We are addressing this letter to the editors of Philosophical Psychology after reading an article they decided to publish in the recent vol. 33, issue 1. The article is by Nathan Cofnas and is entitled “Research on group differences in intelligence: A defense of free inquiry” (2020). The purpose of our letter is not to invite Cofnas’s contribution into a broader dialogue, but to respectfully voice our concerns about the decision to publish the manuscript, which, in our opinion, fails to (...) meet a range of academic quality standards usually expected of academic publications. (shrink)

This letter addresses the editorial decision to publish the article, “Research on group differences in intelligence: A defense of free inquiry” (Cofnas, 2020). Our letter points out several critical problems with Cofnas's article, which we believe should have either disqualified the manuscript upon submission or been addressed during the review process and resulted in substantial revisions.

In this paper, we consider Noël Carroll’s Content Theory (CT) (2015) and argue that a key problem with CT is that it can be interpreted in two distinct ways: as a descriptive theory of aesthetic experience and as a normative prescriptive theory. Although CT is presented as a descriptive theory of experience, much of what Carroll says implies that CT can also be understood as a theory about how one ought to look at artworks. We argue that when (...) understood as a descriptive theory, CT fails to qualify as a meaningful theory of aesthetic experience. We then interpret the theory prescriptively. Ultimately, this second interpretation is also found lacking: if the aim of the theory is to instruct one on how to view art, it is no longer an attempt to characterize the experience of art. We conclude by arguing that the main flaw in CT is its approach: we cannot meaningfully characterize an experience by enumerating the objects that supposedly cause said experience, and any theory that takes such an approach is likely to be unsuccessful. (shrink)

What is the concept of sense developed by Deleuze in his 1969 Logic of Sense? This paper attempts to answer this question analysing the three dimensions of language that Deleuze isolates: the primary order of noises and intensities ; the secondary order of sense ; and the tertiary organisation of propositions. What renders language possible is that which separates sounds from bodies and organises them into propositions, freeing them for the expressive function. Deleuze argues that it is the dimension of (...) sense that brings about this genesis of language, and he analyses in detail the three syntheses that bring about the production of this surface of sense. Yet Deleuze also distinguishes between two types of non-sense: the nonsense of Lewis Carroll's portmanteau words, which remain ensconced in the dimension of sense, and the more profound nonsense of Antonin Artaud's psychotic scream-breaths, which penetrate the almost unbearable world of the primary order of noise and intensities. In the end, the focus of Logic of Sense is less the surface domain of sense than the primary depth of corporeal intensities. What Deleuze calls a ‘minor’ use of language is nothing other than an intensive use of language that constitutes a principle of metamorphosis. (shrink)

Are science and religion compatible when it comes to understanding cosmology (the origin of the universe), biology (the origin of life and of the human species), ethics, and the human mind (minds, brains, souls, and free will)? Do science and religion occupy non-overlapping magisteria? Is Intelligent Design a scientific theory? How do the various faith traditions view the relationship between science and religion? What, if any, are the limits of scientific explanation? What are the most important open questions, problems, or (...) challenges confronting the relationship between science and religion, and what are the prospects for progress? These and other questions are explored in Science and Religion: 5 Questions--a collection of thirty-three interviews based on 5 questions presented to some of the world's most influential and prominent philosophers, scientists, theologians, apologists, and atheists. Contributions by Simon Blackburn, Susan Blackmore, Sean Carroll, William Lane Craig, William Dembski, Daniel C. Dennett, George F.R. Ellis, Owen Flanagan, Owen Gingerich, Rebecca Newberger Goldstein, John F. Haught, Muzaffar Iqbal, Lawrence Krauss, Colin McGinn, Alister McGrath, Mary Midgley, Seyyed Hossein Nasr, Timothy O'Connor, Massimo Pigliucci, John Polkinghorne, James Randi, Alex Rosenberg, Michael Ruse, Robert John Russell, John Searle, Michael Shermer, Victor J. Stenger, Robert Thurman, Michael Tooley, Charles Townes, Peter van Inwagen, Keith Ward, Rabbi David Wolpe. (shrink)

We consider emergence from the perspective of dynamics: states of a system evolving with time. We focus on the role of a decomposition of wholes into parts, and attempt to characterize relationships between levels without reference to whether higher-level properties are “novel” or “unexpected.” We offer a classification of different varieties of emergence, with and without new ontological elements at higher levels. -/- Submitted to a volume on Real Patterns (Tyler Milhouse, ed.), to be published by MIT Press.

Recent debates in psychopathy studies have articulated concerns about false-positives in assessment and research sampling. These are pressing concerns for research progress, since scientific quality depends on sample quality, that is, if we wish to study psychopathy we must be certain that the individuals we study are, in fact, psychopaths. Thus, if conventional assessment tools yield substantial false-positives, this would explain why central research is laden with discrepancies and nonreplicable findings. This paper draws on moral psychology in order to develop (...) tentative theory-driven exclusion criteria applicable in research sampling. Implementing standardized procedures to discriminate between research participants has the potential to yield more homogenous and discrete samples, a vital prerequisite for research progress in etiology, epidemiology, and treatment strategies. (shrink)

Martin E. Rosenberg -/- The Gift of Silence: Towards an Anthropology of Jazz Improvisation as Neuro-Resistance. -/- ABSTRACT: -/- This essay addresses how the complex processes that occur during jazz improvisation enact behaviors that resemble the logic of gift exchange first described by Marcel Mauss. It is possible to bring to bear structural, sociological, political economical, deconstructive or even ethical approaches to what constitutes gift exchange during the performance of jazz. Yet, I would like to shift from focusing this (...) analysis of jazz improvisation with reference to the language of music as symbolic action (which all of these approaches require), to grounding improvisation in embodied and distributed cognition, the performance of which begins with a ritual gift of silence. By silence, I refer to the embodied, yet shared pure duration as felt synchrony within an individual performer, that extends to the members of an ensemble. Thus, I refer to both aesthetic and micro-political implications of embodied, yet also distributed musical cognition in real time. -/- For jazz musicians, embodied silence becomes the initial condition for processes of cognitive bifurcation. For it is bifurcation that attracts us to jazz in the first place. Here I expand my previous work establishing similarities in the behavior of bifurcating systems in physical and cognitive sciences to the unfolding of ambiguity in real time during improvisation with respect to polyphony, polytonality and polyrhythms in the history of jazz from Charlie Parker to Ornette Coleman. We can therefore re-conceptualize jazz improvisation as a subversive antidote for processes of determination identified in a sub-discipline of cultural studies called “cognitive capitalism.” By examining silence from this anthropological perspective, we can conceive of jazz performance as a ritualized resistance to top-down cognitive control immanent with social and digital networks. The ritual enactment that is jazz improvisation points towards an aesthetics of bifurcation that is simultaneously a micro-politics of neuro-resistance. In other words, I argue that freedom of thought requires freedom from thought as an initial condition. -/- Yet, I emphasize the empirical rather than mystical grounds to this gift of silence. The valorization of silence by jazz musicians is not simply etiquette, an ethics of reciprocity for performers exchanging “riffs,” but an initial condition that jazz performers (and, I would argue, listeners) experience in their bodies, thus linking embodied cognition to a collective field of cultural production that emerges from each embodied individual, and yet also pervades the ensemble in ways reminiscent of feedback loops in complex systems. The recent and remarkable research on music and the brain has demonstrated that it is now possible to describe jazz improvisation as possessing both embodied and distributed cognitive properties. The emergent neuronal ensemble behavior within the individual that is visible in jazz improvisors, discovered by the neuroscientists at Johns Hopkins led by Charles Limb, bears striking resemblance to the interactive behaviors of the jazz ensemble itself. Thus, it is by recourse to recent research by myself and others into the cognitive neuroscience of music generally, and jazz improvisation specifically, that the empirical grounds for an anthropology of neuro-resistance become visible. (shrink)

We have a much better understanding of physics than we do of consciousness. I consider ways in which intrinsically mental aspects of fundamental ontology might induce modifications of the known laws of physics, or whether they could be relevant to accounting for consciousness if no such modifications exist. I suggest that our current knowledge of physics should make us skeptical of hypothetical modifications of the known rules, and that without such modifications it’s hard to imagine how intrinsically mental aspects could (...) play a useful explanatory role. Draft version of a paper submitted to Journal of Consciousness Studies, special issue responding to Philip Goff’s Galileo’s Error: Foundations for a New Science of Consciousness. (shrink)

I defend the extremist position that the fundamental ontology of the world consists of a vector in Hilbert space evolving according to the Schrödinger equation. The laws of physics are determined solely by the energy eigenspectrum of the Hamiltonian. The structure of our observed world, including space and fields living within it, should arise as a higher-level emergent description. I sketch how this might come about, although much work remains to be done.

Panqualityism, recently defended by Sam Coleman, is a variety of Russellian monism on which the categorical properties of fundamental physical entities are qualities, or, in Coleman’s exposition, unconscious qualia. Coleman defends a quotationalist, higher-order thought version of panqualityism. The aim of this paper is, first, to demonstrate that a first-order representationalist panqualityism is also available, and to argue positively in its favor. For it shall become apparent that quotationalist and first-order representationalist panqualityism are, in spite of their close similarities, radically (...) different theories: quotationalist panqualityism locates qualities in the subject of an experience, while first-order panqualityism locates qualities in the world. I argue that this makes quotationalist panqualityism implausible and first-order, representationalist panqualityism a highly natural, elegant, and intuitive theory. (shrink)

The Principle of Sufficient Reason (PSR) holds that, for everything that exists or occurs or holds true, there is a reason why that is the case. I consider three possible ways of relating physics to the PSR: past states as reasons for present states, reasons why the laws of physics take the form that they do, and reasons why there is anything at all. In each case I suggest that the PSR is not the best way of thinking about how (...) and why physics works. -/- Invited reflection for The Principle of Sufficient Reason (Oxford Philosophical Concepts), Eds. F. Amijee and M. Della Rocca (forthcoming 2024). (shrink)

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

Some modern cosmological models predict the appearance of Boltzmann Brains: observers who randomly fluctuate out of a thermal bath rather than naturally evolving from a low-entropy Big Bang. A theory in which most observers are of the Boltzmann Brain type is generally thought to be unacceptable, although opinions differ. I argue that such theories are indeed unacceptable: the real problem is with fluctuations into observers who are locally identical to ordinary observers, and their existence cannot be swept under the rug (...) by a choice of probability distributions over observers. The issue is not that the existence of such observers is ruled out by data, but that the theories that predict them are cognitively unstable: they cannot simultaneously be true and justifiably believed. (shrink)

It is commonplace in discussions of modern cosmology to assert that the early universe began in a special state. Conventionally, cosmologists characterize this fine-tuning in terms of the horizon and flatness problems. I argue that the fine-tuning is real, but these problems aren't the best way to think about it: causal disconnection of separated regions isn't the real problem, and flatness isn't a problem at all. Fine-tuning is better understood in terms of a measure on the space of trajectories: given (...) reasonable conditions in the late universe, the fraction of cosmological histories that were smooth at early times is incredibly tiny. This discussion helps clarify what is required by a complete theory of cosmological initial conditions. (shrink)

We study the conservation of energy, or lack thereof, when measurements are performed in quantum mechanics. The expectation value of the Hamiltonian of a system changes when wave functions collapse in accordance with the standard textbook treatment of quantum measurement, but one might imagine that the change in energy is compensated by the measuring apparatus or environment. We show that this is not true; the change in the energy of a state after measurement can be arbitrarily large, independent of the (...) physical measurement process. In Everettian quantum theory, while the expectation value of the Hamiltonian is conserved for the wave function of the universe, it is not constant within individual worlds. It should therefore be possible to experimentally measure violations of conservation of energy, and we suggest an experimental protocol for doing so. (shrink)

Cosmological models that invoke a multiverse - a collection of unobservable regions of space where conditions are very different from the region around us - are controversial, on the grounds that unobservable phenomena shouldn't play a crucial role in legitimate scientific theories. I argue that the way we evaluate multiverse models is precisely the same as the way we evaluate any other models, on the basis of abduction, Bayesian inference, and empirical success. There is no scientifically respectable way to do (...) cosmology without taking into account different possibilities for what the universe might be like outside our horizon. Multiverse theories are utterly conventionally scientific, even if evaluating them can be difficult in practice. (shrink)

Some people oppose abortion on the grounds that fetuses have full moral status and thus a right to not be killed. We argue that special obligations that hold between mother and fetus also hold between parents and their children. We argue that if these special obligations necessitate the sacrifice of bodily autonomy in the case of abortion, then they also necessitate the sacrifice of bodily autonomy in the case of organ donation. If we accept the argument that it is obligatory (...) to override a woman’s bodily autonomy for the sake of an unborn child’s survival, we must continue to override the bodily autonomy of parents to ensure the survival of their living children, until the parent no longer has a special obligation to their child to the same degree as their special obligation to the fetus. And if the life of a child is truly more important than the bodily autonomy of its parents, as must be the case to force women to carry unwanted pregnancies to term, this should remain true until such a time that their children are no longer considered their responsibility. Thus, parity of reasoning suggests that policies compelling the gestation of a fetus should be accompanied by policies compelling organ donation. (shrink)

We argued in a recent issue of this journal that if abortion is restricted,1 then there are parallel obligations for parents to donate body parts to their children. The strength of this obligation to donate is proportional to the strength of the abortion restrictions. If abortion is never permissible, then a parent must always donate any organ if they are a match. If abortion is sometimes permissible and sometimes not, then organ donation is sometimes obligatory and sometimes not. Our argument (...) was based on the following ideas: (a) that a fetus has full moral status, (b) that parents have special obligations to their offspring, fetus or not, and (c) that this special obligation is to protect them. The result is the conclusion that abortion restrictivists cannot also consistently deny that organ donation should be compulsory. (shrink)

We study the question of how to decompose Hilbert space into a preferred tensor-product factorization without any pre-existing structure other than a Hamiltonian operator, in particular the case of a bipartite decomposition into "system" and "environment." Such a decomposition can be defined by looking for subsystems that exhibit quasi-classical behavior. The correct decomposition is one in which pointer states of the system are relatively robust against environmental monitoring (their entanglement with the environment does not continually and dramatically increase) and remain (...) localized around approximately-classical trajectories. We present an in-principle algorithm for finding such a decomposition by minimizing a combination of entanglement growth and internal spreading of the system. Both of these properties are related to locality in different ways. This formalism could be relevant to the emergence of spacetime from quantum entanglement. (shrink)

It seems natural to ask why the universe exists at all. Modern physics suggests that the universe can exist all by itself as a self-contained system, without anything external to create or sustain it. But there might not be an absolute answer to why it exists. I argue that any attempt to account for the existence of something rather than nothing must ultimately bottom out in a set of brute facts; the universe simply is, without ultimate cause or explanation.

Effective Field Theory (EFT) is the successful paradigm underlying modern theoretical physics, including the "Core Theory" of the Standard Model of particle physics plus Einstein's general relativity. I will argue that EFT grants us a unique insight: each EFT model comes with a built-in specification of its domain of applicability. Hence, once a model is tested within some domain (of energies and interaction strengths), we can be confident that it will continue to be accurate within that domain. Currently, the Core (...) Theory has been tested in regimes that include all of the energy scales relevant to the physics of everyday life (biology, chemistry, technology, etc.). Therefore, we have reason to be confident that the laws of physics underlying the phenomena of everyday life are completely known. (shrink)

When Adam Smith published his celebrated writings on economics and moral philosophy he famously referred to the operation of an invisible hand. Adam Smith's Political Philosophy makes visible the invisible hand by examining its significance in Smith's political philosophy and relating it to similar concepts used by other philosophers, revealing a distinctive approach to social theory that stresses the significance of the unintended consequences of human action. This book introduces greater conceptual clarity to the discussion of the (...) invisible hand and the related concept of unintended order in the work of Smith and in political theory more generally. By examining the application of spontaneous order ideas in the work of Smith, Hume, Hayek and Popper, Adam Smith's Political Philosophy traces similarities in approach and from these builds a conceptual, composite model of an invisible hand argument. While setting out a clear model of the idea of spontaneous order the book also builds the case for using the idea of spontaneous order as an explanatory social theory, with chapters on its application in the fields of science, moral philosophy, law and government. (shrink)

Advances in emotion and affective science have yet to translate routinely into psychiatric research and practice. This is unfortunate since emotion and affect are fundamental components of many psychiatric conditions. Rectifying this lack of interdisciplinary integration could thus be a potential avenue for improving psychiatric diagnosis and treatment. In this contribution, we propose and discuss an ontological framework for explicitly capturing the complex interrelations between affective entities and psychiatric disorders, in order to facilitate mapping and integration between affective science and (...) psychiatric diagnostics. We build on and enhance the categorisation of emotion, affect and mood within the previously developed Emotion Ontology, and that of psychiatric disorders in the Mental Disease Ontology. This effort further draws on developments in formal ontology regarding the distinction between normal and abnormal in order to formalize the interconnections. This operational semantic framework is relevant for applications including clarifying psychiatric diagnostic categories, clinical information systems, and the integration and translation of research results across disciplines. (shrink)

This paper seeks to resolve a fairly simple question in ethics: Why do seemingly reasonable people disagree about ethical problems? My paper seeks both to analyze this question and attempts to find a solution. My premise is that disagreement happens because of differences in hierarchical value ranking, or quite simply because some problems are more important to some people than others. Theories of choice, however, influenced by concepts such as "freedom of choice," conceal the hierarchical nature of our choices, leading (...) to confusion over the nature and degree of our ethical disagreements. I propose then that ethical disagreements can be reduced when we understand hierarchy as an essential element in moral choice theory. (shrink)

We provide a derivation of the Born Rule in the context of the Everett (Many-Worlds) approach to quantum mechanics. Our argument is based on the idea of self-locating uncertainty: in the period between the wave function branching via decoherence and an observer registering the outcome of the measurement, that observer can know the state of the universe precisely without knowing which branch they are on. We show that there is a uniquely rational way to apportion credence in such cases, which (...) leads directly to the Born Rule. Our analysis generalizes straightforwardly to cases of combined classical and quantum self-locating uncertainty, as in the cosmological multiverse. (shrink)

The prescriptive force of methodological rules rests, I argue, on the acceptance of scientific theories; that of the most general methodological rules rests on theories in the philosophy of science, which differ from theories in the several sciences only in generality and abstraction. I illustrate these claims by reference to methodological disputes in social science and among philosophers of science. My conclusions substantiate those of Laudan except that I argue for the existence of transtheoretical goals common to all scientists and (...) concrete enough actually to have bearing on methodology. And I argue that Laudan is committed to such goals himself, willy nilly. (shrink)

In Morality & Mathematics, Justin Clarke-Doane argues that it is hard to imagine being "a realist about, for example, the standard model of particle physics, but not about mathematics." I try to explain how that seems very possible from the perspective of a physicist. What is real is the physical world; mathematics starts from descriptions of the natural world and extrapolates from there, but that extrapolation does not imply any independent reality. -/- Submitted to an Analysis Reviews symposium on Clarke-Doane's (...) Morality & Mathematics. (shrink)

I ask whether what we know about the universe from modern physics and cosmology, including fine-tuning, provides compelling evidence for the existence of God, and answer largely in the negative.

A repository of clinically associated Staphylococcus aureus (Sa) isolates is used to semi‐automatically generate a set of application ontologies for specific subfamilies of Sa‐related disease. Each such application ontology is compatible with the Infectious Disease Ontology (IDO) and uses resources from the Open Biomedical Ontology (OBO) Foundry. The set of application ontologies forms a lattice structure beneath the IDO‐Core and IDO‐extension reference ontologies. We show how this lattice can be used to define a strategy for the construction of a new (...) taxonomy of infectious disease incorporating genetic, molecular, and clinical data. We also outline how faceted browsing and query of annotated data is supported using a lattice application ontology. (shrink)

The goal of this essay is to explain how Wittgenstein's philosophy may be helpful for understanding and addressing challenges to cross-cultural communication in educational contexts. In particular, the notions of “hinge,” “intellectual distance,” and “grounds” from On Certainty will be helpful for identifying cultural differences. Wittgenstein's dialogical conception of philosophy in Philosophical Investigations will be helpful for addressing that cultural difference in conversation. While here can be no panacea to address all potential sources of confusion, Wittgenstein's philosophy has strong resources (...) that are helpful for curbing some of our human tendencies to misunderstand other people. (shrink)

Philosophers and theologians acknowledge that "fideism" is difficult to define but rarely agree on what the best characterization of the term is. In this article, I investigate the history of use of "fideism" to explore why its meaning has been so contested and thus why it has not always been helpful for resolving philosophical problems. I trace the use of the term from its origins in French theology to its current uses in philosophy and theology, concluding that "fideism" is helpful (...) in resolving philosophical problems only when philosophers scrupulously acknowledge the tradition of use that informs their understanding of the word. (shrink)

Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...) will become correspondingly difficult to maintain. While descriptive semantic representations are certainly a necessary component to any adequate ontology-based system, so long as ontology engineers rely solely on semantic information, without a sound ontological theory informing their modeling decisions, this goal will surely remain out of reach. In this paper we describe how Language and Computing nv (L&C), along with The Institute for Formal Ontology and Medical Information Sciences (IFOMIS), are working towards developing and implementing just such a theory, combining the open software architecture of L&C’s LinkSuiteTM with the philosophical rigor of IFOMIS’s Basic Formal Ontology. In this way we aim to move beyond the more or less simple controlled vocabularies that have dominated the industry to date. (shrink)

Disgust has been a perennial feature of art from medieval visions of hell to postmodern travesties. The purpose of this chapter is to chart various ways in which disgust functions in artworks both in terms of content and style, canvassing cases in which the content and/or style is literally disgusting in contrast to cases where the disgust serves to characterize the content, often for moral or political or broader cultural purposes.

Recently two distinct forms of rule-utilitarianism have been introduced that differ on how to measure the consequences of rules. Brad Hooker advocates fixed-rate rule-utilitarianism, while Michael Ridge advocates variable-rate rule-utilitarianism. I argue that both of these are inferior to a new proposal, optimum-rate rule-utilitarianism. According to optimum-rate rule-utilitarianism, an ideal code is the code whose optimum acceptance level is no lower than that of any alternative code. I then argue that all three forms of rule-utilitarianism fall prey to two fatal (...) problems that leave us without any viable form of rule-utilitarianism. (shrink)

Ontologies formally represent reality in a way that limits ambiguity and facilitates automated reasoning and data fusion, but is often daunting to the non-technical user. Thus, many researchers have endeavored to hide the formal syntax and semantics of ontologies behind the constructs of Controlled Natural Languages (CNLs), which retain the formal properties of ontologies while simultaneously presenting that information in a comprehensible natural language format. In this paper, we build upon previous work in this field by evaluating prospects of implementing (...) International Technology Alliance Controlled English (ITACE) as a middleware for ontology editing. We also discuss at length a prototype of a natural language conversational interface application designed to facilitate ontology editing via the formulation of CNL constructs. (shrink)

Despite the growth in research in philosophy of religion over the past several decades, recent years have seen a number of critical studies of this subfield in an effort to redirect the methods and topics of inquiry. This article argues that in addition to problems of religious parochialism described by critics such as Wesley Wildman, the subfield is facing a problem of relevance. In responding to this problem, it suggests that philosophers of religion should do three things: first, be critically (...) self-aware about their aims of inquiry; second, investigate concepts used by other philosophers, scientists, and religious studies scholars to identify and dispel confusion about religions; and third, following the model of applied ethics, work to clarify concepts and advance arguments of contemporary practical urgency. (shrink)

Referent Tracking (RT) advocates the use of instance unique identifiers to refer to the entities comprising the subject matter of patient health records. RT promises many benefits to those who use health record data to improve patient care. To further the adoption of the paradigm we provide an illustration of how data from an EHR application needs to be decomposed in order to make it accord with the tenets of RT. We describe the ontological principles on which this decomposition is (...) based in order to allow integration efforts to be applied in similar ways to other EHR applications. We find that an ordinary statement from an EHR contains a surprising amount of “hidden” data that are only revealed by its decomposition according to these principles. (shrink)

The Neurological Disease Ontology (ND) is being developed to provide a comprehensive framework for the representation of neurological diseases (Diehl et al., 2013). ND utilizes the model established by the Ontology for General Medical Science (OGMS) for the representation of entities in medicine and disease (Scheuermann et al., 2009). The goal of ND is to include information for each disease concerning its molecular, genetic, and environmental origins, the processes involved in its etiology and realization, as well as its clinical presentation (...) including signs and symptoms. (shrink)

Recent years have seen an increasing amount of studies of the history of the term “religion” and how it figures in conceptions of “the secular” and of cultural differences generally. A recurrent theme in these studies is that “religion” carries associations with Protestant Christianity and thus is not as universal a category as it might appear. The aim of this paper is to explore some resources in Wittgenstein’s philosophy to obtain greater clarity about the contexts of ascription of religion-status to (...) various phenomena and thus to gain perspective on claims made by scholars who investigate the genealogy of the term. While there is good reason to be circumspect about uncritical use of the term “religion” (no less in philosophizing about religions or conducting interreligious dialogue), I argue that instead of abandoning the term or proffering a critical theory of religion, investigation of ascriptions of religion will help philosophers to perceive more clearly the social dynamics that have led to some- one or thing being called religious and thus avoid equivocations that could obstruct the ends of philosophical inquiry or dialogue. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s LinKBase® (...) is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

We argue that there is significant evidence for reconsidering the possibility that moral judgment constitutes a distinctive category of judgment. We begin by reviewing evidence and arguments from neuroscience and philosophy that seem to indicate that a diversity of brain processes result in verdicts that we ordinarily consider “moral judgments”. We argue that if these findings are correct, this is plausible reason for doubting that all moral judgments necessarily share common features: if diverse brain processes give rise to what we (...) refer to as “moral judgments”, then we have reason to suspect that these judgments may have different features. After advancing this argument, we show that giving up the unity of moral judgment seems to effectively dissolve the internalism/externalism debate concerning motivation within the field of metaethics. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. Finally, (...) we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

The truthmaker theory rests on the thesis that the link between a true judgment and that in the world to which it corresponds is not a one-to-one but rather a one-to-many relation. An analogous thesis in relation to the link between a singular term and that in the world to which it refers is already widely accepted. This is the thesis to the effect that singular reference is marked by vagueness of a sort that is best understood in supervaluationist terms. (...) In what follows we show that the supervaluationist approach to singular reference, when wedded to the truthmaker idea, yields a framework of surprising power, which offers a uniform set of solutions to a range of problems regarding identity, reference and knowledge, problems which have hitherto been dealt with on an ad hoc basis. (shrink)

Ontological realism aims at the development of high quality ontologies that faithfully represent what is general in reality and to use these ontologies to render heterogeneous data collections comparable. To achieve this second goal for clinical research datasets presupposes not merely (1) that the requisite ontologies already exist, but also (2) that the datasets in question are faithful to reality in the dual sense that (a) they denote only particulars and relationships between particulars that do in fact exist and (b) (...) they do this in terms of the types and type-level relationships described in these ontologies. While much attention has been devoted to (1), work on (2), which is the topic of this paper, is comparatively rare. Using Referent Tracking as basis, we describe a technical data wrangling strategy which consists in creating for each dataset a template that, when applied to each particular record in the dataset, leads to the generation of a collection of Referent Tracking Tuples (RTT) built out of unique identifiers for the entities described by means of the data items in the record. The proposed strategy is based on (i) the distinction between data and what data are about, and (ii) the explicit descriptions of portions of reality which RTTs provide and which range not only over the particulars described by data items in a dataset, but also over these data items themselves. This last feature allows us to describe particulars that are only implicitly referred to by the dataset; to provide information about correspondences between data items in a dataset; and to assert which data items are unjustifiably or redundantly present in or absent from the dataset. The approach has been tested on a dataset collected from patients seeking treatment for orofacial pain at two German universities and made available for the NIDCR-funded OPMQoL project. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.