Al-Taftāzānī introduces the Liar Paradox, in a commentary on al-Rāzī, in a short passage that is part of a polemic against the ethical rationalism of the Muʿtazila. In this essay, we consider his remarks and their place in the history of the Liar Paradox in Arabic Logic. In the passage, al-Taftāzānī introduces Liar Cycles into the tradition, gives the paradox a puzzling name—the fallacy of the “irrational root” —which became standard, and suggests a connection between the paradox and what it (...) tells us about truth and falsehood, and arguments for divine voluntarism and what they tell us about the nature of goodness and badness. On this last point, we also discuss a passage from al-Rāzī, which suggests similar connections. (shrink)

We describe the earliest occurrences of the Liar Paradox in the Arabic tradition. e early Mutakallimūn claim the Liar Sentence is both true and false; they also associate the Liar with problems concerning plural subjects, which is somewhat puzzling. Abharī (1200-1265) ascribes an unsatisfiable truth condition to the Liar Sentence—as he puts it, its being true is the conjunction of its being true and false—and so concludes that the sentence is not true. Tūsī (1201-1274) argues that self-referential sentences, like the (...) Liar, are not truth-apt, and defends this claim by appealing to a correspondence theory of truth. Translations of the texts are provided as an appendix. (shrink)

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)

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)

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)

Opponents of presentism have often argued that the presentist has difficulty in accounting for what makes true past-tensed propositions true in a way that is compatible with her metaphysical view of time and reality. The problem is quite general and concerns not only strong truth-maker principles, but also the requirement that truth be grounded in reality. In order to meet the challenge, presentists have proposed many peculiar present aspects of the world as grounds for truths concerning the past, such as (...) uninstantiated haecceities, Meinongian non-existents, ersatz times, and dispositional and distributional properties. The main problem with all such solutions is that any explanation of what grounds a TptP that involves the past is eo ipso a better explanation than any that involves only the present. Thus, the quest for an account of grounding for TptP that is compatible with the presentist ontology and ideology is doomed to be explanatorily deficient with respect to eternalism. In a recent article, Ben Caplan and David Sanson have claimed that presentists should change their strategy and, rather than seeking for exotic grounds for TptP, should adopt a more liberal view of explanation. That is, they should allow themselves to resort to “past directed” explanations, even if they do not accept the past in their ontology and ideology. I argue that such a proposal is not compatible with the tenet that there is a substantial distinction between the ideology of such a version of presentism and that of eternalism. Therefore, the presentist cannot endorse such “deflationist” explanations as an easy way out to the problem of the grounding of TptP. (shrink)