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)

Currently, the widely used notion of activity is increasingly present in computer science. However, because this notion is used in specific contexts, it becomes vague. Here, the notion of activity is scrutinized in various contexts and, accordingly, put in perspective. It is discussed through four scientific disciplines: computer science, biology, economics, and epistemology. The definition of activity usually used in simulation is extended to new qualitative and quantitative definitions. In computer science, biology and economics disciplines, the new simulation activity definition (...) is first applied critically. Then, activity is discussed generally. In epistemology, activity is discussed, in a prospective way, as a possible framework in models of human beliefs and knowledge. (shrink)

Tradução para o português de "Uma espécie de história de minha vida" (A kind of history of my life), ou Carta a um médico (A Letter to a Physician), uma carta escrita por Hume (1711-1776), endereçada em março ou abril de 1734 a um médico não identificado (segundo Norton provavelmente John Arbuthnot ou George Cheyne), na qual Hume pede alguns conselhos para continuar com o seu trabalho filosófico. O título atual é extraído do primeiro parágrafo.A carta foi escrita em 1734, (...) um pouco antes de Hume viajar para Bristol, onde, “forçado a fazer uma rápida incursão em uma vida mais ativa”, conforme relata em sua autobiografia Minha vida, buscou empregar-se no comércio. A importância dessa carta reside no seu caráter autobiográfico e nos comentários que Hume faz sobre seu projeto filosófico. A carta foi publicada originalmente em Life and correspondence of David Hume, John Hill Burton(Ed.), Edinburgh 1846, v. 1, p. 30-39; ela foi reproduzida em The Letters of David Hume. Grey, J. Y. T. (ed.) Oxford: Clarendon Press, 1932, 2v; v.1, n.3, p. 12-18, e pode ser encontrada também em The Cambridge companion to Hume, David Fate Norton, Jacqueline Taylor (ed.) 2 ed. Cambridge University Press, 2009, p. 515-522. Para essa tradução consultamos o texto original conforme apresentado nas duas últimas edições aqui mencionadas. (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_.

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)

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 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_.

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.

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)

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.

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)

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)

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)

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)

Conservation biologists recognize a duty to maintain as much value as possible in ecosystems that are threatened by recent anthropogenic impacts. Until recently the paradigm of contemporary conservation seemed relatively straightforward: the best way to maintain the value of species and ecosystems at a given location was to maintain—or shepherd the system back towards—historical conditions. Among the most difficult theoretical tasks was the determination of “baseline” historical conditions (or trajectories) to return to, recognizing the dynamism of ecosystems over time. However, (...) the rate, scale, and magnitude of contemporary climate change, species introductions, and land-use change make it increasingly impractical to return locations to any kind of historical state. This forces a paradigm shift which is both ongoing and difficult, and necessitates a rigorous evaluation of the scientific and ethical foundations of modern conservation along with a careful reexamination of terminology. Here, I discuss the moral relevance and waning utility of the geographically-based and dichotomous understanding of “native” (or “in situ”) which is an important component of conservation ethics and practice. I then propose a new understanding of nativeness in which a species is native—not to a geographic location—but to a quantifiable set of biotic, climatic, geologic, and topographic conditions (i.e. its niche) that can then map to geographic space. Following this, I demonstrate the unique utility of this concept, which I will refer to as “econativeness,” in thinking through conservation problems—range expansions, range contractions, species introductions, and assisted migration—where the classical understanding of nativeness has become increasingly inadequate for assessing the moral value of species. (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.

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)

We present data and argument to show that in Tetris—a real-time interactive video game—certain cognitive and perceptual problems are more quickly, easily, and reliably solved by performing actions in the world rather than by performing computational actions in the head alone. We have found that some translations and rotations are best understood as being used to implement a plan, or to implement a reaction. To substantiate our position we have implemented a computational laboratory that lets us record keystrokes and game (...) situations, as well as allows us to dynamically create situations. Using the data of over 30 subjects playing 6 games, tachistoscopic tests of some of these subjects, and results from our own successful efforts at building expert systems to play Tetris, we show why knowing how to use one’s environment to enhance speed and robustness are important components in skilled play. (shrink)

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)

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)