How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

A series of papers on different aspects of practical knowledge by Roderick Chisholm, Rudolf Haller, J. C. Nyiri, Eva Picardi, Joachim Schulte Roger Scruton, Barry Smith and Johan Wrede.

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that (...) has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility. (shrink)

The COVID-19 pandemic revealed numerous weaknesses in pandemic preparedness and response, including underfunding, inadequate surveillance, and inequitable distribution of countermeasures. To overcome these weaknesses for future pandemics, WHO released a zero draft of a pandemic treaty in February, 2023, and subsequently a revised bureau's text in May, 2023. COVID-19 made clear that pandemic prevention, preparedness, and response reflect choices and value judgements. These decisions are therefore not a purely scientific or technical exercise, but are fundamentally grounded in ethics. The latest (...) treaty draft reflects these ethical considerations by including a section entitled Guiding Principles and Approaches. Most of these principles are ethical—they establish core values that undergird the treaty. Unfortunately, the treaty draft's set of principles are numerous, overlapping, and show inadequate coherence and consistency. We propose two improvements to this section of the draft pandemic treaty. First, key guiding ethical principles should be clearer and more precise than they currently are. Second, the link between ethical principles and policy implementation should be clearly established and define boundaries on acceptable interpretation, ensuring that signatories abide by these principles. (shrink)

The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.

In May 2010, philosophers, family and friends gathered at the University of Notre Dame to celebrate the career and retirement of Alvin Plantinga, widely recognized as one of the world's leading figures in metaphysics, epistemology, and the philosophy of religion. Plantinga has earned particular respect within the community of Christian philosophers for the pivotal role that he played in the recent renewal and development of philosophy of religion and philosophical theology. Each of the essays in this volume engages with some (...) particular aspect of Plantinga's views on metaphysics, epistemology, or philosophy of religion. Contributors include Michael Bergman, Ernest Sosa, Trenton Merricks, Richard Otte, Peter VanInwagen, Thomas P. Flint, Eleonore Stump, Dean Zimmerman and Nicholas Wolterstorff. The volume also includes responses to each essay by Bas van Fraassen, Stephen Wykstra, David VanderLaan, Robin Collins, Raymond VanArragon, E. J. Coffman, Thomas Crisp, and Donald Smith. (shrink)

Sceptical theists--e.g., William Alston and Michael Bergmann--have claimed that considerations concerning human cognitive limitations are alone sufficient to undermine evidential arguments from evil. We argue that, if the considerations deployed by sceptical theists are sufficient to undermine evidential arguments from evil, then those considerations are also sufficient to undermine inferences that play a crucial role in ordinary moral reasoning. If cogent, our argument suffices to discredit sceptical theist responses to evidential arguments from evil.

Property-identical divine-command theory (PDCT) is the view that being obligatory is identical to being commanded by God in just the way that being water is identical to being H2O. If these identity statements are true, then they express necessary a posteriori truths. PDCT has been defended in Robert M. Adams (1987) and William Alston (1990). More recently Mark C. Murphy (2002) has argued that property-identical divine-command theory is inconsistent with two well-known and well-received theses: the free-command thesis and the supervenience (...) thesis. I show that Murphy's argument is vitiated by mistaken assumptions about the substitutivity of metaphysical identicals in contexts of supervenience. The free-command thesis and the supervenience thesis therefore pose no serious threat to PDCT. (Published Online August 11 2004). (shrink)

Perhaps the most commonly discussed argument against the possibility of extended simples is the argument from heterogeneity. The argument states that, if extended simples are possible, then extended simples which exhibit intrinsic qualitative variation across space (or spacetime) are also possible [Premise 1]. But, the argument goes, it is impossible for an extended simple to exhibit intrinsic qualitative variation across space (or spacetime) [Premise 2]. Thus, extended simples are impossible. I argue that there is a serious problem with the argument (...) from heterogeneity: the best arguments in support of the first premise undermine support for the second. Thus, there appears to be no good reason to accept both premises. (shrink)

A commonly held view is that a central aim of metaphysics is to give a fundamental account of reality which refers only to the fundamental entities. But a puzzle arises. It is at least a working hypothesis for those pursuing the aim that, first, there must be fundamental entities. But, second, it also seems possible that the world has no foundation, with each entity depending on others. These two claims are inconsistent with the widely held third claim that the fundamental (...) just is the foundational. It is tempting to resolve the puzzle by rejecting the first or second claim, perhaps because it is obscure how the third claim might plausibly be challenged. But I develop a new analysis of fundamentality which challenges the third claim by allowing for an entity to be fundamental without being foundational. The analysis, roughly, is that an entity is fundamental just in case not all facts about it are grounded in facts about other entities. The possibility of fundamentality without foundations not only provides for a novel resolution to the puzzle, but has applications to some live debates: for example, it undermines Jonathan Schaffer's modal argument for priority monism. (shrink)

I argue that Anselmians ought to abandon traditional Anselmianism in favor of Moderate Anselmianism. Moderate Anselmianism advances the view that a being x = God iff for every essential property P of x, it is secondarily necessary that x has P, for most essential properties of x, it is not primarily necessary that x has P and the essential properties of x include omnipotence, omniscience, perfect goodness and necessary existence. Traditional Anselmians have no cogent response to most a priori atheological (...) arguments. But a priori atheological arguments present no serious problem for moderate Anselmians. Unlike traditional Anselmianism, Moderate Anselmianism explains why a priori atheological arguments can be convincing and nonetheless illusory. (shrink)

Etic theorizing uses the theorist’s social notions to theorize about their subject. This theorist may claim that Genghis Khan was a war criminal even though his actions predate the enactment of the Geneva Conventions. Brian Epstein considers a modal etic theorist who claims that Genghis Khan would have been a war criminal even if the Geneva Conventions were never enacted. Epstein argues that this has metaphysical import: it requires postulating a novel metaphysical notion of “anchoring”. Drawing from some familiar issues (...) in modal actualism, I argue that modal etic theorizing does not support this postulate. But it does suggest a distinctive kind of modality at work in social reality. (shrink)

ABSTRACT: Recent work in moral theory includes an intriguing new argument that the vagueness of moral properties, together with two well-known and well-received metaethical principles, entails the incredible conclusion that it is impossible to be moral. I show that the argument equivocates between “it is true that A and B are morally indistinguishable” and “it is not false that A and B are morally indistinguishable.” As expected the argument is interesting but unsound. It is therefore not impossible to be moral.RÉSUMÉ: (...) Les travaux récents en théorie morale comprennent un nouvel argument intrigant voulant que le caractère vague des propriétés morales, joint à deux principes métaéthiques bien connus et généralement admis, entraîne une conclusion incroyable, soit qu’il est impossible d’être moral. Je montre que cet argument entretient l’équivoque entre «il est vrai que A et B sont moralement impossibles à distinguer» et «il n’est pas faux que A et B soient moralement impossibles à distinguer». Comme on s’y attendait, l’argument est intéressant mais mal fondé. Il n’est donc pas impossible d’être moral. (shrink)

Ted Sider’s Proportionality of Justice condition requires that any two moral agents instantiating nearly the same moral state be treated in nearly the same way. I provide a countermodel in supervaluation semantics to the proportionality of justice condition. It is possible that moral agents S and S' are in nearly the same moral state, S' is beyond all redemption and S is not. It is consistent with perfect justice then that moral agents that are not beyond redemption go determinately to (...) heaven and moral agents that are beyond all redemption go determinately to hell. I conclude that moral agents that are in nearly the same moral state may be treated in very unequal ways. (shrink)

In this article the standard philosophical method involving intuition-driven conceptual analysis is challenged in a new way. This orthodox approach to philosophy takes analysanda to be the specifications of the content of concepts in the form of sets of necessary and sufficient conditions. Here it is argued that there is no adequate account of what necessary and sufficient conditions are. So, the targets of applications of the standard philosophical method so understood are not sufficiently well understood for this method to (...) be dependable. (shrink)

This paper challenges Williamson's "E = K" thesis on the basis of evidential practice. The main point is that most evidence is only approximately true and so cannot be known if knowledge is factive.

What are the properties of composite objects, and how do the properties of composite objects and the properties of their proper parts relate to one another? The answers to these questions depend upon which view of composition one adopts. One view, which I call the orthodox view, is that composite objects are numerically distinct from their proper parts, individually and collectively. Another view, known as composition as identity, is that composite objects are numerically identical to their proper parts, taken together. (...) I argue that the orthodox view entails that the intuitive picture of composite objects and their properties that most accept is false. Not so for composition as identity. I also show that all of the available alternatives face serious difficulties. This puts composition as identity at an advantage over the orthodox view, at least when it comes to accounting for the properties of composite objects. (shrink)

This paper concerns a distinction between circumstantial truths that hold because of the circumstances and acircumstantial truths that hold regardless of, or transcend, the circumstances. Previous discussions of the distinction tended to focus on its applications, such as to modality, logical truth, and essence. This paper focuses on developing the distinction largely, but not entirely, in abstraction from its potential applications. As such, the paper’s main contribution is to further clarify the distinction itself. An indirect contribution is to help guide (...) its future applications. (shrink)

In a recent paper Shieva Kleinschmidt has argued that if certain scenarios involving extended simple regions are possible (so-called ‘Place Cases’), then no logic of location with only one primitive locative notion (i.e., no ‘parsimonious logic of location’) will suffice to describe all of the locative possibilities. Since almost all existing logics of location are parsimonious (and apparently for good reason) the argument is a considerable obstacle to the development of a satisfactory logic of location. Kleinschmidt suggests that the best (...) way out of the difficulty is to deny the possibility of Place Cases by denying that extended simple regions are possible. I argue that much the same problem arises even in cases not involving extended simple regions or indeed exotic regions of any kind. Thus, simply denying the possibility of extended simple regions will not save parsimonious logics of location. (shrink)

The Oxford Handbook of Metaphysics offers the most authoritative and compelling guide to this diverse and fertile field of philosophy. Twenty-four of the world's most distinguished specialists provide brand-new essays about 'what there is': what kinds of things there are, and what relations hold among entities falling under various categories. They give the latest word on such topics as identity, modality, time, causation, persons and minds, freedom, and vagueness. The Handbook's unrivaled breadth and depth make it the definitive reference work (...) for students and academics across the philosophical spectrum. (shrink)

The social world contains institutions, groups, objects, and more. This essay explores a puzzle about the essences of social items. There is widespread consensus against social essences because of problematic presuppositions often made about them. But it is argued that essence can be freed from these presuppositions and their problems. Even so, a puzzle still arises. In a Platonic spirit, essences in general seem detached from the world. In an Aristotelian spirit, social essences in particular seem embedded in the world. (...) The puzzle is that these inclinations are individually plausible but jointly incompatible. The essay has four aims: to clarify and refine the puzzle; to explore the puzzle's implications for essence in general and for social essences in particular; to illustrate the fruitfulness of the general distinction between detached and embedded; and to develop this distinction to sketch a novel solution to the puzzle. (shrink)

In this paper it is argued that three of the most prominent theories of conditional acceptance face very serious problems. David Lewis' concept of imaging, the Ramsey test and Jonathan Bennett's recent hybrid view all face viscious regresses, or they either employ unanalyzed components or depend upon an implausibly strong version of doxastic voluntarism.

Following Nancy Cartwright and others, I suggest that most (if not all) theories incorporate, or depend on, one or more idealizing assumptions. I then argue that such theories ought to be regimented as counterfactuals, the antecedents of which are simplifying assumptions. If this account of the logic form of theories is granted, then a serious problem arises for Bayesians concerning the prior probabilities of theories that have counterfactual form. If no such probabilities can be assigned, the the posterior probabilities will (...) be undefined, as the latter are defined in terms of the former. I argue here that the most plausible attempts to address the problem of probabilities of conditionals fail to help Bayesians, and, hence, that Bayesians are faced with a new problem. In so far as these proposed solutions fail, I argue that Bayesians must give up Bayesianism or accept the counterintuitive view that no theories that incorporate any idealizations have ever really been confirmed to any extent whatsoever. Moreover, as it appears that the latter horn of this dilemma is highly implausible, we are left with the conclusion that Bayesianism should be rejected, at least as it stands. (shrink)

This paper contains a critical examination of the prospects for analyses of knowledge that weaken the factivity condition such that knowledge implies approximate truth.

This paper challenges the soundness of an argument given in support of a Ramseyan analysis of belief defended by Dokic and Engel in their 2001 book.

This paper explores the prospects of combining two views. The first view is metaphysical rationalism : all things have an explanation. The second view is metaphysical essentialism: there are real essences. The exploration is motivated by a conflict between the views. Metaphysical essentialism posits facts about essences. Metaphysical rationalism demands explanations for all facts. But facts about essences appear to resist explanation. I consider two solutions to the conflict. Exemption solutions attempt to exempt facts about essences from the demand for (...) explanation. Explanation solutions attempt to explain facts about essences. I argue that exemption solutions are less promising than explanation solutions. I then consider how explanation solutions might be developed. I suggest that a “generative” approach is most promising. I tentatively conclude that the prospects for combining metaphysical rationalism and metaphysical essentialism turn on the viability of a generative approach. This sets the agenda for defending the combination as well as the more general project of explaining essences. (shrink)

Knowledge ascriptions of the form ‘S knows that p’ are a central area of research in philosophy. But why do humans think and talk about knowledge? What are knowledge ascriptions for? This article surveys a variety of proposals about the role of knowledge ascriptions and attempts to provide a unified account of these seemingly distinct views.

This paper contains an argument to the effect that possible worlds semantics renders semantic knowledge impossible, no matter what ontological interpretation is given to possible worlds. The essential contention made is that possible worlds semantic knowledge is unsafe and this is shown by a parallel with the preface paradox.

Following the standard practice in sociology, cultural anthropology and history, sociologists, historians of science and some philosophers of science define scientific communities as groups with shared beliefs, values and practices. In this paper it is argued that in real cases the beliefs of the members of such communities often vary significantly in important ways. This has rather dire implications for the convergence defense against the charge of the excessive subjectivity of subjective Bayesianism because that defense requires that communities of Bayesian (...) inquirers share a significant set of modal beliefs. The important implication is then that given the actual variation in modal beliefs across individuals, either Bayesians cannot claim that actual theories have been objectively confirmed or they must accept that such theories have been confirmed relative only to epistemically insignificant communities. (shrink)

This paper is a response to Baumann's comments on "Can Knowledge Really be Non-fative?" In this paper Baumann's suggestions for how those who deny the factivty of knowledge might deal with the argument from inconsistency and explosion are addressed.

This paper shows how the availability heuristic can be used to justify inference to the best explanation in such a way that van Fraassen's infamous "best of a bad lot" objection can be adroitly avoided. With this end in mind, a dynamic and contextual version of the erotetic model of explanation sufficient to ground this response is presented and defended.

In this paper significant challenges are raised with respect to the view that explanation essentially involves unification. These objections are raised specifically with respect to the well-known versions of unificationism developed and defended by Michael Friedman and Philip Kitcher. The objections involve the explanatory regress argument and the concepts of reduction and scientific understanding. Essentially, the contention made here is that these versions of unificationism wrongly assume that reduction secures understanding.

The physicalist credo is that the world is physical. But some phenomena, such as minds, morals, and mathematics, appear to be nonphysical. While an uncompromising physicalism would reject these, a conciliatory physicalism needn’t if it can account for them in terms of an underlying physical basis. Any such account must refer to the nonphysical. But won’t this unavoidable reference to the nonphysical conflict with the physicalist credo? This essay aims to clarify this problem and introduce a novel solution that relies (...) on a distinction between “circumstantial” facts that are based in the circumstances and “acircumstantial” facts that are not. This is used in two ways. First, physicalism is restricted to circumstantial facts: only they must have a physical basis that does not refer to the nonphysical. Second, facts accounting for the nonphysical are not restricted to the circumstantial: they may refer to the nonphysical if they are acircumstantial. Facts about how the physical accounts for the nonphysical therefore do not conflict with the physicalist’s credo. This provides a credible answer to what physicalism could be. (shrink)

This chapter will discuss the relation of physicalism to social ontology, and explores problems that social ontology raises for physicalism. Physicalism is often understood to be the view that all facts—the social ones included—are physical facts, or at least are exhaustively determined by physical facts. While this view is widely endorsed, social phenomena challenge physicalism in several ways, both challenging the coherence of claims of physicalism and raising potential counterexamples.

In this paper, I outline the ways that reification as a pathology of what I call “cybernetic society” shapes the fundamental structures of the self and our shared social reality. Whereas the classical theory of reification was a diagnostic attempt to understand the failure of class consciousness, I believe we must push this thesis further to show how is fundamentally an ontological and not a merely cognitive or epistemic concern. By this I mean that it is a pathology of consciousness (...) as well as social praxis and, as such, infects the ontological substrates of social reality. In effect, reification is a collective rather than merely subjective phenomenon. I explore this dialectic between our subjective and social dimensions of being to show how reification actively shapes self and world. I end with a discussion of how this theory of reification as an ontological concept can be used to overcome it via what I term “ontological coherence,” or the capacity of the self to reflect dialectically on the shapes of sociality that one inhabits, opening it up to evaluative reflection and critique. (shrink)

The main question addressed in this paper is whether some false sentences can constitute evidence for the truth of other propositions. In this paper it is argued that there are good reasons to suspect that at least some false propositions can constitute evidence for the truth of certain other contingent propositions. The paper also introduces a novel condition concerning propositions that constitute evidence that explains a ubiquitous evidential practice and it contains a defense of a particular condition concerning the possession (...) of evidence. The core position adopted here then is that false propositions that are approximately true reports of measurements can constitute evidence for the truth of other propositions. So, it will be argued that evidence is only quasi-factive in this very specific sense. (shrink)

This paper introduces two new paradoxes for standard deontic logic (SDL). They are importantly related to, but distinct from Ross' paradox. These two new paradoxes for SDL are the simple weakening paradox and the complex weakening paradox. Both of these paradoxes arise in virtue of the underlaying logic of SDL and are consequences of the fact that SDL incorporates the principle known as weakening. These two paradoxes then show that SDL has counter-intuitive implications related to disjunctive obligations that arise in (...) virtue of deontic weakening and in virtue of decisions concerning how to discharge such disjunctive obligations. The main result here is then that theorem T1 is a problematic component of SDL that needs to be addressed. (shrink)

Although epistasis is at the center of the Fisher-Wright debate, biologists not involved in the controversy are often unaware that there are actually two different formal definitions of epistasis. We compare concepts of genetic independence in the two theoretical traditions of evolutionary genetics, population genetics and quantitative genetics, and show how independence of gene action (represented by the multiplicative model of population genetics) can be different from the absence of gene interaction (represented by the linear additive model of quantitative genetics). (...) The two formulations converge with weak selection but not with strong selection or, for multiple loci, when the aggregated interaction terms are not negligible. As a result of the different formulations of gene interaction, the presence or absence of linkage disequilibrium,/D/, does not necessarily indicate the presence or absence of fitness epistasis. Indeed, linkage disequilibrium is generated in ‘additive’ models in quantitative genetics whenever two (or more) loci experience simultaneous selection. As a research strategy, it is often practical, for theoretical or experimental reasons, to minimize gene interaction by assuming independence of gene action in regard to fitness, or by assuming linear additive effects of multiple loci on a phenotype. However, minimizing the role of epistasis in theoretical investigations hinders our understanding of the origins of diversity and the evolution of complex phenotypes. (shrink)

This is an editorial introduction to a special issue of Acta Analytica on epistemic luck.

This paper explores two related questions in late Athenian and Alexandrian Neoplatonism. First, how can a philosopher contemplate the eternal Forms while engaging in practical agency in the world? Second, do Neoplatonists provide a consistent account of the philosopher’s progress through the ‘stages of virtue’ (βαθμοί τῶν ἀρετῶν), the conceptual structure that underpins late antique philosophical curricula and hagiography? These questions interact, I suggest, because later Platonists appeal to the stages of virtue and divine maniai (βαθμοί τῶν μανίων) to explain (...) the philosopher’s ability to alternate gracefully between contemplation and embodied agency, and even to engage in both activities at the same moment. I argue that apparently contradictory evidence for the highest stages of virtue can be reconciled satisfactorily, shedding light on two models of ethical and perceptual transformation that are consistent throughout later Neoplatonism. In the first, 'painterly' model, we alternate between a vision of the paradigmatic model and its expression in the media of place and time; in the second, 'dancerly' model, we contemplate in action all at once, like a dancer moving to the music. (shrink)