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)

Los teóricos de la democracia dejaron de lado la pregunta de quién legalmente forma parte del "pueblo" autorizado, pregunta que atraviesa a todas las teoría de la democracia y continuamente vivifica la práctica democrática. Determinar quién constituye el pueblo es un dilema inabordable e incluso imposible de responder democráticamente; no es una pregunta que el pueblo mismo pueda decidir procedimentalmente porque la propia premisa subvierte las premisas de su resolución. Esta paradoja del mandato popular revela que el pueblo para ser (...) mejor comprendido como una demanda política, como un proceso de subjetivación, surge y se desarrolla en distintos contextos democráticos. En Estados Unidos el disputado poder para hablar en beneficio del pueblo deriva de un excedente constitutivo heredado de la era revolucionaria, a partir del hecho de que desde la Revolución el pueblo ha sido por vez primera encarnado por la representación y como exceso de cualquier forma de representación. La autoridad posrevolucionaria del vox populi deriva de esa continuamente reiterada pero nunca realizada referencia a la soberanía del pueblo a partir de la representación, legitimidad a partir de la ley, espíritu a partir de la letra, la palabra a través de la palabra. Este ensayo examina la emergencia histórica de este exceso de democracia en el período revolucionario, y cómo este habilita a una subsecuente historia de "momentos constituyentes", momentos cuando subautorizados -radicales, entidades autocreadas-, se apoderan del manto de la autoridad, cambiando las reglas de la autoridad en ese proceso. Estos pequeños dramas de reclamos de autoridad política para hablar en nombre del pueblo son felices, aun cuando explícitamente rompan con los procedimientos o reglas estatuidas para representar la voz popular. -/- Momentos constituyentes: paradojas y poder popular en los Estados Unidos de América posrevolucionarios [traducción], Revista Argentina de Ciencia Política, N°15, EUDEBA, Buenos Aires, Octubre 2012, pp. 49-74. ISSN: 0329-3092. Introducción de “Constituent Moments: Enacting the People in Postrevolutionary America”, de Jason Frank [Ed.: Duke University Press Books, enero de 2010. ISBN-10: 0822346753; ISBN-13: 978-0822346753]. (shrink)

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

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)

While there are numerous differences between the approaches taken by Maurice Merleau-Ponty and James J. Gibson, the basic motivation of the two thinkers, as well as the internal logic of their respective views, is extraordinarily close. Both were guided throughout their lives by an attempt to overcome the dualism of subject and object, and both devoted considerable attention to their "Gestaltist" predecessors. There can be no doubt but that it is largely because of this common cause that the subsequent (...) development of their ideas is so similar. It is not my objective in what follows merely to demonstrate a similarity between two lines of thought. Instead, I will try to show that each approach gains considerably from attention to the other. There are numerous ways to begin such a project, each about as arbitrary as the next. For present purposes, I shall take as of central importance the question of the character of the perceived world, both in relation to the traditionally opposed mental and material "substances", and in relation to its identification and individuation of things vis a vis one another and vis a vis ourselves. This will implicate especially Gibson's "affordances" and Merleau-Ponty's thesis concerning the "materiality of meaning.". (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)

The aim of this paper is to discuss the “Austro-American” logical empiricism proposed by physicist and philosopher Philipp Frank, particularly his interpretation of Carnap’s Aufbau, which he considered the charter of logical empiricism as a scientific world conception. According to Frank, the Aufbau was to be read as an integration of the ideas of Mach and Poincaré, leading eventually to a pragmatism quite similar to that of the American pragmatist William James. Relying on this peculiar interpretation, Frank (...) intended to bring about a rapprochement between the logical empiricism of the Vienna Circle in exile and American pragmatism. In the course of this project, in the last years of his career, Frank outlined a comprehensive, socially engaged philosophy of science that could serve as a “link between science and philosophy”. (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.

In this paper, I critically evaluate several related, provocative claims made by proponents of data-intensive science and “Big Data” which bear on scientific methodology, especially the claim that scientists will soon no longer have any use for familiar concepts like causation and explanation. After introducing the issue, in section 2, I elaborate on the alleged changes to scientific method that feature prominently in discussions of Big Data. In section 3, I argue that these methodological claims are in tension with a (...) prominent account of scientific method, often called “Inference to the Best Explanation” (IBE). Later on, in section 3, I consider an argument against IBE that will be congenial to proponents of Big Data, namely the argument due to Roche and Sober (2013) that “explanatoriness is evidentially irrelevant”. This argument is based on Bayesianism, one of the most prominent general accounts of theory-confirmation. In section 4, I consider some extant responses to this argument, especially that of Climenhaga (2017). In section 5, I argue that Roche and Sober’s argument does not show that explanatory reasoning is dispensable. In section 6, I argue that there is good reason to think explanatory reasoning will continue to prove indispensable in scientific practice. Drawing on Cicero’s oft-neglected De Divinatione, I formulate what I call the “Ciceronian Causal-nomological Requirement”, (CCR), which states roughly that causal-nomological knowledge is essential for relying on correlations in predictive inference. I defend a version of the CCR by appealing to the challenge of “spurious correlations”, chance correlations which we should not rely upon for predictive inference. In section 7, I offer some concluding remarks. (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.

These essays draw on work in the history and philosophy of science, the philosophy of mind and language, the development of concepts in children, conceptual..

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 examine Cicero’s oft-neglected De Divinatione, a dialogue investigating the legitimacy of the practice of divination. First, I offer a novel analysis of the main arguments for divination given by Quintus, highlighting the fact that he employs two logically distinct argument forms. Next, I turn to the first of the main arguments against divination given by Marcus. Here I show, with the help of modern probabilistic tools, that Marcus’ skeptical response is far from the decisive, proto-naturalistic assault (...) on superstition that it is sometimes portrayed to be. Then, I offer an extended analysis of the second of the main arguments against divination given by Marcus. Inspired by Marcus’ second main argument, I formulate, explicate, and defend a substantive principle of scientific methodology that I call the “Ciceronian Causal-Nomological Requirement” (CCR). Roughly, this principle states that causal knowledge is essential for relying on correlations in predictive inference. Although I go on to argue that Marcus’ application of the CCR in his debate with Quintus is dialectically inadequate, I conclude that De Divinatione deserves its place in Cicero’s philosophical corpus, and that ultimately, its significance for the history and philosophy of science ought to be recognized. (shrink)

Intuitions about intentional action have turned out to be sensitive to normative factors: most people say that an indifferent agent brings about an effect of her action intentionally when it is harmful, but unintentionally when it is beneficial. Joshua Knobe explains this asymmetry, which is known as ‘the Knobe effect’, in terms of the moral valence of the effect, arguing that this explanation generalizes to other asymmetries concerning notions as diverse as deciding and being free. I present an alternative explanation (...) of the Knobe effect in terms of normative reasons. This explanation generalizes to other folk psychological notions such as deciding, but not to such notions as being free. I go on to argue, against Knobe, that offering a unified explanation of all the asymmetries he discusses is in fact undesirable. (shrink)

This paper discusses the finite version of the two envelope paradox. (That is, we treat the paradox against the background assumption that there is only a finite amount of money in the world.).

In this paper the system IL for relative interpretability is studied.

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.

Critical discussion of Jerry Fodor's Concepts: Where Cognitive Science Went Wrong (1998).

Name der Zeitschrift: Nietzsche-Studien Jahrgang: 44 Heft: 1 Seiten: 267-290 In this paper, I examine the possibility of constructing an ontological phenomenology of love by tracing Nietzsche’s questioning about science. I examine how the evolution of Nietzsche’s thinking about science and his increasing suspicion towards it coincide with his interest for the question of love. Although the texts from the early and middle period praise science as an antidote to asceticism, the later texts associate the scientifi c spirit with asceticism. (...) I argue that this shift is motivated by Nietzsche’s realization that asceticism and science share the same fetish of facts. It is now for Nietzsche no longer a matter of proving the so-called facts of the backworlds to be wrong (something science is very capable of doing), but a matter of rejecting the very structure of thought that reduces a shapeless reality into a series of facts, subjects and objects. It is this second attitude that Nietzsche regards as the common core of science and asceticism. From this critique of science and its correlative critique of facts, Nietzsche begins searching for a counter-attitude able to perform the reduction of the factual attitude. This is the attitude he calls love. Although Nietzsche’s concept of love has oft en been elucidated in terms of its object or its subject, I argue that such interpretations precisely defeat Nietzsche’s point, which is to recover a ground that precedes the division of the world into subjects and objects. Love becomes the name of this intra-relationship of being, opening up to new perspectives on Nietzsche’s ontology of the will to power. (shrink)

This paper offers a probabilistic treatment of the conditions for argument cogency as endorsed in informal logic: acceptability, relevance, and sufficiency. Treating a natural language argument as a reason-claim-complex, our analysis identifies content features of defeasible argument on which the RSA conditions depend, namely: change in the commitment to the reason, the reason’s sensitivity and selectivity to the claim, one’s prior commitment to the claim, and the contextually determined thresholds of acceptability for reasons and for claims. Results contrast with, and (...) may indeed serve to correct, the informal understanding and applications of the RSA criteria concerning their conceptual dependence, their function as update-thresholds, and their status as obligatory rather than permissive norms, but also show how these formal and informal normative approachs can in fact align. (shrink)

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)

For each positive n , two alternative axiomatizations of the theory of strings over n alphabetic characters are presented. One class of axiomatizations derives from Tarski's system of the Wahrheitsbegriff and uses the n characters and concatenation as primitives. The other class involves using n character-prefixing operators as primitives and derives from Hermes' Semiotik. All underlying logics are second order. It is shown that, for each n, the two theories are definitionally equivalent [or synonymous in the sense of deBouvere]. It (...) is further shown that each member of one class is synonymous with each member of the other class; thus that all of the theories are definitionally equivalent with each other and with Peano arithmetic. Categoricity of Peano arithmetic then implies categoricity of each of the above theories. (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)

Advocates of moral enhancement through pharmacological, genetic, or other direct interventions sometimes explicitly argue, or assume without argument, that traditional moral education and development is insufficient to bring about moral enhancement. Traditional moral education grounded in a Kohlbergian theory of moral development is indeed unsuitable for that task; however, the psychology of moral development and education has come a long way since then. Recent studies support the view that moral cognition is a higher-order process, unified at a functional level, and (...) that a specific moral faculty does not exist. It is more likely that moral cognition involves a number of different mechanisms, each connected to other cognitive and affective processes. Taking this evidence into account, we propose a novel, empirically informed approach to moral development and education, in children and adults, which is based on a cognitive-affective approach to moral dispositions. This is an interpretative approach that derives from the cognitive-affective personality system (Mischel and Shoda, 1995). This conception individuates moral dispositions by reference to the cognitive and affective processes that realise them. Conceived of in this way, moral dispositions influence an agent's behaviour when they interact with situational factors, such as mood or social context. Understanding moral dispositions in this way lays the groundwork for proposing a range of indirect methods of moral enhancement, techniques that promise similar results as direct interventions whilst posing fewer risks. (shrink)

We introduce two notions–the shadows and the shallows of explanation–in opening up explanation to broader, interdisciplinary investigation. The shadows of explanation refer to past philosophical efforts to provide either a conceptual analysis of explanation or in some other way to pinpoint the essence of explanation. The shallows of explanation refer to the phenomenon of having surprisingly limited everyday, individual cognitive abilities when it comes to explanation. Explanations are ubiquitous, but they typically are not accompanied by the depth that we might, (...) prima facie, expect. We explain the existence of the shadows and shallows of explanation in terms of there being a theoretical abyss between explanation and richer, theoretical structures that are often attributed to people. We offer an account of the shallows, in particular, both in terms of shorn-down, internal, mental machinery, and in terms of an enriched, public symbolic environment, relative to the currently dominant ways of thinking about cognition and the world. (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)

In this chapter, we consider ethical and philosophical aspects of trust in the practice of medicine. We focus on trust within the patient-physician relationship, trust and professionalism, and trust in Western (allopathic) institutions of medicine and medical research. Philosophical approaches to trust contain important insights into medicine as an ethical and social practice. In what follows we explain several philosophical approaches and discuss their strengths and weaknesses in this context. We also highlight some relevant empirical work in the section on (...) trust in the institutions of medicine. It is hoped that the approaches discussed here can be extended to nursing and other topics in the philosophy of medicine. (shrink)

This paper, while neutral on questions about the minimality of truth, argues for the non-minimality of truth-aptness.

Despite the ubiquity of inner speech in our mental lives, methods for objectively assessing inner speech capacities remain underdeveloped. The most common means of assessing inner speech is to present participants with tasks requiring them to silently judge whether two words rhyme. We developed a version of this task to assess the inner speech of a population of patients with aphasia and corresponding language production deficits. As expected, patients’ performance on the silent rhyming task was severely impaired relative to controls. (...) More surprisingly, however, patients’ performance on this task did not correlate with their performance on a variety of other standard tests of overt language abilities. In particular, patients who were generally unimpaired in their abilities to overtly name objects during confrontation naming tasks, and who could reliably judge when two words spoken to them rhymed, were still severely impaired (relative to controls) at completing the silent rhyme task. This seems to suggest that inner speech was more severely impaired in these patients than outer speech. However, these results should also cause us to critically reflect on the relation between inner speech and silent rhyme judgments more generally. (shrink)

In this chapter, we outline the range of argument forms involving causation that can be found in everyday discourse. We also survey empirical work concerned with the generation and evaluation of such arguments. This survey makes clear that there is presently no unified body of research concerned with causal argument. We highlight the benefits of a unified treatment both for those interested in causal cognition and those interested in argumentation, and identify the key challenges that must be met for a (...) full understanding of causal argumentation. (shrink)

It is not a particularly hard thing to want or seek explanations. In fact, explanations seem to be a large and natural part of our cognitive lives. Children ask why and how questions very early in development and seem genuinely to want some sort of answer, despite our often being poorly equipped to provide them at the appropriate level of sophistication and detail. We seek and receive explanations in every sphere of our adult lives, whether it be to understand why (...) a friendship has foundered, why a car will not start, or why ice expands when it freezes. Moreover, correctly or incorrectly, most of the time we think we know when we have or have not received a good explanation. There is a sense both that a given, successful explanation satisfies a cognitive need, and that a questionable or dubious explanation does not. There are also compelling intuitions about what make good explanations in terms of their form, that is, a sense of when they are structured correctly. (shrink)

In this paper, we attempt to show that if Plantinga’s free will defence succeeds, his O Felix Culpa theodicy fails. For if every creaturely essence suffers from transworld depravity, then given that Jesus has a creaturely essence (as we attempt to show), it follows that Incarnation and Atonement worlds cannot be actualized by God, in which case we have anything but a felix culpa.

It is not clear to what the projects of creating an artificial intelligence (AI) that does ethics, is moral, or makes moral judgments amounts. In this paper we discuss some of the extant metaethical theories and debates in moral philosophy by which such projects should be informed, specifically focusing on the project of creating an AI that makes moral judgments. We argue that the scope and aims of that project depend a great deal on antecedent metaethical commitments. Metaethics, therefore, plays (...) the role of an Archimedean fulcrum in this context, very much like the Archimedean role that it is often taken to take in context of normative ethics (Dworkin 1996; Dreier 2002; Fantl 2006; Ehrenberg 2008). (shrink)

This paper discusses ethical issues surrounding Integrated Assessment Models (IAMs) of the economic effects of climate change, and how climate economists acting as policy advisors ought to represent the uncertain possibility of catastrophe. Some climate economists, especially Martin Weitzman, have argued for a precautionary approach where avoiding catastrophe should structure climate economists’ welfare analysis. This paper details ethical arguments that justify this approach, showing how Weitzman’s “fat tail” probabilities of climate catastrophe pose ethical problems for widely used IAMs. The main (...) claim is that economists who ignore or downplay catastrophic risks in their representations of uncertainty likely fall afoul of ethical constraints on scientists acting as policy advisors. Such scientists have duties to honestly articulate uncertainties and manage (some) inductive risks, or the risks of being wrong in different ways. (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.