The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad scope. (...) We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

Where humans can manipulate and integrate the information they receive in subtle and ever changing ways from context to context, computers need structured and context-free background information of a sort which ontologies can help to provide. A domain ontology captures the stable, highly general and commonly accepted core knowledge for an application domain. The domain at issue here is that of the life sciences, in particular molecular biology and bioinformatics. Contemporary life science research includes components drawn from physics, chemistry, mathematics, (...) medicine and many other areas, and all of these dimensions, as well as fundamental philosophical issues, must be taken into account in the construction of a domain ontology. Here we describe the basic features of domain ontologies in the life sciences and show how they can be used. (shrink)

Legal theorists have characterized physical evidence of brain dysfunction as a double-edged sword, wherein the very quality that reduces the defendant’s responsibility for his transgression could simultaneously increase motivations to punish him by virtue of his apparently increased dangerousness. However, empirical evidence of this pattern has been elusive, perhaps owing to a heavy reliance on singular measures that fail to distinguish between plural, often competing internal motivations for punishment. The present study employed a test of the theorized double-edge pattern using (...) a novel approach designed to separate such motivations. We asked a large sample of participants (N = 330) to render criminal sentencing judgments under varying conditions of the defendant’s mental health status (Healthy, Neurobiological Disorder, Psychological Disorder) and the disorder’s treatability (Treatable, Untreatable). As predicted, neurobiological evidence simultaneously elicited shorter prison sentences (i.e., mitigating) and longer terms of involuntary hospitalization (i.e., aggravating) than equivalent psychological evidence. However, these effects were not well explained by motivations to restore treatable defendants to health or to protect society from dangerous persons but instead by deontological motivations pertaining to the defendant’s level of deservingness and possible obligation to provide medical care. This is the first study of its kind to quantitatively demonstrate the paradoxical effect of neuroscientific trial evidence and raises implications for how such evidence is presented and evaluated. (shrink)

The rapidly increasing wealth of genomic data has driven the development of tools to assist in the task of representing and processing information about genes, their products and their functions. One of the most important of these tools is the Gene Ontology (GO), which is being developed in tandem with work on a variety of bioinformatics databases. An examination of the structure of GO, however, reveals a number of problems, which we believe can be resolved by taking account of certain (...) organizing principles drawn from philosophical ontology. We shall explore the results of applying such principles to GO with a view to improving GO’s consistency and coherence and thus its future applicability in the automated processing of biological data. (shrink)

Gilbert Ryle’s distinction between knowledge-how and knowledge-that emerged from his criticism of the “intellectualist legend” that to do something intelligently is “to do a bit of theory and then to do a bit of practice,” and became a philosophical commonplace in the second half of the last century. In this century Jason Stanley has attacked Ryle’s distinction, arguing that “knowing-how is a species of knowing-that,” and accusing Ryle of setting up a straw man in his critique of “intellectualism.” Examining the (...) use of the terms “intellectualism” and “anti-intellectualism” in the first half of the 20th century, in a wide-ranging debate in the social sciences as well as in philosophy, I show that Ryle was not criticizing a straw man, but a live historical position. In the context of this controversy, Ryle’s position represents a third way between “intellectualism” and “anti-intellectualism,” an option that has largely gone missing in the 21st century discussion. This argument illustrates how history can inform the history of philosophy, and how the history of philosophy can inform contemporary philosophical inquiry. (shrink)

Many philosophers of theistic religions claim (1) that there are powerful a posteriori arguments for God’s existence that make it rational to believe that He exists and at the same time maintain (2) that God always has the freedom to do otherwise. In this article, I argue that these two positions are inconsistent because the empirical evidence on which the a posteriori arguments for God’s existence rest can be explained better by positing the existence of a God-like being without the (...) freedom to do otherwise. (shrink)

Considerable variation exists not only in the kinds of transposable elements (TEs) occurring within the genomes of different species, but also in their abundance and distribution. Noting a similarity to the assortment of organisms among ecosystems, some researchers have called for an ecological approach to the study of transposon dynamics. However, there are several ways to adopt such an approach, and it is sometimes unclear what an ecological perspective will add to the existing co-evolutionary framework for explaining transposon-host interactions. This (...) review aims to clarify the conceptual foundations of transposon ecology in order to evaluate its explanatory prospects. We begin by identifying three unanswered questions regarding the abundance and distribution of TEs that potentially call for an ecological explanation. We then offer an operational distinction between evolutionary and ecological approaches to these questions. By determining the amount of variance in transposon abundance and distribution that is explained by ecological and evolutionary factors, respectively, it is possible empirically to assess the prospects for each of these explanatory frameworks. To illustrate how this methodology applies to a concrete example, we analyzed whole-genome data for one set of distantly related mammals and another more closely related group of arthropods. Our expectation was that ecological factors are most informative for explaining differences among individual TE lineages, rather than TE families, and for explaining their distribution among closely related as opposed to distantly related host genomes. We found that, in these data sets, ecological factors do in fact explain most of the variation in TE abundance and distribution among TE lineages across less distantly related host organisms. Evolutionary factors were not significant at these levels. However, the explanatory roles of evolution and ecology become inverted at the level of TE families or among more distantly related genomes. Not only does this example demonstrate the utility of our distinction between ecological and evolutionary perspectives, it further suggests an appropriate explanatory domain for the burgeoning discipline of transposon ecology. The fact that ecological processes appear to be impacting TE lineages over relatively short time scales further raises the possibility that transposons might serve as useful model systems for testing more general hypotheses in ecology. (shrink)

The objection of horrible commands claims that divine command metaethics is doomed to failure because it is committed to the extremely counterintuitive assumption that torture of innocents, rape, and murder would be morally obligatory if God commanded these acts. Morriston, Wielenberg, and Sinnott-Armstrong have argued that formulating this objection in terms of counterpossibles is particularly forceful because it cannot be simply evaded by insisting on God’s necessary perfect moral goodness. I show that divine command metaethics can be defended even against (...) this counterpossible version of the objection of horrible commands because we can explain the truth-value intuitions about the disputed counterpossibles as the result of conversational implicatures. Furthermore, I show that this pragmatics-based defence of divine command metaethics has several advantages over Pruss’s reductio counterargument against the counterpossible version of the objection of horrible commands. (shrink)

Rirchard Rorty has criticized the rigiditiy of the classical ethics of Kant, and he claims that we do not have absolute and universal moral norms.

Stephen Maitzen argues that divine command metaethics must be mistaken because it is committed to the implausible assumption that the sentence ‘God is good’ is a tautology. In this article, I show that a charitable interpretation of R. M. Adams’ version of divine command metaethics is not committed to accept this assumption. I conclude that Maitzen’s objection merely manages to refute a strawman version of divine command metaethics.

In this essay we analyze the question of the origin of purpose. Due to the overwhelming success of science in explaining phenomena, it is often asked, when, and how science could explain purpose and consciousness by use of purely mechanical laws. Here I argue that such a reduction is impossible.

Review of Kremer's book on Barry Miller's approach to God. (I have discussed Miller's argument from contingency in other publications.).

The Polish philosophy of mathematics in the 19th century is not a well-researched topic. For this period, only five philosophers are usually mentioned, namely Jan Śniadecki, Józef Maria Hoene-Wroński, Henryk Struve, Samuel Dickstein, and Edward Stamm. This limited and incomplete perspective does not allow us to develop a well-balanced picture of the Polish philosophy of mathematics and gauge its influence on 19th- and 20th-century Polish philosophy in general. To somewhat complete our picture of the history of the Polish philosophy of (...) mathematics in those times, we here present the profiles of some lesser-known Polish Romantic philosophers of the 19th century, namely Karol Libelt, Bronisław Trentowski, and Józef Kremer. We discuss their contributions to the philosophy of mathematics and their metaphysical perspectives, and we also show how their metaphysical ideas have found some continuity in the studies of some Catholic philosophers. (shrink)

In the introduction to the special volume, Gilbert Ryle: Intelligence, Practice and Skill, Julia Tanney introduces the contributions of Michael Kremer, Stina Bäckström and Martin Gustafsson, and Will Small, each of which indicates concern about the appropriation of Ryle’s distinction between knowing-how and knowing-that in seminal work in contemporary epistemology. Expressing agreement with the authors that something has gone awry in these borrowings from Ryle, Tanney takes this criticism to a deeper level. She argues that the very notion of (...) content-bearing, causally-efficacious mental states, let alone representational states of knowledge-that or knowledge-how, embodies the very presuppositions that Ryle calls into question in his rejection of classical theories of meaning and his related warning of the type-errors involved in conflating rational and mechanistic explanation. That these mental posits are presupposed, unchallenged, in today’s debates make his arguments against intellectualism particularly difficult to discern. (shrink)

This paper reconstructs Susan Stebbing’s account of intelligent dealing with a problem and defends this account against charges that it relies on a “censurable kind” of intellectualism. This charge was made in Stebbing’s own time by Laird and Wittgenstein. Michael Kremer has recently made the case that Stebbing is also a proximate target of Gilbert Ryle’s attack on intellectualism. This paper argues that Stebbing should indeed be counted as an intellectualist since she holds that intelligent dealing with a problem (...) requires propositional thought. Yet, for Stebbing, thinking is an activity of a whole person and is enabled and constrained by their dispositions. This complex picture of a thinker enables Stebbing’s account to resist arguments targeting certain forms of intellectualism such as Ryle’s regress argument. It also helps her to respond to the charge that she overemphasizes the importance of intellectual failures. On the picture that emerges, Stebbing offers a strikingly modern epistemology that incorporates the social features of a person as well as their purely intellectual features. (shrink)

Much has been written on the relative merits of different readings of Wittgenstein's Tractatus Logico-Philosophicus. The recent renewal of the debate has almost exclusively been concerned with variants of the ineffabilist (metaphysical) reading of TL-P - notable such readings have been advanced by Elizabeth Anscombe, P. M. S. Hacker and H. O. Mounce - and the recently advanced variants of therapeutic (resolute) readings - notable advocates of which are James Conant, Cora Diamond, Juliet Floyd and Michael Kremer. During this (...) debate, there have been a number of writers who have tried to develop a third way, incorporating what they see as insights and avoiding what they see as flaws in both the ineffabilist and resolute readings. The most prominent advocates of these elucidatory readings of TL-P are Dan Hutto (2003) and Marie McGinn (1999). In this paper we subject Hutto's and McGinn's readings of TL-P to critical scrutiny. We find that in seeking to occupy the middle ground they ultimately find themselves committed to (and in the process commit Wittgenstein to) the very ineffabilism they (and Wittgenstein) are seeking to overcome. (shrink)

The aim of my paper is to describe and evaluate different conceptions of holism in Ludwig Wittgenstein’s Tractatus Logico-Philosophicus. I distinguish three readings of holistic elements in this work: i) Minimal Holism (E. Anscombe, M. Black, D. Pears); ii) Moderate Holism (J. Conant, C. Diamond, G. Ryle); and iii) Radical Holism (G. Bar-Elli, M. Kremer, P. Livingston). The conclusion is that the most viable option is Moderate Holism since it embraces the logico-syntactical notion of use, rejects an anachronistic interpretation (...) of Tractatarian ontology and allows us to see that the holistic elements are complementary to the initial atomism of the work. Moreover, I point to the consequences of the topic for the overall reading of Wittgenstein’s early and late work. (shrink)