I propose and defend a novel view called “de se consequentialism,” which is noteworthy for two reasons. First, it demonstrates—contra Doug Portmore, Mark Schroeder, Campbell Brown, and Michael Smith, among others—that agent-neutral consequentialism is consistent with agent-centered constraints. Second, it clarifies the nature of agent-centered constraints, thereby meriting attention from even dedicated nonconsequentialists. Scrutiny reveals that moral theories in general, whether consequentialist or not, incorporate constraints by assessing states in a first-personal guise. Consequently, de se consequentialism enacts constraints through (...) the very same feature that nonconsequentialist theories do. (shrink)

We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge (...) 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. (shrink)

Report on Dagstuhl Seminar 07132, Schloss Dagstuhl, March 27-30 , 2007.

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. (shrink)

The Planteome project provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology, and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides (...) access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. (shrink)

In this dialogue, we discuss the contrast between inexorable physical laws and the semiotic freedom of life. We agree that material and symbolic structures require complementary descriptions, as do the many hierarchical levels of their organizations. We try to clarify our concepts of laws, constraints, rules, symbols, memory, interpreters, and semiotic control. We briefly describe our different personal backgrounds that led us to a biosemiotic approach, and we speculate on the future directions of biosemiotics.

Next SectionThis article argues against two dominant accounts of the nature of nostalgia. These views assume that nostalgia depends, in some way, on comparing a present situation with a past one. However, neither does justice to the full range of recognizably nostalgic experiences available to us – in particular, ‘Proustian’ nostalgia directed at involuntary autobiographical memories. Therefore, the accounts in question fail. I conclude by considering an evaluative puzzle raised by Proustian nostalgia when it is directed at memories that the (...) nostalgist herself regards as non-veridical. (shrink)

Our approach is based on a tri-partite method of integrating psychodynamic hypotheses, cognitive subliminal processes, and psychophysiological alpha power measures. We present ten social phobic subjects with three individually selected groups of words representing unconscious conflict, conscious symptom experience, and Osgood Semantic negative valence words used as a control word group. The unconscious conflict and conscious symptom words, presented subliminally and supraliminally, act as primes preceding the conscious symptom and control words presented as supraliminal targets. With alpha power as a (...) marker of inhibitory brain activity, we show that unconscious conflict primes, only when presented subliminally, have a unique inhibitory effect on conscious symptom targets. This effect is absent when the unconscious conflict primes are presented supraliminally, or when the target is the control words. Unconscious conflict prime effects were found to correlate with a measure of repressiveness in a similar previous study (Shevrin et al., 1992, 1996). Conscious symptom primes have no inhibitory effect when presented subliminally. Inhibitory effects with conscious symptom primes are present, but only when the primes are supraliminal, and they did not correlate with repressiveness in a previous study (Shevrin et al., 1992, 1996). We conclude that while the inhibition following supraliminal conscious symptom primes is due to conscious threat bias, the inhibition following subliminal unconscious conflict primes provides a neurological blueprint for dynamic repression: it is only activated subliminally by an individual's unconscious conflict and has an inhibitory effect specific only to the conscious symptom. These novel findings constitute neuroscientific evidence for the psychoanalytic concepts of unconscious conflict and repression, while extending neuroscience theory and methods into the realm of personal, psychological meaning. (shrink)

REMARKS ON EVOLUTION AND TIME-SCALES, Graham Cairns-Smith; HODGSON'S BLACK BOX, Thomas Clark; DO HODGSON'S PROPOSITIONS UNIQUELY CHARACTERIZE FREE WILL?, Ravi Gomatam; WHAT SHOULD WE RETAIN FROM A PLAIN PERSON'S CONCEPT OF FREE WILL?, Gilberto Gomes; ISOLATING DISPARATE CHALLENGES TO HODGSON'S ACCOUNT OF FREE WILL, Liberty Jaswal; FREE AGENCY AND LAWS OF NATURE, Robert Kane; SCIENCE VERSUS REALIZATION OF VALUE, NOT DETERMINISM VERSUS CHOICE, Nicholas Maxwell; COMMENTS ON HODGSON, J.J.C. Smart; THE VIEW FROM WITHIN, Sean Spence; COMMENTARY ON HODGSON, Henry (...) Stapp. (shrink)

This review essay assesses Michael Jackson’s ongoing project of staging an encounter between anthropology and philosophy in two books: Lifeworlds (2013) and As Wide as the World Is Wise (2016). Considering his philosophical enrichment of ethnographic theory and method, this essay addresses foundational questions about the prospects and practices of interdisciplinary engagement. It also suggests future avenues for continued dialogue between philosophy and anthropology.

: In the epistemology of the late Wittgenstein, a central place is given to the notion of the hinge: an arational commitment that provides a foundation of some sort for the rest of our beliefs. Quasi-fideism is an approach to the epistemology of religion that argues that religious belief is on an epistemic par with other sorts of belief inasmuch as religious and non-religious beliefs all rely on hinges. I consider in this paper what it takes to find the appropriate (...) hinge for a quasi-fideist approach to the epistemology of religion. (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)

This article presents a case for human rights feminism as providing us with an effective, but too often under-recognized model for achieving equality in our society. From out of the context of recent feminism, with specific focus on Judith Butler, the author argues that the move to universal human rights is compatible with the critical tradition of identity politics as a means of realizing the goal of gender equality.

I argue that the self is simple metaphysically, whilst being complex psychologically and that the persona that links these moments might be dubbed ”creativity’ or ”imagination’. This theory is trinitarian because it ascribes to the self these three ”features’ or ”moments’ and they bear at least some analogy with the Persons of the Trinity, as understood within the neo- platonic, Augustinian tradition.

The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)

Here we present what we believe is a novel account of what languages are, along with an axiomatically rich representation of languages and language-related data that is based on this account. We propose an account of languages as aggregates of dispositions distributed across aggregates of persons, and in doing so we address linguistic competences and the processes that realize them. This paves the way for representing additional types of language-related entities. Like demographic data of other sorts, data about languages may (...) be of use to researchers in a number of areas, including biomedical research. Data on the languages used in clinical encounters are typically included in medical records, and capture an important factor in patient-provider interactions. Like many types of patient and demographic data, data on a person’s preferred and primary languages are organized in different ways by different systems. This can be a barrier to data integration. We believe that a robust framework for representing language in general and preferred and primary language in particular – which has been lacking in ontologies thus far – can promote more successful integration of language-related data from disparate data sources. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users. (shrink)

The chapter introduces and characterizes the notion of fittingness. It charts the history of the relation and its relevance to contemporary debates in normative and metanormative philosophy and proceeds to survey issues to do with fittingness covered in the volume’s chapters, including the nature and epistemology of fittingness, the relations between fittingness and reasons, the normativity of fittingness, fittingness and value theory, and the role of fittingness in theorizing about responsibility. The chapter concludes with a brief discussion of issues to (...) do with fittingness that aren’t covered extensively by the volume’s chapters in order to indicate avenues for further research. (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)

While intimately familiar, gender eludes theorizing. We argue that well-known challenges to gender’s analysis originate in a subtle ambiguity: questions about gender sometimes express questions about gender categories themselves (e.g., womanhood, manhood, and so on), while at other times expressing questions about what makes someone a member of these categories. Distinguishing these questions accentuates gender’s connections to morality, making a novel “antirealist” view of gender, or as we call it, “unrealist” view, especially natural. Gender’s relations to identity, sex, and social (...) position are illuminated along the way. Taking cues from both historical and contemporary debates in metaethics about the roles that attitudes can play in metaphysical and semantic analysis, we introduce and begin developing a comprehensive non-ameliorative framework for explicating gender’s nature and our thought and talk about it. In a slogan, on the view we defend, you belong to the gender category to which you intrinsically desire to belong. (shrink)

Many theistic religions place a high value on faith in God and some traditions regard it as a virtue. However, philosophers commonly assign either very little value to faith in God or significant negative value, or even view it as a vice. Progress in assessing whether and when faith in God can be valuable or disvaluable, virtuous or vicious, rational or irrational, or otherwise apt or inapt requires understanding what faith in God is. This Special Issue on the normative appraisal (...) of faith in God for Religious Studies includes nine articles, from a diverse range of perspectives, which explore issues related to the core questions ‘What is faith in God?’ and ‘What normative questions about faith in God need to be addressed?’ In this Introduction, we briefly introduce each article. (shrink)

It has recently been argued that when one conducts an inquiry into some question one ought to suspend belief with respect to that question. But what about hunches? In this short note, a hunch about the cause of a phenomenon is described. The hunch plays a role in the inquiry into the cause of the phenomenon. It appears that the hunch constitutes a belief that need not be suspended during the inquiry even though belief about the precise cause of the (...) phenomenon is suspended. (shrink)

The goal of the 2010 Ontology Summit was to address the current shortage of persons with ontology expertise by developing a strategy for the education of ontologists. To achieve this goal we studied how ontologists are currently trained, the requirements identified by organizations that hire ontologists, and developments that might impact the training of ontologists in the future. We developed recommendations for the body of knowledge that should be taught and the skills that should be developed by future ontologists; these (...) recommendations are intended as guidelines for institutions and organizations that may consider establishing a program for training ontologists. Further, we recommend a number of specific actions for the community to pursue. (shrink)

This article constructively retrieves St. Anselm of Canterbury’s theory of retributive justice and provides a defense of what can be called the retributive model of hell. In the first part of this article, we develop the place of retributive punishment in Anselm’s thinking and discuss how and when retributive punishment is a good thing. In the second part, we apply Anselm’s thinking on retributive justice to the problem of hell and provide a defense of how hell, defined as a state (...) of receiving retributive, damnatory, and irreversible punishment, is good. We then address a series of objections. Despite some criticism that both Anselm and the retributive model of hell receive in the contemporary literature, Anselm’s account of retributive justice can make unique and constructive contributions to the contemporary discussion of hell; by retrieving and applying Anselm’s thought to the problem of hell, we intend to kill two birds with one stone. (shrink)

Recent work by Peijnenburg, Atkinson, and Herzberg suggests that infinitists who accept a probabilistic construal of justification can overcome significant challenges to their position by attending to mathematical treatments of infinite probabilistic regresses. In this essay, it is argued that care must be taken when assessing the significance of these formal results. Though valuable lessons can be drawn from these mathematical exercises (many of which are not disputed here), the essay argues that it is entirely unclear that the form of (...) infinitism that results meets a basic requirement: namely, providing an account of infinite chains of propositions qua reasons made available to agents. (shrink)

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

In this short essay, we sketch a theory of faith that features resilience in the face of challenges to relying on those in whom you have faith. We argue that it handles a variety of both religious and secular faith-data, e.g., the value of faith in relationships of mutual faith and faithfulness, how the Christian and Hebrew scriptures portray pístis and ʾĕmûnāh, and the character of faith as it is often expressed in popular secular venues.

This article examines where Kant stands on the question of the redistribution of wealth and income both nationally and globally. Kant is rightly seen as a radical reformer of the world order from a political standpoint seeking a republican, federative worldwide system; can he also be seen as wanting to bring about an equally dramatic shift from an economic perspective? To answer this question we have first of all to address the question of whether he is an egalitarian or an (...) inegalitarian at the national level. Certainly there are certain social and material inequalities within a civil society Kant is prepared to accept and there are some he is not. This would imply that he would affirm certain inequalities at an international level and that there are others upon which he would recommend action. Thus the question arises as to whether or not it is appropriate for Kantians to regard the current enormous inequalities in wealth and income between individuals living in different parts of the globe as scandalous and in need of change. The paper throughout relates the problem of distributive justice within the state to the problem of distributive justice amongst states, arguing that this approach is warranted by Kant's own method. Particular attention is paid to how Kant's own approach to political philosophy may be deployed to underpin a change to a distinctive type of international distributive justice. (shrink)

Inflicting harm is generally preferable to inflicting death. If you must choose between the two, you should generally choose to harm. But prenatal harm seems different. If a mother must choose between harming her fetus or aborting it, she may choose either, at least in many cases. So it seems that prenatal harm is particularly objectionable, sometimes on a par with death. This paper offers an explanation of why prenatal harm seems particularly objectionable by drawing an analogy to the all-or-nothing (...) problem. It then argues that this analogy offers independent support for the ‘voluntarist’ view that at least some parental role obligations are grounded in the choice to be a parent. (shrink)

This paper brings Sellars’ synoptic vision of philosophy into contact with elements of Quine’s naturalism. The implications of the synoptic view for the method of analysis are presented. Sellars’ metaphysical naturalism is supplemented with the meta-philosophical and epistemological naturalism of Quine. The issue of epistemic normativity is addressed within a naturalistic context. The possibility of a conflict between naturalism and realism is considered.

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)

Why should we refrain from doing things that, taken collectively, are environmentally destructive, if our individual acts seem almost certain to make no difference? According to the expected consequences approach, we should refrain from doing these things because our individual acts have small risks of causing great harm, which outweigh the expected benefits of performing them. Several authors have argued convincingly that this provides a plausible account of our moral reasons to do things like vote for policies that will reduce (...) our countries’ greenhouse gas emissions, adopt plant-based diets, and otherwise reduce our individual emissions. But this approach has recently been challenged by authors like Bernward Gesang and Julia Nefsky. Gesang contends that it may be genuinely impossible for our individual emissions to make a morally relevant difference. Nefsky argues more generally that the expected consequences approach cannot adequately explain our reasons not to do things if there is no precise fact of the matter about whether their outcomes are harmful. -/- In the following chapter, author Howard Nye defends the expected consequences approach against these objections. Nye contends that Gesang has shown at most that our emissions could have metaphysically indeterministic effects that lack precise objective chances. He argues, moreover, that the expected consequences approach can draw upon existing extensions to cases of indeterminism and imprecise probabilities to deliver the result that we have the same moral reasons to reduce our emissions in Gesang’s scenario as in deterministic scenarios. Nye also shows how the expected consequences approach can draw upon these extensions to handle Nefsky’s concern about the absence of precise facts concerning whether the outcomes of certain acts are harmful. The author concludes that the expected consequences approach provides a fully adequate account of our moral reasons to take both political and personal action to reduce our ecological footprints. (shrink)

Klein’s account of epistemic justification, infinitism, supplies a novel solution to the regress problem. We argue that concentrating on the normative aspect of justification exposes a number of unpalatable consequences for infinitism, all of which warrant rejecting the position. As an intermediary step, we develop a stronger version of the ‘finite minds’ objection.

Truth in a correspondence sense is objective in two ways. It is objective because the relation of correspondence is objective and because the facts to which truths correspond are objective. Truth about artifacts is problematic because artifacts are intentionally designed to perform certain functions, and so are not entirely mind independent. Against this, it is argued in this paper that truth about artifacts is perfectly objective despite the role played by intention and purpose in the production of artifacts.

This is a brief exploration of the notion of an objective fact. The form of objectivity at issue is distinct from epistemic objectivity or objectivity about truth. It is an ontological form of objectivity. Objective facts may obtain whether or not we know, believe or are aware of them. They depend upon objects, for example, on the properties that objects have or the relationships into which objects enter. Setting scepticism to one side, there is a perfectly mundane sense in which (...) we may come to have knowledge or fail to have knowledge of such facts. We must perceive objective facts from a perspective, but this does not enter into the facts. Nor does the fact that we must describe facts using language mean that facts are language-dependent. (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 National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and (...) terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data. (shrink)

Faith in God conflicts with reason—or so we’re told. We focus on two arguments for this conclusion. After evaluating three criticisms of them, we identify an assumption they share, namely that faith in God requires belief that God exists. Whether the assumption is true depends on what faith is. We sketch a theory of faith that allows for both faith in God without belief that God exists, and faith in God while in belief-cancelling doubt God’s existence. We then argue that (...) our theory, unlike the theory of Thomas Aquinas, makes sense of four central items of faith-data: (i) pístis in the Synoptics, (ii) ʾemunāh in the Hebrew scriptures, (iii) exemplars of faith in God, including Abraham, Jesus, and Mother Teresa, and (iv) the widespread experience of people of faith today. We close by assessing revisions of the two arguments we began with, revisions that align with our theory of faith, and find them dubious, at best. (shrink)

The current COVID-19 pandemic and the previous SARS/MERS outbreaks of 2003 and 2012 have resulted in a series of major global public health crises. We argue that in the interest of developing effective and safe vaccines and drugs and to better understand coronaviruses and associated disease mechenisms it is necessary to integrate the large and exponentially growing body of heterogeneous coronavirus data. Ontologies play an important role in standard-based knowledge and data representation, integration, sharing, and analysis. Accordingly, we initiated the (...) development of the community-based Coronavirus Infectious Disease Ontology in early 2020. -/- As an Open Biomedical Ontology (OBO) library ontology, CIDO is open source and interoperable with other existing OBO ontologies. CIDO is aligned with the Basic Formal Ontology and Viral Infectious Disease Ontology. CIDO has imported terms from over 30 OBO ontologies. For example, CIDO imports all SARS-CoV-2 protein terms from the Protein Ontology, COVID-19-related phenotype terms from the Human Phenotype Ontology, and over 100 COVID-19 terms for vaccines (both authorized and in clinical trial) from the Vaccine Ontology. CIDO systematically represents variants of SARS-CoV-2 viruses and over 300 amino acid substitutions therein, along with over 300 diagnostic kits and methods. CIDO also describes hundreds of host-coronavirus protein-protein interactions (PPIs) and the drugs that target proteins in these PPIs. CIDO has been used to model COVID-19 related phenomena in areas such as epidemiology. The scope of CIDO was evaluated by visual analysis supported by a summarization network method. CIDO has been used in various applications such as term standardization, inference, natural language processing (NLP) and clinical data integration. We have applied the amino acid variant knowledge present in CIDO to analyze differences between SARS-CoV-2 Delta and Omicron variants. CIDO's integrative host-coronavirus PPIs and drug-target knowledge has also been used to support drug repurposing for COVID-19 treatment. -/- CIDO represents entities and relations in the domain of coronavirus diseases with a special focus on COVID-19. It supports shared knowledge representation, data and metadata standardization and integration, and has been used in a range of applications. (shrink)

A major point of debate about morally good motives concerns an ambiguity in the truism that good and strong-willed people desire to do what is right. This debate is shaped by the assumption that “what’s right” combines in only two ways with “desire,” leading to distinct de dicto and de re readings of the truism. However, a third reading of such expressions is possible, first identified by Janet Fodor, which has gone wholly unappreciated by philosophers in this debate. I identify (...) Fodor’s nonspecific reading of “desire to do what’s right” and briefly discuss its merits. (shrink)

This paper provides an axiomatic formalization of a theory of foundational relations between three categories of entities: individuals, universals, and collections. We deal with a variety of relations between entities in these categories, including the is-a relation among universals and the part-of relation among individuals as well as cross-category relations such as instance-of, member-of, and partition-of. We show that an adequate understanding of the formal properties of such relations – in particular their behavior with respect to time – is critical (...) for formal ontology. We provide examples to support this thesis from the domain of biomedicine. (shrink)

One of the most intriguing claims in Sven Rosenkranz’s Justification as Ignorance is that Timothy Williamson’s celebrated anti-luminosity argument can be resisted when it comes to the condition ~K~KP—the condition that one is in no position to know that one is in no position to know P. In this paper, I critically assess this claim.

A descriptive polytheist thinks there are at least two gods. John Hick and Richard Swinburne are descriptive polytheists. In this respect, they are like Thomas Aquinas and many other theists. What sets Swinburne and Hick apart from Aquinas, however, is that unlike him they are normative polytheists. That is, Swinburne and Hick think that it is right that we, or at least some of us, worship more than one god. However, the evidence available to me shows that only Swinburne, and (...) not Hick, is a cultic polytheist: he actually worships more than one god. I conclude that only Swinburne is a polytheist par excellence. (shrink)

The paper presents some thoughts about how an account of rationality might be recovered from what might have first appeared as anti-rationalistic ideas in the work of Kuhn and Feyerabend. The paper draws inspiration from some suggestions of Bernstein and Rorty, as well well as Brown's theory of rationality.

This paper presents a particularist and naturalist response to epistemic relativism. The response is based on an analysis of the source of epistemic relativism, according to which epistemic relativism is closely related to Pyrrhonian scepticism. The paper starts with a characterization of epistemic relativism. Such relativism is explicitly distinguished from epistemological contextualism. Next the paper presents an argument for epistemic relativism that is based on the Pyrrhonian problem of the criterion. It then considers a response to the problem of the (...) criterion proposed by Roderick Chisholm, which is based on epistemological particularism. After sketching Chisholm’s approach, a response to epistemic relativism is presented which combines Chisholm’s particularism with epistemic naturalism and reliabilism. A number of objections to the position are then considered. The paper ends with remarks about the relationship between particularism and the naturalistic response proposed to epistemic relativism. (shrink)