respect and minimizes harm. Put simply, the debate about trigger warnings has followed the trajectory of many debates (...) in the public sphere: The issue has largely been framed by highly committed opponents and proponents whose positions represent the extremes of the spectrum. Lost has been the nuance that an issue like trigger warnings necessarily requires. This article examines trigger warnings—particularly the call for trigger warnings on university campuses—from a pluralistic ethical perspective and addresses the question: When, if ever, are trigger warnings ethically appropriate? (shrink)

Introduction and translation of “The Four Phases of Philosophy” by Franz Brentano.

Intellectual property law tends to be viewed as the only (or most significant) mechanism for achieving policy goals relating to innovation assets. Yet more creative and effective solutions are often available. When analysed from a transdisciplinary perspective, relying on the cooperative efforts of researchers from fields other than law, innovation governance is characterized not simply as the product of legal rules, but as a function of the interaction of legal rules, practices and institutions. When policy-makers seek to identify conditions under (...) which the creation, use and exchange of innovation assets flourishes, care should be taken to focus on this combination of factors. This article describes the development of an ontology—a computerized method of representing knowledge as concepts and relations between concepts—to convey such understanding. Policy makers (and researchers) are provided with an organized, accessible representation of innovation governance that enriches their understanding and improves their decision-making. (shrink)

In this paper I aim to undermine Stoic and Neo-Stoic readings of Benedict de Spinoza by examining the latter’s strong agreements with Epicurus (a notable opponent of the Stoics) on the nature and ethical role of pleasure in living a happy life. Ultimately, I show that Spinoza and Epicurus are committed to three central claims which the Stoics reject: (1) pleasure holds a necessary connection to healthy natural being, (2) pleasure manifests healthy being through positive changes in state and states (...) of healthy being per se, and (3) pleasure is by nature good. The Stoics reject these three claims due to their views on pleasant sensations as preferred moral indifferents and passionate pleasures as diseases of the soul, views which Spinoza (due to the abovementioned commitments) is strongly opposed to, thereby placing him (at least on the subject of pleasure) outside the realm of merely following or improving on Stoic doctrines. From this comparative analysis we also gain deeper insight into both Spinoza’s engagement with ancient Greek philosophy and the value of Epicureanism and Spinozism in helping us achieve and maintain happiness in the present day, particularly with respect to the benefits and harms of bodily and mental pleasures. (shrink)

The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...) to include all green plants. The PO was the first multi-species anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. There are about 2.2 million annotations linking PO terms to over 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and Quantitative Traits Loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users, and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. (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)

Focusing principally on the once-feted philosophical movement of object-oriented ontology (OOO), this article examines the ways in which this movement fits into a broader “speculative turn,” which seeks to reverse the purportedly wrongheaded emphasis of post-Kantian critical philosophy upon the finitude of the subject and to once again unleash the fecund potentialities of speculative thought. Identifying several incongruities and tensions that traverse this project, it is argued that OOO exemplifies the difficulties faced when attempting to articulate a decidedly pre-critical metaphysics.

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

We critically engage two traditional views of scientific data and outline a novel philosophical view that we call the pragmatic-representational view of data. On the PR view, data are representations that are the product of a process of inquiry, and they should be evaluated in terms of their adequacy or fitness for particular purposes. Some important implications of the PR view for data assessment, related to misrepresentation, context-sensitivity, and complementary use, are highlighted. The PR view provides insight into the common (...) but little-discussed practices of iteratively reusing and repurposing data, which result in many datasets’ having a phylogeny—an origin and complex evolutionary history—that is relevant to their evaluation and future use. We relate these insights to the open-data and data-rescue movements, and highlight several future avenues of research that build on the PR view of data. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

In a recent paper in this journal Duncan Pritchard responds to an objection to the modal account of risk pressed by Ebert, Smith and Durbach ( 2020 ). In this paper, I expand upon the objection and argue that it still stands. I go on to consider a more general question raised by this exchange – whether risk is ‘objective’, or whether it is something that varies from one perspective to another.

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (shrink)

This essay is a response to Luis M. Augusto’s intriguing paper on the rift between mainstream and formal ontology. I will show that there are in fact two questions at issue here: 1. concerning the links between mainstream and formal approaches within philosophy, and 2. concerning the application of philosophy (and especially philosophical ontology) in support of information-driven research for example in the life sciences.

Ontologies describe reality in specific domains in ways that can bridge various disciplines and languages. They allow easier access and integration of information that is collected by different groups. Ontologies are currently used in the biomedical sciences, geography, and law. A Biomedical Ethics Ontology would benefit members of ethics committees who deal with protocols and consent forms spanning numerous fields of inquiry. There already exists the Ontology for Biomedical Investigations (OBI); the proposed BMEO would interoperate with OBI, creating a powerful (...) information tool. We define a domain ontology and begin to construct a BMEO, focused on the process of evaluating human research protocols. Finally, we show how our BMEO can have practical applications for ethics committees. This paper describes ongoing research and a strategy for its broader continuation and cooperation. (shrink)

Gilles Deleuze was one of the most influential philosophers of the twentieth-century, and Smith is widely recognized to be one of his most penetrating interpreters, as well as an important philosophical voice in his own right. Combining his most important pieces over the last fifteen years along with two new essays, this book is Smith 's definitive treatise on Deleuze. The essays are divided into four sections, which cover Deleuze's use of the history of philosophy, an overview of (...) his philosophical system, an analysis of several Deleuzian concepts, as well as an assessment of his position within contemporary philosophy. (shrink)

Both ‘Sachverhalt’ and ‘state of affairs’ seem to have been derived from the juridical ‘status’ in the sense of 'status rerum' meaning: state or constitution of things. ‘Status’ signifies also in an extended sense ‘the way things stand, the condition or peculiarity of a thing in regard to its circumstances, position, order’. We describe the history of usage of ‘Sachverhalt’ from these beginnings, addressing the role of Goclenius, Lotze, Stumpf, Husserl and Adolf Reinach, whose theory of the relations between judgment (...) and Sachverhalt served as one starting point for the development of Reinach’s theory of speech acts in 1913. (shrink)

The analytical philosophy of the last hundred years has been heavily influenced by a doctrine to the effect that the key to the correct understanding of reality is captured syntactically in the ‘Fa’ (or, in more sophisticated versions, in the ‘Rab’) of standard first order predicate logic. Here ‘F’ stands for what is general in reality and ‘a’ for what is individual. Hence “f(a)ntology”. Because predicate logic has exactly two syntactically different kinds of referring expressions—‘F’, ‘G’, ‘R’, etc., and ‘a’, (...) ‘b’, ‘c’, etc.—so reality must consist of exactly two correspondingly different kinds of entity: the general (properties, concepts) and the particular (things, objects). We describe the historical influence of this view, and also show how standard first-order predicate logic can be used for the logical formalization of a more adequate “six category ontology”, which recognizes, at the level of both particulars and universals, not only things or objects but also events and qualities. (shrink)

This book explores a question central to philosophy--namely, what does it take for a belief to be justified or rational? According to a widespread view, whether one has justification for believing a proposition is determined by how probable that proposition is, given one's evidence. In this book this view is rejected and replaced with another: in order for one to have justification for believing a proposition, one's evidence must normically support it--roughly, one's evidence must make the falsity of that proposition (...) abnormal in the sense of calling for special, independent explanation. This conception of justification bears upon a range of topics in epistemology and beyond. Ultimately, this way of looking at justification guides us to a new, unfamiliar picture of how we should respond to our evidence and manage our own fallibility. This picture is developed here. (shrink)