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)
Vann McGee has presented a putative counterexample to modus ponens. After clarifying that McGee actually targets an epistemic version of such a principle, I show that, contrary to a view commonly held in the literature, assuming the material conditional as an interpretation of the natural language conditional “if … then …” does not dissolve the puzzle. Indeed, I provide a slightly modified version of McGee’s famous election scenario in which (1) the relevant features of the scenario are (...) preserved and (2) both (epistemic) modus ponens and modus tollens fail, even if we assume the material conditional. I go on to note that in the modified scenario (which I call “the restaurant scenario”) (epistemic) conjunction introduction does not hold. More specifically, I show that the restaurant scenario is actually a version of the lottery scenario Kyburg uses in his Lottery Paradox. One main conclusion ensues, according to which we should expect a unified solution to both McGee’s puzzle and the Lottery Paradox. This conclusion defies the existing accounts of McGee’s puzzle. (shrink)
Paul Horwich (1990) once suggested restricting the T-Schema to the maximally consistent set of its instances. But Vann McGee (1992) proved that there are multiple incompatible such sets, none of which, given minimal assumptions, is recursively axiomatizable. The analogous view for set theory---that Naïve Comprehension should be restricted according to consistency maxims---has recently been defended by Laurence Goldstein (2006; 2013). It can be traced back to W.V.O. Quine(1951), who held that Naïve Comprehension embodies the only really intuitive conception of (...) set and should be restricted as little as possible. The view might even have been held by Ernst Zermelo (1908), who,according to Penelope Maddy (1988), subscribed to a ‘one step back from disaster’ rule of thumb: if a natural principle leads to contra-diction, the principle should be weakened just enough to block the contradiction. We prove a generalization of McGee’s Theorem, anduse it to show that the situation for set theory is the same as that for truth: there are multiple incompatible sets of instances of Naïve Comprehension, none of which, given minimal assumptions, is recursively axiomatizable. This shows that the view adumbrated by Goldstein, Quine and perhaps Zermelo is untenable. (shrink)
I argue that we should solve the Lottery Paradox by denying that rational belief is closed under classical logic. To reach this conclusion, I build on my previous result that (a slight variant of) McGee’s election scenario is a lottery scenario (see Lissia 2019). Indeed, this result implies that the sensible ways to deal with McGee’s scenario are the same as the sensible ways to deal with the lottery scenario: we should either reject the Lockean Thesis or Belief (...) Closure. After recalling my argument to this conclusion, I demonstrate that a McGee-like example (which is just, in fact, Carroll’s barbershop paradox) can be provided in which the Lockean Thesis plays no role: this proves that denying Belief Closure is the right way to deal with both McGee’s scenario and the Lottery Paradox. A straightforward consequence of my approach is that Carroll’s puzzle is solved, too. (shrink)
Recently four different papers have suggested that the supervaluational solution to the Problem of the Many is flawed. Stephen Schiffer (1998, 2000a, 2000b) has argued that the theory cannot account for reports of speech involving vague singular terms. Vann McGee and Brian McLaughlin (2000) say that theory cannot, yet, account for vague singular beliefs. Neil McKinnon (2002) has argued that we cannot provide a plausible theory of when precisifications are acceptable, which the supervaluational theory needs. And Roy Sorensen (2000) (...) argues that supervaluationism is inconsistent with a directly referential theory of names. McGee and McLaughlin see the problem they raise as a cause for further research, but the other authors all take the problems they raise to provide sufficient reasons to jettison supervaluationism. I will argue that none of these problems provide such a reason, though the arguments are valuable critiques. In many cases, we must make some adjustments to the supervaluational theory to meet the posed challenges. The goal of this paper is to make those adjustments, and meet the challenges. (shrink)
Tarski's Undefinability of Truth Theorem comes in two versions: that no consistent theory which interprets Robinson's Arithmetic (Q) can prove all instances of the T-Scheme and hence define truth; and that no such theory, if sound, can even express truth. In this note, I prove corresponding limitative results for validity. While Peano Arithmetic already has the resources to define a predicate expressing logical validity, as Jeff Ketland has recently pointed out (2012, Validity as a primitive. Analysis 72: 421-30), no theory (...) which interprets Q closed under the standard structural rules can define nor express validity, on pain of triviality. The results put pressure on the widespread view that there is an asymmetry between truth and validity, viz. that while the former cannot be defined within the language, the latter can. I argue that Vann McGee's and Hartry Field's arguments for the asymmetry view are problematic. (shrink)
This paper gives a definition of self-reference on the basis of the dependence relation given by Leitgeb (2005), and the dependence digraph by Beringer & Schindler (2015). Unlike the usual discussion about self-reference of paradoxes centering around Yablo's paradox and its variants, I focus on the paradoxes of finitary characteristic, which are given again by use of Leitgeb's dependence relation. They are called 'locally finite paradoxes', satisfying that any sentence in these paradoxes can depend on finitely many sentences. I prove (...) that all locally finite paradoxes are self-referential in the sense that there is a directed cycle in their dependence digraphs. This paper also studies the 'circularity dependence' of paradoxes, which was introduced by Hsiung (2014). I prove that the locally finite paradoxes have circularity dependence in the sense that they are paradoxical only in the digraph containing a proper cycle. The proofs of the two results are based directly on König's infinity lemma. In contrast, this paper also shows that Yablo's paradox and its nested variant are non-self-referential, and neither McGee's paradox nor the omega-cycle liar paradox has circularity dependence. (shrink)
Chancy modus ponens is the following inference scheme: ‘probably φ’, ‘if φ, then ψ’, therefore, ‘probably ψ’. I argue that Chancy modus ponens is invalid in general. I further argue that the invalidity of Chancy modus ponens sheds new light on the alleged counterexample to modus ponens presented by McGee. I close by observing that, although Chancy modus ponens is invalid in general, we can recover a restricted sense in which this scheme of inference is valid.
McGee argued that modus ponens was invalid for the natural language conditional ‘If…then…’. Many subsequent responses have argued that, while McGee’s examples show that modus ponens fails to preserve truth, they do not show that modus ponens fails to preserve rational full acceptance, and thus modus ponens may still be valid in the latter informational sense. I show that when we turn our attention from indicative conditionals to subjunctive conditionals, we find that modus ponens does not preserve either (...) truth or rational full acceptance, and thus is not valid in either sense. In concluding I briefly consider how we can account for these facts. (shrink)
In a recent pair of publications, Richard Bradley has offered two novel no-go theorems involving the principle of Preservation for conditionals, which guarantees that one’s prior conditional beliefs will exhibit a certain degree of inertia in the face of a change in one’s non-conditional beliefs. We first note that Bradley’s original discussions of these results—in which he finds motivation for rejecting Preservation, first in a principle of Commutativity, then in a doxastic analogue of the rule of modus ponens —are problematic (...) in a significant number of respects. We then turn to a recent U-turn on his part, in which he winds up rescinding his commitment to modus ponens, on the grounds of a tension with the rule of Import-Export for conditionals. Here we offer an important positive contribution to the literature, settling the following crucial question that Bradley leaves unanswered: assuming that one gives up on full-blown modus ponens on the grounds of its incompatibility with Import-Export, what weakened version of the principle should one be settling for instead? Our discussion of the issue turns out to unearth an interesting connection between epistemic undermining and the apparent failures of modus ponens in McGee’s famous counterexamples. (shrink)
*This work is no longer under development* Two major themes in the literature on indicative conditionals are that the content of indicative conditionals typically depends on what is known;1 that conditionals are intimately related to conditional probabilities.2 In possible world semantics for counterfactual conditionals, a standard assumption is that conditionals whose antecedents are metaphysically impossible are vacuously true.3 This aspect has recently been brought to the fore, and defended by Tim Williamson, who uses it in to characterize alethic necessity by (...) exploiting such equivalences as: A⇔¬A A. One might wish to postulate an analogous connection for indicative conditionals, with indicatives whose antecedents are epistemically impossible being vacuously true: and indeed, the modal account of indicative conditionals of Brian Weatherson has exactly this feature.4 This allows one to characterize an epistemic modal by the equivalence A⇔¬A→A. For simplicity, in what follows we write A as KA and think of it as expressing that subject S knows that A.5 The connection to probability has received much attention. Stalnaker suggested, as a way of articulating the ‘Ramsey Test’, the following very general schema for indicative conditionals relative to some probability function P: P = P 1For example, Nolan ; Weatherson ; Gillies. 2For example Stalnaker ; McGee ; Adams. 3Lewis. See Nolan for criticism. 4‘epistemically possible’ here means incompatible with what is known. 5This idea was suggested to me in conversation by John Hawthorne. I do not know of it being explored in print. The plausibility of this characterization will depend on the exact sense of ‘epistemically possible’ in play—if it is compatibility with what a single subject knows, then can be read ‘the relevant subject knows that p’. If it is more delicately formulated, we might be able to read as the epistemic modal ‘must’. (shrink)
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