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)

The paper presents the outlines of an ontology of plans and guidelines, which is then used as the basis for a framework for implementing guideline-based systems for the management of workflow in health care organizations. The framework has a number of special features, above all in that it enables us to represent in formal terms assignments of work-items both to individuals and to teams and to tailor guideline to specific contexts of application in health care organizations. It is designed also (...) to enable implementations to do justice to the fact that the processes carried out in health care organizations may deviate in different ways from the norms set forth in corresponding guideline definitions. This means that implementations built in conformity with the framework will be marked by a type of flexibility that might make them more likely to be accepted by healthcare professionals than are standard guideline-based management systems. (shrink)

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

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)

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)

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)

The National Center for Biomedical Ontology is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists, funded by the National Institutes of Health (NIH) Roadmap, to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create (...) new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease. (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)

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)

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)

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)

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)

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.

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.

Background: Current practice frequently fails to provide care consistent with the preferences of decisionally-incapacitated patients. It also imposes significant emotional burden on their surrogates. Algorithmic-based patient preference predictors (PPPs) have been proposed as a possible way to address these two concerns. While previous research found that patients strongly support the use of PPPs, the views of surrogates are unknown. The present study thus assessed the views of experienced surrogates regarding the possible use of PPPs as a means to help make (...) treatment decisions for decisionally-incapacitated patients. -/- Methods: This qualitative study used semi-structured interviews to determine the views of experienced surrogates [n=26] who were identified from two academic medical centers and two community hospitals. The primary outcomes were respondents’ overall level of support for the idea of using PPPs and the themes related to their views on how a PPP should be used, if at all, in practice. -/- Results: Overall, 21 participants supported the idea of using PPPs. The remaining five indicated that they would not use a PPP because they made decisions based on the patient’s best interests, not based on substituted judgment. Major themes which emerged were that surrogates, not the patient’s preferences, should determine how treatment decisions are made, and concern that PPPs might be used to deny expensive care or be biased against minority groups. -/- Conclusions: Surrogates, like patients, strongly support the idea of using PPPs to help make treatment decisions for decisionally-incapacitated patients. These findings provide support for developing a PPP and assessing it in practice. At the same time, patients and surrogates disagree over whose preferences should determine how treatment decisions are made, including whether to use a PPP. These findings reveal a fundamental disagreement regarding the guiding principles for surrogate decision-making. Future research is needed to assess this disagreement and consider ways to address it. (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)

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)

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.

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)

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 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)

This paper explores the relationship between scepticism and epistemic relativism in the context of recent history and philosophy of science. More specifically, it seeks to show that significant treatments of epistemic relativism by influential figures in the history and philosophy of science draw upon the Pyrrhonian problem of the criterion. The paper begins with a presentation of the problem of the criterion as it occurs in the work of Sextus Empiricus. It is then shown that significant treatments of epistemic relativism (...) in recent history and philosophy of science (critical rationalism, historical philosophy of science and the strong programme) draw upon the problem of the criterion. It is briefly suggested that a particularist response to the problem of the criterion may be put to good use against epistemic relativism. (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)

What is faith? Lara Buchak has done as much as anyone recently to answer our question in a sensible and instructive fashion. As it turns out, her writings reveal two theories of faith, an early one and a later one (or, if you like, two versions of the same theory). In what follows, we aim to do three things. First, we will state and assess Buchak’s early theory, highlighting both its good-making and bad-making features. Second, we will do the same (...) for her later theory, noting improvements on the early one. Third, we will mark various choice points in theorizing about faith, and we will argue for specific choices at those points, culminating in what we regard as a better, alternative theory of faith. Our critical aims, therefore, are ultimately constructive. By theorizing about faith with Lara Buchak, we aim to contribute to our common understanding of what faith is. (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)

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)

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)

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)

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)

In lieu of an abstract, here is a brief excerpt of the content:Plato on Knowledge as a Power1Nicholas D. SmithAt 471C4 in Plato’s Republic, the argument takes a sudden turn when Glaucon becomes impatient with all of the specific prescriptions Socrates has been making, and asks to return to the issue Socrates had earlier set aside—whether or not the city he was describing could ever be brought into being. In response to Glaucon’s impatient question, Socrates articulates his “third wave of (...) paradox” (472ag–7), namely, that the ills of the cities will never be ended until either philosophers become rulers or rulers become philosophers (473c11–d6). Glaucon immediately responds that such a view is likely to be greeted with violence and scorn (473e6–474a4), and so Socrates must hasten to explain his odd claim. His explanation, it turns out, is that true philosophers have an enormous cognitive advantage over non-philosophers—philosophers have and use knowledge (ἐπιστήμη), whereas non-philosophers have and use only opinion (δόξα).2 This distinction, between επιστήμη and δόξα, turns out: to be a distinction between two different cognitive powers (δυνάμεις—477d7–e3). And different powers, Plato clearly tells us, apply to or take as their objects (Plato says they are “ἐπί”) different things (477dl).In this paper, I shall argue that the relationship between the cognitive powers and their various objects has been fundamentally misunderstood, which has led scholars into one or more misinterpretations of important and explicit features of the text. At the heart of these misunderstandings, I claim, is [End Page 145] their shared misconception of the relation between the cognitive power and its objects as interpretable in terms of the relationship between a cognitive stale and what the content of that state is of or about.3 One consequence of the view for which I shall argue is that what has come to be known as the “two-worlds theory”4 of Plato’s epistemology is seriously mistaken, but no less mistaken than the alternatives given by its recent critics. Another consequence that I shall draw from my argument is that Plato should be understood neither as a kind of foundationalist with regard to knowledge and warrant, as some have supposed him to be,5 nor as a coherentist, as others have supposed,6 but, rather, as a kind of causal reliabilist. [End Page 146]1. KNOWLEDGE AS A POWERScholarly interpretations of Plato’s epistemology have routinely sought to understand the relationships between each cognitive power of Republic Book V and the objects of the ἐφ’ ᾦ (“what it is related to”) condition by which it is differentiated from other δυνάμεις as Plato’s way of telling us what each sort of cognition is of or aboul. 7 So, for example, we find Gail Fine using the expressions “belief [δόξα] is set over [Fine’s translation of Plato’s ἐπί] …” and “knowledge is set over …” interchangeably with “belief is of …” or “belief is about…” and “knowledge is of …” or “knowledge is about …”8 Against the “two-worlds theory,” Fine argues that, for Plato, there can be knowledge of sensibles and beliefs about Forms. Accordingly, since she assimilates the power-ἐπί-object set of relations to the cognilion-of/about-object relation, she concludes—in order to account for knowledge of sensibles and beliefs about Forms—that the objects of knowledge and opinion must be propositions. Plato’s claims that knowledge is ἐπί what is, whereas opinion is ἐπί what is and is not, Fine understands as, “One can only know true propositions; one can believe both true and false propositions.”9 We shall see later that this “veridical” understanding of what Plato means to identify as “what is,” and “what is and is not” fails to account for important and explicit elements of Plato’s exposition of the epistemological and metaphysical distinctions he is making. For now, it is enough to note that Fine understands the ἐφ’ᾦ) relation in terms of our cognition-of/about-object relation. One finds the same assimilation made by those who advance existential readings of Plato’s “is” and “is not,”10 as [End Page 147] well as those who have urged that we adopt predicative readings of “is” and “is not.”11But I think there are very serious problems with this assimilation. Plato is very... (shrink)

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)

I defend the widely-held view that morally worthy action need not be motivated by a desire to promote rightness as such. Some have recently come to reject this view, arguing that desires for rightness as such are necessary for avoiding a certain kind of luck thought incompatible with morally worthy action. I show that those who defend desires for rightness as such on the basis of this argument misunderstand the relationship between moral worth and the kind of luck that their (...) argument employs. Consequently, the argument provides no reason to doubt the popular view that a desire for rightness as such is no part of virtue. I conclude by suggesting that a family of worries about merely accidentally right action presuppose one side of the recent debate about objectivism and perspectivism about moral rightness. (shrink)

This is a response to Dragan Jakowljewitsch's 'The Successes of Science and Scientific-Theoretical Realism: A Less Than Direct Connection'.

This is a survey of theories of scientific method which opens the book "After Popper, Kuhn and Feyerabend: Recent Issues in Theories of Scientific Method".

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)

This paper describes the position of scientific realism and presents the basic lines of argument for the position. Simply put, scientific realism is the view that the aim of science is knowledge of the truth about observable and unobservable aspects of a mind-independent, objective reality. Scientific realism is supported by several distinct lines of argument. It derives from a non-anthropocentric conception of our place in the natural world, and it is grounded in the epistemology and metaphysics of common sense. Further, (...) the success of science entitles us to infer both the approximate truth of mature scientific theories and the truth-conduciveness of the methods of science. (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)

The paper presents a realist account of the epistemic objectivity of science. Epistemic objectivity is distinguished from ontological objectivity and the objectivity of truth. As background, T.S. Kuhn’s idea that scientific theory-choice is based on shared scientific values with a role for both objective and subjective factors is discussed. Kuhn’s values are epistemologically ungrounded, hence provide a minimal sense of objectivity. A robust account of epistemic objectivity on which methodological norms are reliable means of arriving at the truth is presented. (...) The problem remains that deliberative judgement is required to determine the relevance and relative significance of a range of methodological norms. A role is sketched for cognitive virtues which may be exercised in the course of the deliberative judgement. (shrink)

When people are making certain medical decisions – especially potentially transformative ones – the specter of regret may color their choices. In this paper, I ask: can predicting that we will regret a decision in the future serve any justificatory role in our present decision-making? And if so, what role? While there are many pitfalls to such reasoning, I ultimately conclude that considering future retrospective emotions like regret in our decisionmaking can be both rational and authentic. Rather than indicating that (...) one is about to make a mistake or that there is some underlying value that one already cares about but is overlooking, the prediction that one will regret a decision in the future makes one confront how her present values and priorities may change as a result of her choice in ways she cannot presently anticipate. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance a (...) proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (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)

Philosophers have recently come to focus on explaining the phenomenon of ​bad beliefs,​ beliefs that are apparently true and well-evidenced but nevertheless objectionable. Despite this recent focus, a consensus is already forming around a particular explanation of these beliefs’ badness called ​moral encroachment​, according to which, roughly, the moral stakes engendered by bad beliefs make them particularly difficult to justify. This paper advances an alternative account not just of bad beliefs but of bad attitudes more generally according to which bad (...) beliefs’ badness originates not in a failure of sufficient evidence but in a failure to respond adequately to reasons. I motivate this alternative account through an analogy to recent discussions of moral worth centered on the well-known grocer case from Kant’s ​Groundwork​, and by showing that this analogy permits the proposed account to generalize to bad attitudes beyond belief. The paper concludes by contrasting the implications of moral encroachment and of the proposed account for bad attitudes’ blameworthiness. (shrink)

Springer. We find in contemporary culture starkly contrasting estimates of the value of faith. On the one hand, for many people, faith is a virtue or positive human value, something associated with understanding, hope, and love, something to be inculcated, maintained, and cherished. On the other hand, for many people, faith is a vice, something associated with dogmatism, arrogance, and close-mindedness, something to be avoided at all costs. The papers included in this special (double) issue on approaches to faith explore (...) questions about faith in a variety of settings through a diverse range of examples, both secular and religious. The attempt to deepen our understanding of faith in the context of ordinary human relationships (e.g., between parents and children, friends, generals and their armies, business partners, citizens and the state), a commitment to ideals, or the pursuit of significant goals is clearly of general philosophical interest, as is the examination of potential connections between faith and topics such as trust or reliance. (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)

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.

Searle’s tool for understanding culture, law and society is the opposition between brute reality and institutional reality, or in other words between: observer-independent features of the world, such as force, mass and gravitational attraction, and observer-relative features of the world, such as money, property, marriage and government. The question posed here is: under which of these two headings do moral concepts fall? This is an important question because there are moral facts – for example pertaining to guilt and responsibility – (...) which hover uncomfortably close to the boundary between the observer-relative and the observer-independent. By means of a thought experiment involving an imagined Chinese society in which guilt is determined by the random throwing of sticks, I seek to show that moral concepts threaten the foundations of Searle’s philosophy of social reality. (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)