The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to (...) existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource providing details on the people, policies, and issues being addressed in association with OBI. (shrink)

Throughout the biological and biomedical sciences there is a growing need for, prescriptive ‘minimum information’ (MI) checklists specifying the key information to include when reporting experimental results are beginning to find favor with experimentalists, analysts, publishers and funders alike. Such checklists aim to ensure that methods, data, analyses and results are described to a level sufficient to support the unambiguous interpretation, sophisticated search, reanalysis and experimental corroboration and reuse of data sets, facilitating the extraction of maximum value from data sets (...) them. However, such ‘minimum information’ MI checklists are usually developed independently by groups working within representatives of particular biologically- or technologically-delineated domains. Consequently, an overview of the full range of checklists can be difficult to establish without intensive searching, and even tracking thetheir individual evolution of single checklists may be a non-trivial exercise. Checklists are also inevitably partially redundant when measured one against another, and where they overlap is far from straightforward. Furthermore, conflicts in scope and arbitrary decisions on wording and sub-structuring make integration difficult. This presents inhibit their use in combination. Overall, these issues present significant difficulties for the users of checklists, especially those in areas such as systems biology, who routinely combine information from multiple biological domains and technology platforms. To address all of the above, we present MIBBI (Minimum Information for Biological and Biomedical Investigations); a web-based communal resource for such checklists, designed to act as a ‘one-stop shop’ for those exploring the range of extant checklist projects, and to foster collaborative, integrative development and ultimately promote gradual integration of checklists. (shrink)

Cognitivism in respect to the arts refers to a constellation of positions that share in common the idea that artworks often bear, in addition to aesthetic value, a significant kind of cognitive value. In this paper I concentrate on three things: (i) the challenge of understanding exactly what one must do if one wishes to defend a cognitivist view of the arts; (ii) common anti-cognitivist arguments; and (iii) promising recent attempts to defend cognitivism.

What is the relation between works of fiction and the acquisition of knowledge?

A viable theory of literary humanism must do justice to the idea that literature offers cognitive rewards to the careful reader. There are, however, powerful arguments to the effect that literature is at best only capable of offering idle visions of a world already well known. In this essay I argue that there is a form of cognitive awareness left unmentioned in the traditional vocabulary of knowledge acquisition, a form of awareness literature is particularly capable of offering. Thus even if (...) it is the case that literature has nothing interesting to give us in the way of knowledge, the literary humanist can consistently maintain that literary experience is thoroughly cognitive. (shrink)

It is often assumed that literary meaning is essentially linguistic in nature and that literary interpretation is therefore a purely linguistic affair. This essay identifies a variety of literary meaning that cannot be reduced to linguistic meaning. Meaning of this sort is generated not by a communicative act so much as through a creative one: the construction of a fictional world. The way in which a fictional world can bear meaning turns out to be strikingly unlike the way a sentence (...) can, and this, I argue, has important implications for the theory of interpretation. (shrink)

This paper attempts to reconcile two apparently opposed ways of thinking about the imagination and its relationship to literature, one which casts it as essentially concerned with fiction-making and the other with culture-making. The literary imagination’s power to create fictions is what gives it its most obvious claim to “autonomy”, as Kant would have it: its freedom to venture out in often wild and spectacular excess of reality. The argument of this paper is that we can locate the literary imagination’s (...) complementary power of cultural articulation in this fictional activity. The suggestion is that we should conceive of the literary imagination as expressing its interests in culture not mimetically but by producing a certain kind of meaning. This meaning is irreducibly narratological, and understanding it helps us to see the role of narrative in bringing into harmony the literary imagination’s interests in both the imaginary and the real. (shrink)

The chapter presents Anselm’s incompatibilist account of human freedom within the context of his theodicy and presents two arguments against his account. Both arguments aim to show there is a genuine conflict between his account of freedom and the role of God’s grace in making agents just. The first argument, the problem of harmonization, highlights the conflict within the soteriological context where an agent changes from being unjust to being just. The second argument, the problem of just creation, highlights the (...) conflict within the context of the creation of agents prior to the presence of evil. Holding fixed his incompatibilist account and the necessity of divine grace, the upshot of both arguments is that Anselm must endorse a version of Pelagianism. (shrink)

This paper raises a slightly uncomfortable question: are some delusional subjects responsible for their delusions? This question is uncomfortable because we typically think that the answer is pretty clearly just ‘no’. However, we also accept that self-deception is paradigmatically intentional behavior for which the self-deceiver is prima facie blameworthy. Thus, if there is overlap between self-deception and delusion, this will put pressure on our initial answer. This paper argues that there is indeed such overlap by offering a novel philosophical account (...) of self-deception. The account offered is independently plausible and avoids the main problems that plague other views. It also yields the result that some delusional subjects are self-deceived. The conclusion is not, however, that those subjects are blameworthy. Rather, a distinction is made between blameworthiness and ‘attributability’. States or actions can be significantly attributable to a subject—in the sense that they are expressions of their wills—without it being the case that the subject is blameworthy, if the subject has an appropriate excuse. Understanding delusions within this framework of responsibility and excuses not only illuminates the ways in which the processes of delusional belief formation and maintenance are continuous with ‘ordinary’ processes of belief formation and maintenance, it also provides a way of understanding the innocence of the delusional subject that does not involve the denial of agency. (shrink)

Philosophers of literature do not take much of an interest in autobiography.1 In one sense this is not surprising. As a certain prejudice has it, autobiography is, along with biography, the preferred reading of people who do not really like to read. The very words can conjure up images of what one finds on bookshelves in Florida retirement communities and in underfunded public libraries, books with titles like Under the Rainbow: The Real Liza Minnelli or Me: Stories of My Life (...) (Katharine Hepburn).2 Hardly rousing material, at least from the philosophical point of view. But on a moment’s reflection, it becomes clear that the initial prejudice is unfounded. Never mind the fact that there are obviously .. (shrink)

This is the first book-length attempt to find the answer, by one author, since Sartre in his 1948 book with the same title.

Xenotransplantation has the potential to alter the U.S. transplant system in profound ways. However, this emerging “spare parts” solution spearheaded by biotechnology companies raises concerns about its impact on the organ shortage, healthcare systems, population health, and health inequalities. We contend that xenotransplantation may have limited benefits in improving health, could prove prohibitively expensive for many, and may divert resources away from proven public health measures. Additionally, it carries the risk of perpetuating stigma. Xenotransplantation may thereby exacerbate existing healthcare inequities (...) across racial, ethnic, socio‐economic, and geographic lines. To mitigate these risks, we contend that public health expert input is integral for xenotransplant policy development and outreach and that this underscores the importance of federal government investment in transplant infrastructure. (shrink)

Philosophers ask just whose expression, if anyone’s, we hear in lyric poetry. Walton provides a novel possibility: it’s the reader who “uses” the poem (just as a speech giver uses a speech) who makes the language expressive. But worries arise once we consider poems in particular social or political settings, those which require a strong self-other distinction, or those with expressions that should not be disassociated from the subjects whose experience they draw from. One way to meet this challenge is (...) to consider the poem expressive of a plural subject, which frees us from looking for a particular individual whose voice we hear in the work, whether she be fictional or actual. Some lyrics give voice to a group whose experience is attended to in the work. This may be done through a posited fictional speaker, but the ontology of the speaker is shown to be less important. Attending to a group whose concerns are voiced allows us to explain how poems can manage to address our-worldly concerns even when lacking actual persons whose expressions we encounter in the poems. (shrink)

Some properties are causally relevant for a certain effect, others are not. In this paper we describe a problem for our understanding of this notion and then offer a solution in terms of the notion of a program explanation.

There is little question as to whether there is good boring art, though its existence raises a number of questions for both the philosophy of art and the philosophy of emotions. How can boredom ever be a desideratum of art? How can our standing commitments concerning the nature of aesthetic experience and artistic value accommodate the existence of boring art? How can being bored constitute an appropriate mode of engagement with a work of art as a work of art? More (...) broadly, how can there be works of art whose very success requires the experience of boredom? Our goal in this paper is threefold. After offering a brief survey of kinds of boring art, we: i) derive a set of questions that we argue constitutes the philosophical problem of boring art; ii) elaborate an empirically informed theory of boredom that furnishes the philosophical problem with a deeper sense of the affect at the heart of the phenomenon; and iii) conclude by offering and defending a solution to the problem that explains why and how artworks might wish to make the experience of boredom key to their aesthetic and artistic success. (shrink)

There are infinitely many ways the world might be, and there may well be infinitely many people in it. These facts raise moral paradoxes. We explore a conflict between two highly attractive principles: a Pareto principle that says that what is better for everyone is better overall, and a statewise dominance principle that says that what is sure to turn out better is better on balance. We refine and generalize this paradox, showing that the problem is faced by many theories (...) of interpersonal aggregation besides utilitarianism, and by many decision theories besides expected value theory. Considering the range of consistent responses, we find all of them to be quite radical. (shrink)

In this paper, I offer an analysis of the radical disagreement over the adequacy of string theory. The prominence of string theory despite its notorious lack of empirical support is sometimes explained as a troubling case of science gone awry, driven largely by sociological mechanisms such as groupthink (e.g. Smolin 2006). Others, such as Dawid (2013), explain the controversy by positing a methodological revolution of sorts, according to which string theorists have quietly turned to nonempirical methods of theory assessment given (...) the technological inability to directly test the theory. The appropriate response, according to Dawid, is to acknowledge this development and widen the canons of acceptable scientific methods. As I’ll argue, however, the current situation in fundamental physics does not require either of these responses. Rather, as I’ll suggest, much of the controversy stems from a failure to properly distinguish the “context of justification” from the “context of pursuit”. Both those who accuse string theorists of betraying the scientific method and those who advocate an enlarged conception of scientific methodology objectionably conflate epistemic justification with judgements of pursuit-worthiness. Once we get clear about this distinction and about the different norms governing the two contexts, the current situation in fundamental physics becomes much less puzzling. After defending this diagnosis of the controversy, I’ll show how the argument patterns that have been posited by Dawid as constituting an emergent methodological revolution in science are better off if reworked as arguments belonging to the context of pursuit. (shrink)

In this paper, I consider the relationship between Inference to the Best Explanation and Bayesianism, both of which are well-known accounts of the nature of scientific inference. In Sect. 2, I give a brief overview of Bayesianism and IBE. In Sect. 3, I argue that IBE in its most prominently defended forms is difficult to reconcile with Bayesianism because not all of the items that feature on popular lists of “explanatory virtues”—by means of which IBE ranks competing explanations—have confirmational import. (...) Rather, some of the items that feature on these lists are “informational virtues”—properties that do not make a hypothesis \ more probable than some competitor \ given evidence E, but that, roughly-speaking, give that hypothesis greater informative content. In Sect. 4, I consider as a response to my argument a recent version of compatibilism which argues that IBE can provide further normative constraints on the objectively correct probability function. I argue that this response does not succeed, owing to the difficulty of defending with any generality such further normative constraints. Lastly, in Sect. 5, I propose that IBE should be regarded, not as a theory of scientific inference, but rather as a theory of when we ought to “accept” H, where the acceptability of H is fixed by the goals of science and concerns whether H is worthy of commitment as research program. In this way, IBE and Bayesianism, as I will show, can be made compatible, and thus the Bayesian and the proponent of IBE can be friends. (shrink)

Definition of the problem The umbrella term “explicability” refers to the reduction of opacity of artificial intelligence (AI) systems. These efforts are challenging for medical AI applications because higher accuracy often comes at the cost of increased opacity. This entails ethical tensions because physicians and patients desire to trace how results are produced without compromising the performance of AI systems. The centrality of explicability within the informed consent process for medical AI systems compels an ethical reflection on the trade-offs. Which (...) levels of explicability are needed to obtain informed consent when utilizing medical AI? Arguments We proceed in five steps: First, we map the terms commonly associated with explicability as described in the ethics and computer science literature, i.e., disclosure, intelligibility, interpretability, and explainability. Second, we conduct a conceptual analysis of the ethical requirements for explicability when it comes to informed consent. Third, we distinguish hurdles for explicability in terms of epistemic and explanatory opacity. Fourth, this then allows to conclude the level of explicability physicians must reach and what patients can expect. In a final step, we show how the identified levels of explicability can technically be met from the perspective of computer science. Throughout our work, we take diagnostic AI systems in radiology as an example. Conclusion We determined four levels of explicability that need to be distinguished for ethically defensible informed consent processes and showed how developers of medical AI can technically meet these requirements. (shrink)

Recent years have witnessed intensive efforts to specify which requirements ethical artificial intelligence (AI) must meet. General guidelines for ethical AI consider a varying number of principles important. A frequent novel element in these guidelines, that we have bundled together under the term explicability, aims to reduce the black-box character of machine learning algorithms. The centrality of this element invites reflection on the conceptual relation between explicability and the four bioethical principles. This is important because the application of general ethical (...) frameworks to clinical decision-making entails conceptual questions: Is explicability a free-standing principle? Is it already covered by the well-established four bioethical principles? Or is it an independent value that needs to be recognized as such in medical practice? We discuss these questions in a conceptual-ethical analysis, which builds upon the findings of an empirical document analysis. On the example of the medical specialty of radiology, we analyze the position of radiological associations on the ethical use of medical AI. We address three questions: Are there references to explicability or a similar concept? What are the reasons for such inclusion? Which ethical concepts are referred to? (shrink)

In this article, I will provide a critical overview of the form of non-deductive reasoning commonly known as “Inference to the Best Explanation” (IBE). Roughly speaking, according to IBE, we ought to infer the hypothesis that provides the best explanation of our evidence. In section 2, I survey some contemporary formulations of IBE and highlight some of its putative applications. In section 3, I distinguish IBE from C.S. Peirce’s notion of abduction. After underlining some of the essential elements of IBE, (...) the rest of the entry is organized around an examination of various problems that IBE confronts, along with some extant attempts to address these problems. In section 4, I consider the question of when a fact requires an explanation, since presumably IBE applies only in cases where some explanation is called for. In section 5, I consider the difficult question of how we ought to understand IBE in light of the fact that among philosophers, there is significant disagreement about what constitutes an explanation. In section 6, I consider different strategies for justifying the truth-conduciveness of the explanatory virtues, e.g., simplicity, unification, scope, etc., criteria which play an indispensable role in any given application of IBE. In section 7, I survey some of the most recent literature on IBE, much of which consists of investigations of the status of IBE from the standpoint of the Bayesian philosophy of science. (shrink)

The Preface Paradox is often discussed for its implications for rational belief. Much less discussed is a variant of the Preface Paradox for knowledge. In this paper, I argue that the most plausible closure-friendly resolution to the Preface Paradox for Knowledge is to say that in any given context, we do not know much. I call this view “Socraticism”. I argue that Socraticism is the most plausible view on two accounts—(1) this view is compatible with the claim that most of (...) our knowledge ascriptions are true, and (2) provided that (1) is true, the costs of accepting Socraticism are much less than the costs of accepting any other resolution to the Paradox. I argue for (1) in Section 2 by developing a question-sensitive contextualist model for knowledge that shows how Socraticism is compatible with the claim that most of our knowledge ascriptions are true. I also argue how this contextualist model can achieve this result where other contextualist models fail. I then consider other closure-friendly solutions to the paradox in Section 3 and show how accepting those solutions forces us to give up a number of plausible epistemic principles. (shrink)

We develop a Bayesian framework for thinking about the way evidence about the here and now can bear on hypotheses about the qualitative character of the world as a whole, including hypotheses according to which the total population of the world is infinite. We show how this framework makes sense of the practice cosmologists have recently adopted in their reasoning about such hypotheses.

Philosophy &Public Affairs, Volume 46, Issue 4, Page 363-383, Fall 2018.