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)

There is a difference between merely thinking that P and really grasping that P. For example, Jackson's (1982) black-and-white Mary cannot (before leaving her black-and-white room) fully grasp what it means to say that fire engines are red, but she can perfectly well entertain the thought that fire engines are red. The contrast between merely thinking and grasping is especially salient in the context of certain moral decisions. For example, an individual who grasps the plight of starving children thanks (...) to evocative images seems much more likely to donate for the children's benefit than someone who is merely told about their plight. This paper offers a phenomenal account of grasping according to which grasping a content (whether a proposition or concept) consists in one's thoughts about the content being constituted by phenomenal experiences of constituents of the content. This account improves on earlier phenomenal accounts of grasping (Bourget 2017a, 2018) by allowing for partial grasping and generalizing to concepts. The paper also addresses objections to phenomenal accounts of grasping, including the objection that recent developments in AI technology show that consciousness is irrelevant to grasping and understanding. (shrink)

The principle of alternate possibilities (PAP), making the ability to do otherwise a necessary condition for moral responsibility, is supposed by Harry Frankfurt, John Fischer, and others to succumb to a peculiar kind of counterexample. The paper reviews the main problems with the counterexample that have surfaced over the years, and shows how most can be addressed within the terms of the current debate. But one problem seems ineliminable: because Frankfurt''s example relies on a counterfactual intervener to preclude alternatives to (...) the person''s action, it is not possible for it to preclude all alternatives (intervention that is contingent upon a trigger cannot bring it about that the trigger never occurred). This makes it possible for the determined PAPist to maintain that some pre-intervention deviation is always available to ground moral responsibility. In reply, the critic of PAP can examine all the candidate deviations and argue their irrelevance to moral responsibility (a daunting prospect); or the critic can dispense with counterfactual intervention altogether. The paper pursues the second of these strategies, developing three examples of noncounterfactual intervention in which (i) the agent has no alternatives (and a fortiori no morally relevant alternatives), yet (ii) there is just as much reason to think that the agent is morally responsible as there was in Frankfurt''s original example. The new counterexamples do suffer from one liability, but this is insufficient in the end to repair PAP''s conceptual connection between moral responsibility and alternate possibilities. (shrink)

This is a contribution to an Author Meets Critics special issue on John Martin Fischer's _Our Fate: Essays on God and Free Will_.

Can free agency exist within a Minkowskian "block universe"? A negative answer to this question has been labeled 'chronogeometrical fatalism'. I look at five theses associated with Minkowskian space-time which have been thought to entail chronogeometrical fatalism, and argue that none of them delivers the goods.

I first argue that the Matrix trilogy is a Gnostic cyber-epic; I then use this interpretive lens to review the films' treatment of fundamental questions in epistemology, metaphysics, and value theory.

The principle that one cannot deliberate over what one already knows is going to happen, when suitably qualified, has seemed to many philosophers to be about as secure a truth as one is likely to find in this life. Fortunately, it poses little restriction on human deliberation, since the conditions which would trigger its prohibition seldom arise for us: our knowledge of the future is intermittent at best, and those things of which we do have advance knowledge are not the (...) sorts of things over which we would deliberate in any case. But matters appear to stand otherwise with an all-knowing agent such as God is traditionally conceived to be; for what an omniprescient deity ‘already knows is going to happen’ is everything that is going to happen; and if He cannot deliberate over such things, there is nothing over which He can deliberate. (shrink)

The paper explores possible resources available to Plotinus for responding to Plato's famous "Third Man Argument" in the _Parmenides_.

The paper that follows continues a discussion with Tomis Kapitan in the pages of this journal over the compatibility of divine agency with divine foreknowledge. I had earlier argued against two premises in Kapitan's case for omniscient impotence: (i) that intentionally A-ing presupposes prior acquisition of the intention to A, and (ii) that acquiring the intention to A presupposes prior ignorance whether one will A. In response to my criticisms, Kapitan has recently offered new defences for these two premises. I (...) show in reply why neither defence succeeds in rehabilitating the case against omniscient agency. (Note that the very first sentence of the published version has a misprint: instead of "To claim that divine foreknowledge is inconsistent with divine agency has been pressed with increasing frequency of late . . .", it should read, "_The_ claim . . ."!). (shrink)

The traditional doctrine of divine omniscience ascribes to God the fully exercised power to know all truths. but why is God’s excellence with respect to knowing not treated on a par with his excellence with respect to doing, where the latter requires only that God have the power to do all things? The prima facie problem with divine ”omni-knowledgeability’ -- roughly, being able to know whatever one wants to know whenever one wants to know it -- is that knowledge requires (...) an internal representation, whereas mere ”knowledgeability’ does not. I argue to the contrary that knowledge does not require an internal representation, and that even if it did, an omni-knowledgeable God would satisfy this requirement. omni-knowledgeability therefore represents a distinct understanding of God’s cognitive excellence while satisfying the traditional insistence on full omniscience. (shrink)

The most serious challenge to Frankfurt-type counterexamples to the Principle of Alternate Possibilities (PAP) comes in the form of a dilemma: either the counterexample presupposes determinism, in which case it begs the question; or it does not presuppose determinism, in which case it fails to deliver on its promise to eliminate all alternatives that might plausibly be thought to satisfy PAP. I respond to this challenge with a counterexample in which considering an alternative course of action is a necessary condition (...) for deciding to act otherwise, and the agent does not in fact consider the alternative. I call this a “buffer case,” because the morally relevant alternative is “buffered” by the requirement that the agent first consider the alternative. Suppose further that the agent’s considering an alternative action—entering the buffer zone—is what would trigger the counterfactual intervener. Then it would appear that PAP-relevant alternatives are out of reach. I defend this counterexample to PAP against three objections: that considering an alternative is itself a morally relevant alternative; that buffer cases can be shown to contain other alternatives that arguably satisfy PAP; and that even if the agent’s present access to PAP-relevant alternatives were eliminated, PAP could still be satisfied in virtue of earlier alternatives. I conclude that alternative possibilities are a normal symptom, but not an essential constituent, of moral agency. (shrink)

One strategy in recent discussions of theological fatalism is to draw on Harry Frankfurt’s famous counterexamples to the principle of alternate possibilities (PAP) to defend human freedom from divine foreknowledge. For those who endorse this line, “Frankfurt counterexamples” are supposed to show that PAP is false, and this conclusion is then extended to the foreknowledge case. This makes it critical to determine whether Frankfurt counterexamples perform as advertised, an issue recently debated in this journal via a pair of articles by (...) David Widerker and John Martin Fischer. I suggest that this debate can be avoided: divine foreknowledge is itself aparadigmatic counterexample to PAP, requiring no support from suspect Frankfurt counterexamples. (shrink)

The computational genomics community has come increasingly to rely on the methodology of creating annotations of scientific literature using terms from controlled structured vocabularies such as the Gene Ontology (GO). We here address the question of what such annotations signify and of how they are created by working biologists. Our goal is to promote a better understanding of how the results of experiments are captured in annotations in the hope that this will lead to better representations of biological reality through (...) both the annotation process and ontology development, and in more informed use of the GO resources by experimental scientists. (shrink)

This paper seeks to rehabilitate St. Augustine’s widely dismissed response to the alleged incompatibility of divine foreknowledge and free will. This requires taking a fresh look at his analysis in On Free Choice of the Will, and arguing its relevance to the current debate. Along the way, mistaken interpretations of Augustine are rebutted, his real solution is developed and defended, a reason for his not anticipating Boethius’s a temporalist solution is suggested, a favorable comparison with Ockham is made, rival solutions (...) are rejected, and the aporetic nature of the problem is explained. (shrink)

I distinguish between a _metaphysical_ problem generated by the argument for theological fatalism, and a _theological_ problem posed by the argument. Some responses to the argument, including ones associated with Boethius, Aquinas and Ockham, address only the theological problem. Even if such responses succeed in showing that God's foreknowledge doesn't threaten human freedom, they fail to take the full measure of the argument for theological fatalism, since the metaphysical problem remains to be solved.

Instead of the half-century old foundational feud between set theory and category theory, this paper argues that they are theories about two different complementary types of universals. The set-theoretic antinomies forced naïve set theory to be reformulated using some iterative notion of a set so that a set would always have higher type or rank than its members. Then the universal u_{F}={x|F(x)} for a property F() could never be self-predicative in the sense of u_{F}∈u_{F}. But the mathematical theory of categories, (...) dating from the mid-twentieth century, includes a theory of always-self-predicative universals--which can be seen as forming the "other bookend" to the never-self-predicative universals of set theory. The self-predicative universals of category theory show that the problem in the antinomies was not self-predication per se, but negated self-predication. They also provide a model (in the Platonic Heaven of mathematics) for the self-predicative strand of Plato's Theory of Forms as well as for the idea of a "concrete universal" in Hegel and similar ideas of paradigmatic exemplars in ordinary thought. (shrink)

Open theists deny that God knows future contingents. Most open theists justify this denial by adopting the position that there are no future contingent truths to be known. In this paper we examine some of the arguments put forward for this position in two recent articles in this journal, one by Dale Tuggy and one by Alan Rhoda, Gregory Boyd, and Thomas Belt. The arguments concern time, modality, and the semantics of ‘will’ statements. We explain why we find none of (...) these arguments persuasive. This wide road leads only to destruction. (shrink)

According to the thesis of divine ‘middle knowledge’, first propounded by the Jesuit theologian Luis de Molina in the sixteenth century, subjunctive conditionals stating how free agents would freely respond under counter-factual conditions may be straightforwardly true, and thus serve as the objects of divine knowledge. This thesis has provoked considerable controversy, and the recent revival of interest in middle knowledge, initiated by Anthony Kenny, Robert Adams and Alvin Plantinga in the 1970s, has led to two ongoing debates. One is (...) a theoretical debate over the very intelligibility of middle knowledge;1 the other is a practical debate over its philosophical and theological utility.2. (shrink)

Gilbert Harman’s famous principle of Clutter Avoidance commands that “one should not clutter one’s mind with trivialities". Many epistemologists have been inclined to accept Harman’s principle, or something like it. This is significant because the principle appears to have robust implications for our overall picture of epistemic normativity. Jane Friedman (2018) has recently argued that one potential implication is that there are no genuine purely evidential norms on belief revision. In this paper, we present some new objections to a suitably (...) formulated version of the clutter principle qua norm on belief revision. Moreover, we argue that the clutter principle is best understood as a norm on non-doxastic stages of inquiry. In our view, it is a norm of asking and considering questions rather than a norm of settling on an answer to a question by forming a belief. (shrink)

Our aim in this entry is to articulate the state of the art in the moral psychology of personal identity. We begin by discussing the major philosophical theories of personal identity, including their shortcomings. We then turn to recent psychological work on personal identity and the self, investigations that often illuminate our person-related normative concerns. We conclude by discussing the implications of this psychological work for some contemporary philosophical theories and suggesting fruitful areas for future work on personal identity.

To discover how to couple reflection with reaction we have been studying how people play the computer game Tetris. Our basic intuition is that the job of the reasoned is to monitor the environment and the agent’s behavior over time to discover trends or deviations from the agent’s normative policy and tune the priorities of the Attentional system accordingly.

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

Contém informações sobre as obras mais experimentais e ousadas da vanguarda histórica dos anos 20. Com uma extensa antologia de ensaios críticos colecionados e reproduzidos pela primeira vez.

Is the societal-level of analysis sufficient today to understand the values of those in the global workforce? Or are individual-level analyses more appropriate for assessing the influence of values on ethical behaviors across country workforces? Using multi-level analyses for a 48-society sample, we test the utility of both the societal-level and individual-level dimensions of collectivism and individualism values for predicting ethical behaviors of business professionals. Our values-based behavioral analysis indicates that values at the individual-level make a more significant contribution to (...) explaining variance in ethical behaviors than do values at the societal-level. Implicitly, our findings question the soundness of using societal-level values measures. Implications for international business research are discussed. (shrink)

An experiment was performed to test the hypothesis that people sometimes take physical actions to make themselves more effective problem solvers. The task was to generate all possible words that could be formed from seven Scrabble letters. In one condition, participants could use their hands to manipulate the letters, and in another condition, they could not. Results show that more words were generated with physical manipulation than without. However, an interaction was obtained between the physical manipulation conditions and the specific (...) letter sets chosen, indicating that physical manipulation helps more for generating words in some circumstances than in others. Overall, our findings can be explained in terms of an interactive search process in which external, physical activity effectively complements internal, cognitive activity. Within this framework, the interaction can be explained in terms of the relative difficulty of generating words from the letters given in the different sets. (shrink)